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  • richardmitnick 10:42 am on November 13, 2017 Permalink | Reply
    Tags: A Johns Hopkins biologist has deputized an army of "citizen scientists" to collect samples out in the field, , , JHU - Johns Hopkins University, The cosmos is too vast and too crowded with the hundreds of billions or perhaps trillions of galaxies filled with stars and planets for there not to be life out there somewhere, We found some colonization and are working now to upload it all to the Rockiology website   

    From Hopkins: “Johns Hopkins researcher enlists citizen scientists to track down rocks harboring earthly ‘extraterrestrials'” 

    Johns Hopkins
    Johns Hopkins University

    Nov 9, 2017
    Arthur Hirsch

    1
    To collect and examine rocks that could house microbes, a Johns Hopkins biologist has deputized an army of “citizen scientists” to collect samples out in the field. Image credit: Darci J. Harland

    In a small New Mexico town called Truth or Consequences, a pair of homeschooled brothers are on the hunt for extraterrestrials.

    With their mom and a small group of other families, Caleb, 10, and Corban, 6, scour the scrubby desert ground at the base of nearby Turtle Back Mountain, searching for certain kinds of rocks that could be home to microorganisms so resilient and so tough that they might be able to survive outside their rock hosts and live on other planets or moons.

    2
    Corban Harland, 6, inspects a rock, looking for the telltale green haze that indicates the presence of microbes called extremophiles.
    Image credit: Darci J. Harland

    These citizen scientists were deputized by Johns Hopkins biologist Jocelyne DiRuggiero—who specializes in astrobiology, or the study of the origins, evolution, and distribution of life in the universe—through her crowdsourcing research project, Rockiology. DiRuggiero believes that rocks in deserts and other extreme locations around the world could be home to single-cell microbes that may shed light on whether life could exist outside of our planet.

    After all, suggests DiRuggiero, the cosmos is too vast and too crowded with the hundreds of billions or perhaps trillions of galaxies filled with stars and planets for there not to be life out there somewhere.

    But the hunt begins at home.

    To learn more about these microbes, named extremophiles for the extreme conditions in which they live, DiRuggiero needs to collect samples. To gather those samples, she needs help reaching the most dry, barren places on Earth: deserts, dry valleys in Antarctica, places that resemble other planets.

    “We can go to some places and collect rocks, but we can’t go everywhere,” said DiRuggiero, an associate research professor in the Department of Biology in the Krieger School of Arts and Sciences. “We try to be creative and conserve resources.”

    That’s where sleuths like Caleb, Corban, and their mom, Darci J. Harland, come in. While scouting for home-school projects, Harland came across the Rockiology website, which features instructions on what sort of rocks the researchers are seeking, what characteristics to look for, and how to send in photos of the rocks—and perhaps eventually the rocks themselves—along with information on where they were found.


    Video: David Schmelick and Deirdre Hammer

    “I’ve always enjoyed getting kids out into the field to collect data, not just talking about it,” said Harland, who is a former public school science and English teacher and university professor of education. “And what better way to do that than to collect data for an actual scientist who needs your help?”

    Locations that are potentially rich with extremophile-housing rocks are very dry, very salty, or both. The Atacama desert in Chile, for instance, with its expanses of desolate, reddish terrain—cracked in some spots, littered with stones in others, and broken with jagged cliffs and rock formations—could easily pass for Mars.

    DiRuggiero has conducted several rock-collecting expeditions there, discovering a number of Atacama sodium chloride rocks that have been “colonized,” as she likes to put it, by microbes. In the exposed innards of a cracked rock, the colonies give away their position in a faint green haze on the white surface. There the creatures find refuge from the more dry, sunny, and windy conditions in the desert.

    So far Harland, her sons, and other homeschool families have taken basic lessons in rocks, extremophiles, and DiRuggiero’s work, and they have embarked on sample-gathering expeditions to Turtle Back Mountain.

    “We found some colonization and are working now to upload it all to the Rockiology website,” Harland said in an email. “Being able to communicate with the scientist on this project has been very rewarding both for me and for the students. They were careful in their data collection, knowing it was ‘for real.'”

    Microbes that can live in a salt rock might help a scientist learn something about creatures living in, say, briny water. That could be significant for astrobiologists wondering about the prospect of liquid water on Mars, which could be a sign that the place could support life. If water exists there as a liquid it is likely to be very salty, perhaps toxic.

    The hunt goes on for more information about extremophiles, the search party now expanded to include anyone who signs on for citizen Rockiology.

    See the full article here .

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    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

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  • richardmitnick 3:34 pm on July 31, 2017 Permalink | Reply
    Tags: 3-D microscope gives Johns Hopkins scientists a clearer view, , , JHU - Johns Hopkins University, , ,   

    From Hopkins: “3-D microscope gives Johns Hopkins scientists a clearer view” 

    Johns Hopkins
    Johns Hopkins University

    7.31.17
    Jill Rosen

    1
    Light-sheet technology allows researchers like Kavli Neuroscience Discovery Institute fellow Audrey Branch to observe how cells, ducts, or veins connect without damaging the cells in the sample Image credit: Will Kirk / Homewood Photography.

    Audrey Branch is trying to learn more about aging by studying old and young brains. Specifically, she’s interested in how cells connect to form memories and what might be going wrong with those connections when older people start to forget things.

    Until recently, getting at that question meant months of tedious specimen preparation. And even then, the very prep that made getting a glimpse of the brain’s core possible—slicing what’s already tiny into thousands of pieces—very likely destroyed the delicate connections the Johns Hopkins neuroscientist needed to see.

    That changed this spring when a new, three-dimensional microscope arrived at the university’s Homewood campus, a cutting-edge tool that not only condenses what had been months of work into just hours, but allows researchers unprecedented views of organs, tissue, and even live specimens.

    Just practicing with it, Branch knew it was a game-changer. She cried when she saw the first pictures of a mouse brain, its individual neurons glowing red, and its spindly dendrites, too—showing quite clearly the links between those cells.

    “It feels so amazing to see the brain in a way that no one has ever seen it before,” she said. “It’s pretty much the greatest thing I’ve ever experienced in science.”

    The selective plane florescence light sheet microscope arrived on campus in April, one of the first in operation on the East Coast and the only one in Maryland. Purchased with a grant from the National Institutes of Health, it cost $360,000.

    Unlike other microscopes, this one illuminates specimens from the side, shooting two perfectly aligned planes of light across an object, illuminating a wafer-thin slice of the whole while the camera captures the image—thousands of times over as the specimen moves through the light. When the images are displayed together, the result is a three-dimensional image or video clip of the full object, sort of like the more familiar CAT scan.

    The technology is very new, but Michael McCaffery, director of the university’s Integrated Imaging Center, expects researchers everywhere will be using it within a few years. Just among the Johns Hopkins community, word of the light sheet is already out and scientists have been lining up to use it—even if that requires the minor inconvenience of bringing specimens over from the medical campus.

    “People really want to use this,” McCaffery said. “It fills a niche that until now was unavailable at Hopkins. Simply, there was no instrument that allowed a researcher to take a whole organ, brain, or cardiac muscle, and image them in three-dimensions, in their entirety.”

    The light sheet is the latest advance in modern microscopy—a world that’s been evolving since fluorescence microscopy became the standard in the 1960s. Now, most researchers use confocal microscopes, which use lasers to illuminate a sample point by point—only extremely tiny samples will work—then create computerized images, pixel by pixel.

    Confocals produce vivid, high-resolution images, but the sample size limitations—nothing thicker than about 70 microns, which is about as wide as a strand of human hair—severely handicapped scientists.

    The new light sheet allows samples up to 12 to 15 millimeters, or about a half an inch. Researchers can study much larger samples, even entire organs. And because the samples don’t have to be cut up, researchers like Branch who are interested in how cells, ducts, or veins connect have a chance to observe them, unspoiled.

    “It’s a very big deal for researchers, particularly those interested in the science of connectomics,” McCaffery said. “Mapping the neuronal connections of the brain is the holy grail of neurology.”

    It’s certainly Branch’s holy grail.

    Branch is a Kavli Neuroscience Discovery Institute fellow working in the Krieger School of Arts and Sciences. She wants to know how newborn neurons, which are key to making memories, connect to other cells in the brain—and how those connections might change as people age.

    Scientists know the number of newborn neurons declines with age, and that likely has something to do with why short-term memory declines with age. What Branch wants to do is audit these newborn cells in a young brain, determining how many there are, where they are, and what other cells they communicate with. She can compare that with an older brain and possibly see which connections have broken when memory loss occurs. If she can target the broken connections, there could be a way to treat the area with a drug and stop or slow cognitive decline.

    Branch has been practicing on the light sheet with mouse brains, and she plans to formally investigate her hypothesis with rat brains, which are bigger and more human-like.

    If she didn’t have the light sheet, Branch would have to slice the brain, which is about the size of an olive pit, into tissue-thin sections—about 250 pieces. Each slice would need to be stained, mounted onto a slide, and then imaged. Each of those images would need to be manually assembled into a composite to approximate the whole.

    All of this work would take about a month. Since Branch’s experiment involves 30 brains, it would take her about two and a half years, “if,” she says, “that’s all I did day in and day out.”

    Worse yet, by slicing the brain, she would lose most of the newborn neurons she needed to find, and probably all of the connections. She figures if she had marked 50 newborn neurons, she’d be lucky to find five.

    “It would be impossible to find the connections,” she says. “And it would be impossible to get an idea of who each of those cells is talking to. Maybe it’s not important, but I’m guessing that’s not the case. Neurons in isolation aren’t interesting; it’s who they’re talking to, it’s how they’re wired.

    “I was just going to have to estimate. I’d have missed a lot of the picture, and that’s all anyone’s been able to do.”

    Guy Bar-Klein, a neuroscientist working in the Hal Dietz Lab at the School of Medicine, has been crossing town to spend time at Homewood’s Dunning Hall with the light sheet to study blood vessels in the heart and brain, hoping to better understand what causes aneurysms.

    Without the light-sheet technology, his view would be limited to a minuscule section of tissue, much too small to get a true sense of its vasculature. Now, he has been looking at samples with intact blood vessels, making it possible to spot and track aneurysms—and possibly pinpoint the underlying issues that caused it to form.

    “It’s very exciting,” Bar-Klein said. “I think it gives us a very substantial advantage in understanding the signaling involved in aneurysm formation.”

    Michael Noë, a pathology resident who studies pancreatic cancer, hopes the light sheet’s three-dimensional perspective will allow him to see relationships between tumors and the surrounding nerves and blood vessels. Tumors often grow around nerves, and Noë expects the new perspective of cancerous ducts and nerves could shed light on why.

    “For almost 200 years, pathologists looked at tissue the same way,” he says. “Three-dimensional is almost a whole new world for us. There is a lot of excitement in the department of pathology to apply this technology for the first time to human samples.”

    Before researchers can view tissue of any sort with the light-sheet, their samples must be treated to make them translucent, so the microscope’s light can pass through and create an image. Noë has developed a protocol for clearing human tissue and tumors, work he’s hoping to publish.

    Branch expects to have 3-D images of all 30 of her rat brains in three to six months.

    She’ll see every newborn neuron. She’ll see each dendrite. And hopefully, she’ll find answers – she already knows she’ll find more questions.

    “The technology makes it easier to have confidence about our findings,” she says, “It also opens up an opportunity to ask even more questions — things that before, we didn’t even know we could ask.”

    See the full article here .

    Please help promote STEM in your local schools.
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    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

     
  • richardmitnick 9:30 am on July 12, 2017 Permalink | Reply
    Tags: , , How old are your cells? New method determines cell age more accurately, JHU - Johns Hopkins University, , The biophysical qualities of cells such as cell movements and structural features make better measures of functional age than other factors including cell secretions and cell energy   

    From Hopkins: “How old are your cells? New method determines cell age more accurately” 

    Johns Hopkins
    Johns Hopkins University

    7.11.17
    Arthur Hirsch

    1
    Glandular tissue at 20x magnification. Image credit: Getty Images.

    Sure, you know how old you are, but what about your cells? Are they the same age? Are they older, younger? Why does it matter?

    Led by scientists at Johns Hopkins University, a team of researchers is reporting progress in developing a method to accurately determine the functional age of cells, a step that could eventually help clinicians evaluate and recommend ways to delay some health effects of aging and potentially improve other treatments, including skin graft matching and predicting prospects for wound healing.

    In the current issue of Nature Biomedical Engineering, lead author Jude M. Phillip, who conducted this research while completing his doctorate in chemical and biomolecular engineering at Johns Hopkins, reports success in creating a system that considers a wide array of cellular and molecular factors in one comprehensive aging assessment.

    These results show that the biophysical qualities of cells, such as cell movements and structural features, make better measures of functional age than other factors, including cell secretions and cell energy.

    The multidisciplinary team of engineers and clinicians examined dermal cells from just underneath the surface of the skin taken from both males and females between the ages of 2 and 96.

    The researchers from Johns Hopkins, Yale University, and the National Cancer Institute of the National Institutes of Health hoped to devise a system that, through computational analysis, could take the measure of various factors of cellular and molecular functions. From that information, they hoped to determine the biological age of individuals more accurately using their cells, in contrast to previous studies, which makes use of gross physiology, or examining cellular mechanisms such as DNA methylation.

    “We combined some classic biomolecular hallmarks of aging, and sought to further elucidate the role of biophysical properties of aging cells, all in one study,” said Phillip, now a post-doctoral fellow at Weill Cornell Medicine.

    Researchers trying to understand aging have, up until now, focused on factors such as tissue and organ function and on molecular-level studies of genetics and of epigenetics, meaning heritable traits that are not traced to DNA. The level in between—cells—has received relatively little attention, the researchers wrote.

    This research was meant to correct for that omission by considering the biophysical attributes of cells, including such factors as the cells’ ability to move, maintain flexibility, and structure. This focus emerges from the understanding that changes associated with aging at the physiological level—such as diminished lung capacity, grip strength, and mean pressure in the arteries—”tend to be secondary to changes in the cells themselves, thus advocating the value of cell-based technologies to assess biological age,” the research team wrote.

    For example, older cells are more rigid and do not move as well as younger cells, which, among other consequences, most likely contributes to the slower wound healing commonly seen in older people, said Denis Wirtz, the senior author and Johns Hopkins’ vice provost for research. Wirtz and Phillip conducted their research in the Johns Hopkins Institute for NanoBioTechnology.

    From the analysis, they were able to stratify individuals’ samples into three groups: those whose cells roughly reflected their chronological age, those whose cells were functionally older, and those whose cells were functionally younger. The results also showed that the so-called biophysical factors of cells determined a more accurate measure of age than biomolecular factors such as cell secretions, cell energy, and the organization of DNA.

    Phillip explained that this better accuracy from the biophysical factors most likely results from the orchestration of many biomolecular factors. He compared it to the more complete picture you get looking at a forest from a distance without binoculars.

    “With binoculars you can see details about the individual trees, the color and shapes of the leaves, the roughness of the bark, the type of tree, but without the binoculars you can now see the density of the trees, and whether there is a barren plot, or a group or dying trees,” Phillip said. “This is something you may miss with the binoculars, unless you are looking at the correct spot.”

    The more accurate system could eventually enable clinicians to see aging in cells before a patient experiences age-related health decline. This in turn could allow doctors to recommend treatments or changes in life habits, such as exercise or diet changes, Wirtz said. Phillip said the work could potentially help clinicians produce more successful skin grafts by matching cell characteristics of the donor and the graft site. Other potential applications range from toxicology screening for cosmetics and topical therapeutics to predicting progression of some age-related diseases.

    The researchers acknowledge that the system needs further testing with a larger cell sample, but the results are robust and encouraging. Conducted along with clinicians such as Jeremy Walston, the Raymond and Anna Lublin Professor of Geriatric Medicine, and co-director of the Biology of Healthy Aging program at the Johns Hopkins School of Medicine, this work promises to allow clinicians to measure a person’s health in the present and the future.

    “It opens the door to finally be able to track how a person is doing at the cellular level,” Wirtz said.

    Added Phillip: “This platform is also more than just a cellular age predictor; it has the ability to do so much more in terms of assessing an individual’s cellular health.”

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

     
  • richardmitnick 9:51 pm on July 1, 2017 Permalink | Reply
    Tags: Cloning Thousands of Genes for Massive Protein Libraries, , JHU - Johns Hopkins University, LASSO (long-adapter single-strand oligonucleotide) probes, New DNA-based LASSO molecule probe can bind target genome regions for functional cloning and analysis, , University of Trento   

    From Rutgers: “Cloning Thousands of Genes for Massive Protein Libraries” 

    Rutgers University
    Rutgers University

    June 26, 2017
    Todd B. Bates

    1
    New DNA-based LASSO molecule probe can bind target genome regions for functional cloning and analysis. Photo: Jennifer E. Fairman/JHU

    Discovering the function of a gene requires cloning a DNA sequence and expressing it. Until now, this was performed on a one-gene-at-a-time basis, causing a bottleneck. Scientists at Rutgers University-New Brunswick in collaboration with Johns Hopkins University and Harvard Medical School have invented a technology to clone thousands of genes simultaneously and create massive libraries of proteins from DNA samples, potentially ushering in a new era of functional genomics.

    “We think that the rapid, affordable, and high-throughput cloning of proteins and other genetic elements will greatly accelerate biological research to discover functions of molecules encoded by genomes and match the pace at which new genome sequencing data is coming out,” said Biju Parekkadan, an associate professor in the Department of Biomedical Engineering at Rutgers University-New Brunswick.

    In a study published online today in the journal Nature Biomedical Engineering, the researchers showed that their technology – LASSO (long-adapter single-strand oligonucleotide) probes – can capture and clone thousands of long DNA fragments at once.

    As a proof-of-concept, the researchers cloned more than 3,000 DNA fragments from E. coli bacteria, commonly used as a model organism with a catalogued genome sequence available.

    “We captured about 95 percent of the gene targets we set out to capture, many of which were very large in DNA length, which has been challenging in the past,” Parekkadan said. “I think there will certainly be more improvements over time.”

    They can now take a genome sequence (or many of them) and make a protein library for screening with unprecedented speed, cost-effectiveness and precision, allowing rapid discovery of potentially beneficial biomolecules from a genome.

    In conducting their research, they coincidentally solved a longstanding problem in the genome sequencing field. When it comes to genetic sequencing of individual genomes, today’s gold standard is to sequence small pieces of DNA one by one and overlay them to map out the full genome code. But short reads can be hard to interpret during the overlaying process and there hasn’t been a way to sequence long fragments of DNA in a targeted and more efficient way. LASSO probes can do just this, capturing DNA targets of more than 1,000 base pairs in length where the current format captures about 100 base pairs.

    The team also reported the capture and cloning of the first protein library, or suite of proteins, from a human microbiome sample. Shedding light on the human microbiome at a molecular level is a first step toward improving precision medicine efforts that affect the microbial communities that colonize our gut, skin and lungs, Parekkadan added. Precision medicine requires a deep and functional understanding, at a molecular level, of the drivers of healthy and disease-forming microbiota.

    Today, the pharmaceutical industry screens synthetic chemical libraries of thousands of molecules to find one that may have a medicinal effect, said Parekkadan, who joined Rutgers’ School of Engineering in January.

    “Our vision is to apply the same approach but rapidly screen non-synthetic, biological or ‘natural’ molecules cloned from human or other genomes, including those of plants, animals and microbes,” he said. “This could transform pharmaceutical drug discovery into biopharmaceutical drug discovery with much more effort.”

    The next phase, which is underway, is to improve the cloning process, build libraries and discover therapeutic proteins found in our genomes, Parekkadan said.

    Other authors include Lorenzo Tosi, Viswanadham Sridhara, Yunlong Yang, Dongli Guan and Polina Shpilker of Harvard Medical School; Nicola Segata of the University of Trento in Trento, Italy; and H. Benjamin Larman of Johns Hopkins University.

    See the full article here .

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    Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

    Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

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  • richardmitnick 9:39 am on June 23, 2017 Permalink | Reply
    Tags: Adegoke Olubusi, , JHU - Johns Hopkins University, Johns Hopkins grad from Nigeria wants to help hospitals in West Africa go digital, , OneMedical   

    From Hopkins: “Johns Hopkins grad from Nigeria wants to help hospitals in West Africa go digital” 

    Johns Hopkins
    Johns Hopkins University

    6.22.17
    Katie Pearce

    1
    Adegoke Olubusi. No image credit.

    OneMedical, founded by WSE alum Adegoke Olubusi, among 15 finalists in Cisco Global Problem Solver Challenge

    Though paper-based health care is a thing of the past for many hospitals and clinics around the world, in West Africa it’s still the dominant standard.
    Adegoke Olubusi wants to change that.

    The tech entrepreneur, a recent graduate of the Johns Hopkins Whiting School of Engineering, started OneMedical to help hospitals in West Africa go digital. His team has already begun that process in Nigeria, partnering with more than a dozen hospitals.

    Now OneMedical is looking at big opportunity for new funding: the Cisco Global Problem Solver Challenge. The team is one of 15 finalists in the digital innovation challenge, which includes a $10,000 People’s Choice Award open for votes through June 28.

    Olubusi, who was born and raised in Nigeria before moving to Maryland for school about a decade ago, has visited his home country often in recent years to work on tech projects like KingsChat, a leading social media platform in Africa.

    When his work brought him to hospitals, Olubusi says he found “chaos” in their record-keeping, complicating everything from patient data and billing to inventory. “It’s all on paper—it’s messy, inefficient, and there’s no way to analyze the data,” he says.

    But in launching a startup to address these problems, he and his team knew they couldn’t simply transplant U.S. standards into hospitals that had never used electronic records before.

    2
    The training interface of OneMedical. No image credit.

    “We thought, ‘How can we make something simple and easy to adopt for hospitals to operate more efficiently?'” says Olubusi, who has also previously worked as an analyst for eBay, PayPal, and Goldman Sachs.

    So he and his team—including rising Johns Hopkins junior Sami Ayele—sat down with health care workers in Nigeria to develop prototypes.

    “Eventually that turned into an actual idea for a business, and a concept that a lot of people loved,” Olubusi says.

    OneMedical offers a user-friendly platform to help hospitals simplify records and streamline processes, with the goal of improving both quality of care and profit margins. It includes a searchable database of patient records, along with features for tracking finances, staff, and medical supplies. The system runs offline at hospitals and syncs to the cloud when there’s an Internet connection available, and it’s accessible through any smart device or operating system.

    Hospitals partnering with OneMedical in this early stage are seeing results such as shorter patient wait times and decreased workload for medical staff, the team says. Meanwhile, a waitlist is growing, with more than 25 facilities in Nigeria hoping to get on board.

    OneMedical aspires to reach 125 facilities within the next year, ultimately fanning out to other parts of West Africa. The startup is currently part of the Y Combinator accelerator program and last year won Etisalat’s Innovation Award.

    Now, with the Cisco Global Problem Solver Challenge, the team is vying for a shot at a $100,000 grand prize, among other possibilities. OneMedical stood out from the more than 1,000 startups applying to land in the finals of the global competition, which seeks digital solutions to tackle economic, social, and environmental challenges.

    OneMedical’s entry for Cisco’s $10,000 People’s Choice award includes a video pitch from Olubusi and partner Nick Moore. Votes from the public can be cast online through June 28, and Cisco will announce the winners from all categories on June 29.

    OneMedical can be reached at team@onemedical.ng.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

     
  • richardmitnick 9:20 am on June 5, 2017 Permalink | Reply
    Tags: , , Idea Lab projects focus on leadership and community building de-escalation and career skills, JHU - Johns Hopkins University   

    From Hopkins: “Idea Lab projects focus on leadership and community building, de-escalation, career skills” 

    Johns Hopkins
    Johns Hopkins University

    June 1, 2017
    Sandra Alexander

    Six more projects submitted this spring to the Idea Lab, Johns Hopkins’ online crowdsourcing platform, have been selected to receive funding, joining five other proposals that will be funded because they received the most online votes.

    A committee selected three proposals from among the many that were submitted to the Ten by Twenty Challenge, which is issued each year by JHU President Ronald J. Daniels and draws its themes from the priorities outlined in the university’s vision for the future. This year the challenge called for ideas to foster individual excellence.

    Project Charmify (JHED login required for project links), a nonprofit initiative run by JHU undergraduates, will teach high school students from Baltimore’s Old Town neighborhood leadership and community development skills and then help them create programs that support community needs in underutilized spaces. Activities may include an outdoor movie night, a community garden, and workshops to coincide with the neighborhood’s open air market. The Project Charmify team has already completed a pilot program with support from JHU’s Social Innovation Lab. They said in their proposal they will use the $20,000 funding from the Ten by Twenty Challenge to move to the next phase and “help those who grew up in Baltimore realize their potential to become the city’s next generation of community leaders.”

    Baltimore is also the focus of 7 in the City: A Multimedia Journalism Project, which will receive $10,000 to create films and written profiles that explore what it is like to be a 7-year-old growing up in the city. The two-semester class will involve students from the Krieger School’s Advanced Academic Program’s MA in Writing and MA in Science Writing programs, Morgan State University’s School of Global Journalism, and JHU’s Department of Film and Media Studies, and will look specifically at public health issues, race, class, and educational and economic disparities.

    Staff of the Sheridan Libraries proposed Mining and Dining: Exploring Text Mining Tools in a Fun Setting in response to feedback from graduate students suggesting that it would be helpful to their careers to better understand the tools and methodologies of textual analysis. With $2,367 in Idea Lab funding, library staff will organize a series of informal workshops over lunch to introduce participants to digital scholarship tools.

    Three more winners were also chosen to receive $2,500 Diversity Innovation Grants, which are awarded by the Diversity Leadership Council using the Idea Lab as a submission platform.

    The Student Research Ambassador Program seeks to address the underrepresentation of students from diverse and low-income backgrounds in academic research. It will be administered by the Krieger School’s director of undergraduate research and will create a network of graduate and undergraduate researchers who share information on finding faculty mentors, locating funding, and writing proposals with peers, among other topics.

    Members of the Black Faculty and Staff Association and JHU students plan to provide a De-escalation Workshop to students in Baltimore City public schools and after-school programs. According to the proposal, “The rate of catastrophic deaths for our city youth increases as the weather turns warm, and many are left on their own without supervision while their parents are working.” The workshop will discuss how the police assess threats and how to communicate with police and others to calm a situation.

    The Information Hub for Latinos will be part of the Hopkins Latino Alliance Community Initiative and will collect information and resources on a new website and app. The project team said in its proposal it will work with Johns Hopkins-affiliated organizations and community leaders to gather information on events, scholarships, grants, summer opportunities, affinity groups, and health promotion.

    All of the 2017 submissions and comments are available with a JHED login credential on the Idea Lab website.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

     
  • richardmitnick 3:28 pm on May 26, 2017 Permalink | Reply
    Tags: , , , JHU - Johns Hopkins University,   

    From Hopkins: “FDA approves cancer drug for personalized immunotherapy approach” 

    Johns Hopkins
    Johns Hopkins University

    5.25.17
    Vanessa Wasta

    1
    T-cells attacking a cancer cell. Image credit: istock

    Earlier this week, for the first time, a drug was FDA-approved for cancer based on disease genetics rather than type.

    Developed from 30 years of basic research at Johns Hopkins and its Bloomberg–Kimmel Institute, the drug, pembroluzimab, now can be used for colon, pancreatic, stomach, ovarian, and other cancers if genetic testing reveals defects in so-called mismatch repair genes.

    Experts at the Bloomberg–Kimmel Institute designed the first clinical trial to test the theory that patients whose tumors have defects in mismatch repair genes may respond better to immunotherapy. Results of the trial were presented and published in 2015 at the American Society of Clinical Oncology Annual Meeting and published online by The New England Journal of Medicine.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

     
  • richardmitnick 3:20 pm on May 26, 2017 Permalink | Reply
    Tags: , , JHU - Johns Hopkins University,   

    From Hopkins: “New cellular target may put the brakes on cancer’s ability to spread” 

    Johns Hopkins
    Johns Hopkins University

    5.26.17
    Phil Sneiderman

    Johns Hopkins-led team finds promising way to disrupt signals that trigger metastasis

    1
    Bladder cancer, transitional cell carcinoma. Image credit: rightdx

    A team led by Johns Hopkins researchers has discovered a biochemical signaling process that causes densely packed cancer cells to break away from a tumor and spread the disease elsewhere in the body.

    In their study, published online today in Nature Communications, the team also reported that the combined use of two existing drugs disrupts this process and appears to significantly slow cancer’s tendency to travel, a behavior called metastasis.

    The new findings are important, the researchers said, because 90 percent of cancer deaths are caused by metastasis, and anything that derails this activity could improve the prognosis for patients. The crucial new signaling process turned up when the team took a closer look at cellular events that promote metastasis.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

     
  • richardmitnick 12:59 pm on May 13, 2017 Permalink | Reply
    Tags: , , JHU - Johns Hopkins University,   

    From Hopkins: “New study sheds light on why cancer often strikes those with healthy lifestyles” 

    Johns Hopkins
    Johns Hopkins University

    Mar 23, 2017
    Vanessa Wasta

    1
    Yellow breast cancer cell on a red background. Wikimedia Commons

    A new study by scientists at Johns Hopkins provides evidence that random, unpredictable DNA copying “mistakes” account for nearly two-thirds of the mutations that cause cancer.

    The researchers say their conclusions are supported by epidemiologic studies showing that approximately 40 percent of cancers can be prevented by avoiding unhealthy environments and lifestyles. But among the factors driving the new study, they add, is that cancer often strikes people who follow all the rules of healthy living—nonsmoker, healthy diet, healthy weight, little or no exposure to known carcinogens—and have no family history of the disease, prompting the pained question, “Why me?”

    “It is well-known that we must avoid environmental factors such as smoking to decrease our risk of getting cancer. But it is not as well-known that each time a normal cell divides and copies its DNA to produce two new cells, it makes multiple mistakes,” says Cristian Tomasetti, assistant professor of biostatistics at the Johns Hopkins Kimmel Cancer Center and the Johns Hopkins Bloomberg School of Public Health. “These copying mistakes are a potent source of cancer mutations that historically have been scientifically undervalued, and this new work provides the first estimate of the fraction of mutations caused by these mistakes.”

    Adds Bert Vogelstein, co-director of the Ludwig Center at the Kimmel Cancer Center: “We need to continue to encourage people to avoid environmental agents and lifestyles that increase their risk of developing cancer mutations. However, many people will still develop cancers due to these random DNA copying errors, and better methods to detect all cancers earlier, while they are still curable, are urgently needed,”

    Tomasetti and Vogelstein’s research will be published Friday [3.23.17] in the journal Science.

    Current and future efforts to reduce known environmental risk factors, they say, will have major impacts on cancer incidence in the U.S and abroad. But they say the new study confirms that too little scientific attention is given to early detection strategies that would address the large number of cancers caused by random DNA copying errors.

    “These cancers will occur no matter how perfect the environment,” Vogelstein says.

    Current and future efforts to reduce known environmental risk factors, they say, will have major impacts on cancer incidence in the U.S and abroad. But they say the new study confirms that too little scientific attention is given to early detection strategies that would address the large number of cancers caused by random DNA copying errors.

    “These cancers will occur no matter how perfect the environment,” Vogelstein says.

    In a previous study authored by Tomasetti and Vogelstein in the Jan. 2, 2015, issue of Science, the pair reported that DNA copying errors could explain why certain cancers in the U.S., such as those of the colon, occur more commonly than other cancers, such as brain cancer.

    In the new study, the researchers addressed a different question: What fraction of mutations in cancer are due to these DNA copying errors?

    To answer this question, the scientists took a close look at the mutations that drive abnormal cell growth among 32 cancer types. They developed a new mathematical model using DNA sequencing data from The Cancer Genome Atlas and epidemiologic data from the Cancer Research UK database.

    According to the researchers, it generally takes two or more critical gene mutations for cancer to occur. In a person, these mutations can be due to random DNA copying errors, the environment, or inherited genes. Knowing this, Tomasetti and Vogelstein used their mathematical model to show, for example, that when critical mutations in pancreatic cancers are added together, 77 percent of them are due to random DNA copying errors, 18 percent to environmental factors (such as smoking), and the remaining 5 percent to heredity.

    In other cancer types, such as those of the prostate, brain, or bone, more than 95 percent of the mutations are due to random copying errors.

    Lung cancer, they note, presents a different picture: 65 percent of all the mutations are due to environmental factors, mostly smoking, and 35 percent are due to DNA copying errors. Inherited factors are not known to play a role in lung cancers.

    Looking across all 32 cancer types studied, the researchers estimate that 66 percent of cancer mutations result from copying errors, 29 percent can be attributed to lifestyle or environmental factors, and the remaining 5 percent are inherited.

    The scientists say their approach is akin to attempts to sort out why “typos” occur when typing a 20-volume book: being tired while typing, which represents environmental exposures; a stuck or missing key in the keyboard, which represent inherited factors; and other typographical errors that randomly occur, which represent DNA copying errors.

    “You can reduce your chance of typographical errors by making sure you’re not drowsy while typing and that your keyboard isn’t missing some keys,” Vogelstein says. “But typos will still occur, because no one can type perfectly. Similarly, mutations will occur, no matter what your environment is, but you can take steps to minimize those mutations by limiting your exposure to hazardous substances and unhealthy lifestyles.”

    Tomasetti and Vogelstein’s 2015 study created vigorous debate from scientists who argued that their previously published analysis did not include breast or prostate cancers, and it reflected only cancer incidence in the United States.

    Tomasetti and Vogelstein now report a similar pattern worldwide, however, supporting their conclusions. They reasoned that the more cells divide, the higher the potential for so-called copying mistakes in the DNA of cells in an organ. They compared total numbers of stem cell divisions with cancer incidence data collected by the International Agency for Research on Cancer on 423 registries of cancer patients from 68 countries other than the United States, representing 4.8 billion people, or more than half of the world’s population. This time, the researchers were also able to include data from breast and prostate cancers. They found a strong correlation between cancer incidence and normal cell divisions among 17 cancer types, regardless of the countries’ environment or stage of economic development.

    Tomasetti says these random DNA copying errors will only get more important as societies face aging populations, prolonging the opportunity for our cells to make more and more DNA copying errors. And because these errors contribute to a large fraction of cancer, Vogelstein says that people with cancer who have avoided known risk factors should be comforted by their findings.

    “It’s not your fault,” says Vogelstein. “Nothing you did or didn’t do was responsible for your illness.”

    In addition to Tomasetti and Vogelstein, Lu Li, a doctoral student in Tomasetti’s laboratory in the Department of Biostatistics at the Johns Hopkins Bloomberg School of Public Health, also contributed to the research.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

     
  • richardmitnick 10:56 am on April 21, 2017 Permalink | Reply
    Tags: , , HOUR - Hopkins Office for Undergraduate Research, JHU - Johns Hopkins University   

    From Hopkins: “A new home for undergraduate research at Johns Hopkins” 

    Johns Hopkins
    Johns Hopkins University

    4.19.17
    Katie Pearce

    1
    Excerpt from time-lapse photography project by PURA awardee Ambrose Tang. Image credit: Ambrose Tang

    There is no tidy definition for the word “research” when it comes to the varied pursuits taking place across Johns Hopkins University.

    “What it calls to mind for many people is bench science, and obviously Hopkins has a lot of that, but we take a broader view,” says Feilim Mac Gabhann, director of the new Hopkins Office for Undergraduate Research [HOUR]. He says research can take the form of “any creative endeavor that brings new knowledge or new insights that weren’t there before.”

    That expansiveness will be on full display at Friday’s DREAMS event, the new office’s inaugural event, which will showcase undergraduate research at the Homewood campus.

    The 250-plus presentations will include, for example, a photography project from Peabody Institute junior Ambrose Tang, who won a grant to explore time-lapse techniques in capturing scenes of his home city of Hong Kong. The end result will present like a film, though he recorded no video—it’s a textured quilt of still photos, with 24 images making up every one second of footage.

    Also presenting at the showcase is Danait Yemane, a public health studies senior whose research took the form of cultural investigation. She traveled to Eritrea, where her parents were born, to learn firsthand about the impacts of the country’s compulsory military service. While the conscriptions are meant to be finite, Yemane found they’d become a long-time occupation for many Eritreans who shared their stories with her.

    The DREAMS event—which takes place April 21 from 1 to 4 p.m. in Goldfarb Gym—covers disciplines across Johns Hopkins, including engineering, science, medicine, and the arts and humanities. Presentation topics include cancer research, medieval artwork, urban gardening, robotics, and immigration, and presenters include recent awardees of the PURA program, which provides $2,500 research stipends. Both Tang and Yemane were recipients last year.

    The Hopkins Office for Undergraduate Research—HOUR, for short—launched in March under Vice Provost for Research Denis Wirtz with the mission to create a broad, centralized support structure for undergraduates to pursue their research.

    “I believe in the university being a real living thing that is larger than one lab, or one department, or one school,” says Mac Gabhann, who is an associate professor of biomedical engineering and part of JHU’s Institute for Computational Medicine.

    To help connect students to research opportunities both inside and outside of Hopkins, HOUR is building out a new database listing available grants and summer research programs.

    One summer program they’re highlighting is CIRCUIT, which allows undergraduates of any background to take part in brain-mapping research at the Johns Hopkins Applied Physics Laboratory. The program provides a $5,000 stipend for living expenses.

    Such stipends, HOUR recognizes, are critical for reducing the barriers for fledgling young researchers. That’s the principle behind another new offering, the STAR program, which provides $4,000 stipends for summer research of the student’s choice within any Hopkins partnership, in Baltimore or beyond.

    HOUR also intends to serve an educational role of its own. A range of training materials, such as videos and tutorials, will help students learn about every step of the research process, from applying for grants and preparing budgets to making public presentations.

    To stay in the loop with new opportunities from HOUR, follow them on Twitter and Facebook. Registration for the DREAMS event is open through April 19, and though deadlines have passed for the CIRCUIT and STAR programs, new application cycles will open next winter.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

     
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