A research assistant uses a pipette to change media that feed trays of human embryonic stem cell cultures in a UW—Madison research lab.
Photo: Jeff Miller. With about lines of code, a Morgridge Institute for Research team has unleashed a fast, simple and predictive text-mining tool that may turbocharge big biomedical pursuits such as drug repurposing and stem cell treatments. Within hours, it can scan the more than 30 million papers online in Europe PMC and provide ranked associations for select target terms and key phrases. The summit showcases new applications in bioinformatics that are improving health care.
The scientists emphasize that while their queries focused on biomedicine, KinderMiner can be applied to any discipline — the only constant is the need for a massive corpus to search. The next step will be to create an online search interface available for the scientific community. To test KinderMining, the team chose two scientific projects that prove to be time consuming and often intractable.
The first is identifying relevant transcription factors to reprogram stem cells, and the second is finding potential drugs with off-label benefits or adverse effects. For cell reprogramming, there are about 2, known transcription factors that might be useful in changing a cell from one state to another, such as creating induced pluripotent stem iPS cells from skin cells.
They used KinderMining on three reprogramming efforts that are well established in research literature: creating iPS cells, creating cardiomyocytes, and maturation of liver cells.Assistenza domiciliare anziani e nuclei familiari in difficoltà
To show the predictive power of the algorithm, the team censored the literature by date, taking out all papers beginning two years before the published dates of each discovery. They queried only up to for iPS cells, for cardiomyocytes and for liver cells. The results in all three tests identified numerous relevant transcription factors in the top 20 hits — again, from a potential pool of more than 2, factors. This is a substantial benefit to the wet lab scientists, given that the factors likely need to act in combination.
For instance, if one needs to test all 2, factors four at a time, it represents billion experiments — clearly outside the realm of possibility. Now if scientists test 10 factors four at a time, it requires a manageable experiments, Stewart says. They compared their results against a state of the art data mining tool called Mogrify, and the KinderMining results overlap on a large proportion of accurate hits.
The second big test involved scanning Europe PMC to identify drugs that have the effect of reducing blood glucose. Of the top 50 drugs found, 43 are known diabetes treatments, but the team found seven drugs that either raise or lower blood glucose as a secondary, off-label effect.Kafka docker production
Those hits are especially important as they demonstrate possible prediction of repurposed drug targets. Repurposed drugs make up about 30 percent of all new drugs or vaccines approved by the U. Food and Drug Administration. David Page, a co-author on the study and a professor of biostatistics and medical informatics at UW—Madison, says he is excited about the potential of KinderMiner to identify promising drugs to repurpose. Kuusisto and Page have received approval to use approximately 10 million de-identified electronic health records from the Veterans Administration to continue the drug repurposing work, examining several drug effects such as lowering of cholesterol levels or blood pressure.
Tags: datadrugshealth careMorgridge Institute for Researchresearchstem cells. University of Wisconsin—Madison. Ron Stewart. Finn Kuusisto. Share via Facebook. Share via Twitter.
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Include any more information that will help us locate the issue and fix it faster for you. Data visualization has always been an important aspect of CASA's research output. With this in mind, I spend much time and effort on the visual representation of my findings, and this is reflected well in the structure of our course.
Building on an introduction to Geographic Information Science, an applied class in digital visualization techniques, a wide range of software packages and techniques, and an optional introduction to the Processing language for people without previous programming experience, I am frequently encouraged to produce visual representations to illustrate and explore a particular scenario or data set. Professors and peers in class then review my work.
I learned a lot just from watching others, and from having my own work critiqued. One commonality is the heavy reliance on computational methods, be it in the acquisition of data, the analysis, or the presentation of insights.
In more than one group project my colleagues and I were making use of online collaboration softwares to produce and refine documents while we were meeting. This works well when everyone is in the same room, but this has also helped me bridge physical distances. After having experienced the benefits of document editors with live collaboration modes like Google Docs, Piratepad, or Prezisingle-person editors seem almost obsolete now.Microphone kit
Such multi-modal teamwork takes a bit of practice, but once it flows it feels magical. In he moved to London to work at the Internet startup Last. Relatively recent cultural trends along with many technological advances have led to dramatic increases in the area of capture. One specific domain that has seen fantastic technological advances is the capture of DNA sequence data.
The process of sequencing DNA involves translating an organism's DNA into the sequence of nucleobases bases of which it is composed.
While the methods for sequencing DNA have changed over the years, almost all have involved some process of breaking the DNA into small fragments and identifying the sequence of bases for each fragment using chemical markers. These small fragments are then reassembled into one large sequence. Early methods required extraordinary amounts of manual labor and were very expensive, but in the first automated DNA sequencer was introduced. These machines continued to get faster and cheaper at an incredible rate.
In fact, the task of sequencing the human genome, a sequence of more than 3 billion base pairs, began in and a rough draft was completed in Using more modern sequencers, this task could be completed in under a week and at a tiny fraction of the cost. With the help of automated DNA sequencers, increasingly massive quantities of genetic data are becoming available for all kinds of biological and medical research with each passing year.
Enjoy affordable access to over 18 million articles from more than 15, peer-reviewed journals. Get unlimited, online access to over 18 million full-text articles from more than 15, scientific journals. See the journals in your area. You can share this free article with as many people as you like with the url below!For his first weekend with the SPCO, his infectious energy meets Sibelius at his most introspective, anxious and uncertain.
The interpretation offered by Kuusisto and the SPCO was both earthy and ethereal, mysterious and disarmingly honest.
From hypnotic loping lines to dance rhythms both gleeful and propulsive, it was a delight, even when acting concertmaster Ruggero Allifranchini snapped a string on his violin, running off and replacing it with the speed of a Grand Prix pit crew. It proved such a success that the standing Stillwater crowd received an encore, a Nordic folk tune that had a lot of Celtic blood in it, performed by Kuusisto alone. If audiences call for more at other concerts this weekend, perhaps the SPCO strings can join the Finnish fiddler for an impromptu jam session that splices improvisational ideas from the worlds of folk and classical.
That sounds like fun. When and where: 8 p. Paul; 2 p. On the rooftop terrace of her Tehran apartment building, year-old Mojgan Hosseini's fingers pluck the strings of her qanun, an ancient stringed instrument, bringing life to an Iranian capital stilled by the coronavirus. The Minnesota Orchestra's season will feature 31 returning and debuting guest soloists and 12 guest conductors. Announced Friday, the season also features a special event in which Vanska and the orchestra will be joined Tuesday, April 21, on CBS.
The concert was recorded in January after the Grammy Awards. Sheila E. The St. Paul Chamber Orchestra announced Thursday that it will cancel all concerts through the end of the season, which would have ended June 14, due to the COVID outbreak. Minnesota Public Radio is inviting everyone across the state to join in Bring the Sing Home at p.
Soul Asylum, Chris Hawkey and Nur-D are among the Minnesota musical acts set to perform on a virtual benefit concert at p. Post was not sent - check your email addresses! Sorry, your blog cannot share posts by email.He also regularly directs the Tapiola Sinfonietta, and the Scottish and Swedish chamber orchestras. Kuusisto returns as violinist-director-conductor to the Tapiola Sinfonietta, and the Norwegian, Swedish and Scottish chamber orchestras.
The violinist brought considerable sweep to long lines, showed complete technical command and illuminated the overall architecture. Their performance was always unassuming and intelligent in delineating the phrasing and textures. It was the Proms debut of Pekka Kuusisto, the maverick Finnish violinist, improbably playing the Tchaikovsky Concerto. Tempos, freed from the weight of Romantic emotion and vibrato, suddenly danced, and melodies relocated from ballroom to barn shook off maturity for lightfooted youth.
Gilbert, the proprietor of the biennial, beamed. He played the Nielsen as though it had been written for him — actually he played it as though he had written it himself, so thoroughly did he inhabit this odd, compelling music… Kuusisto made every twist and turn of the score make sense, and conductor Mena was with him every step of the way. His rich full-bodied sound was mirrored by the orchestra with some lyrical contributions from the brass and playful exchanges with the woodwind section.
Frankly spectacular. After the final bravura notes, the audience just exploded, into an ovation that sounded less like sedate symphony-goers and more like the 12 th Man. This collaboration represented an inventive reimagining of the classical sound and offered the opportunity to hear this music afresh.
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Learn how we count contributions. Less More. You signed in with another tab or window.Pekka Kuusisto born 7 October in Espoo is a Finnish musician. Kuusisto comes from a musical lineage.
His grandfather was a composer and organist, his father is a jazz musician who has composed operas, and his mother is a music teacher. In he enrolled in the Sibelius Academy in Helsinkiand he began to study with Tuomas Haapanen there in InKuusisto became the first Finn to win the International Jean Sibelius Violin Competition and was also awarded a special prize for the best performance of the Sibelius violin concerto.
He has won other prizes, concertised widely, and recorded works for the Ondine label. Kuusisto works with musicians of many different backgrounds.
He regularly performs with electronics, giving concerts consisting of mostly improvised material.
During the past few years, he has frequently performed a solo recital program consisting of the Partita in D minor by Johann Sebastian Bach and electronic improvisations on funeral chorales. The traditional music of Finland serves as a source of inspiration for Kuusisto, and his approach to the violin has changed substantially since he became more involved with folk music and its performers.
Kuusisto also writes music, but mostly for small ensembles where he is one of the performers. He composed the music for the album Kiestinkiwith lyrics by Paula Vesala. Kuusisto has written music for a collaboration between himself, his brother Jaakko Kuusisto and the vocal ensemble Rajaton, themed on climate change.
He has also arranged Sibelius's string quartet Voces intimae for chamber orchestra. In classical circles, Kuusisto is internationally renowned both as soloist and director and is recognised for his fresh approach to the repertoire.
A strong advocate of new music, he regularly collaborates with contemporary composers and in the —13 season gave the world premiere of Sebastian Fagerlund's Violin Concerto, written for him and commissioned by the Tampere Philharmonic Orchestra.
Kuusisto seeks to engage with people across the artistic spectrum, working on new interpretations of existing repertoire alongside original works. He regularly directs ensembles from the violin, including the Australian, London, Irish, Mahler and Saint Paul chamber orchestras, as well as the Amsterdam Sinfonietta. He gave the world premiere of Olli Mustonen's Sonata for Violin and Piano with the composer at the Wigmore Hall in springand later the same year toured Europe with his traditional music group, The Luomu Players.
He also gave duo performances with juggler Jay Gilligan, joined the vocal group Rajaton and performed with Finnish schlager legend Paula Koivuniemi. He oversaw the programming for the Avanti! Summer Sounds Festival and continues to work regularly with Tapiola Sinfonietta, where he was formerly Artistic Partner Kuusisto was featured in the film 4 as the soloist of the winter quarter of a quartet of young musicians from around the world playing Vivaldi 's The Four Seasons.
Kuusisto has also composed the music for the animated show, Moominvalley TV seriesalong with Samuli Kosminen. That same year, Kuusisto was the main solist during the Prinsengrachtconcertan annual open-air concert held on the Prinsengracht in Amsterdam .
The televised version attracked From Wikipedia, the free encyclopedia. Finnish musician. For the Finnish ice hockey player, see Pekka Kuusisto ice hockey. EspooFinland. Ilkka Kuusistocomposer father.
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