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Daily Archives: January 26, 2022
Quantum Computing in Silicon Breaks a Crucial Threshold for the First Time – Singularity Hub
Posted: January 26, 2022 at 9:55 am
Quantum computers made from the same raw materials as standard computer chips hold obvious promise, but so far theyve struggled with high error rates. That seems set to change after new research showed silicon qubits are now accurate enough to run a popular error-correcting code.
The quantum computers that garner all the headlines today tend to be made using superconducting qubits, such as those from Google and IBM, or trapped ions, such as those from IonQ and Honeywell. But despite their impressive feats, they take up entire rooms and have to be painstakingly handcrafted by some of the worlds brightest minds.
Thats why others are keen to piggyback on the miniaturization and fabrication breakthroughs weve made with conventional computer chips by building quantum processors out of silicon. Research has been going on in this area for years, and its unsurprisingly the route that Intel is taking in the quantum race. But despite progress, silicon qubits have been plagued by high error rates that have limited their usefulness.
The delicate nature of quantum states means that errors are a problem for all of these technologies, and error-correction schemes will be required for any of them to reach significant scale. But these schemes will only work if the error rates can be kept sufficiently low; essentially, you need to be able to correct errors faster than they appear.
The most promising family of error-correction schemes today are known as surface codes and they require operations on, or between, qubits to operate with a fidelity above 99 percent. That has long eluded silicon qubits, but in the latest issue of Nature three separate groups report breaking this crucial threshold.
The first two papers from researchers at RIKEN in Japan and QuTech, a collaboration between Delft University of Technology and the Netherlands Organization for Applied Scientific Research, use quantum dots for qubits. These are tiny traps made out of semiconductors that house a single electron. Information can be encoded into the qubits by manipulating the electrons spin, a fundamental property of elementary particles.
The key to both groups breakthroughs was primarily down to careful engineering of the qubits and control systems. But the QuTech group also used a diagnostic tool developed by researchers at Sandia National Laboratories to debug and fine-tune their system, while the RIKEN team discovered that upping the speed of operations boosted fidelity.
A third group from the University of New South Wales took a slightly different approach, using phosphorus atoms embedded into a silicon lattice as their qubits. These atoms can hold their quantum state for extremely long times compared to most other qubits, but the tradeoff is that its hard to get them to interact. The groups solution was to entangle two of these phosphorus atoms with an electron, which enables them to talk to each other.
All three groups were able to achieve fidelities above 99 percent for both single qubit and two-qubit operations, which crosses the error-correction threshold. They even managed to carry out some basic proof-of-principle calculations using their systems. Nonetheless, they are still a long way from making a fault-tolerant quantum processor out of silicon.
Achieving high-fidelity qubit operations is only one of the requirements for effective error correction. The other is having a large number of spare qubits that can be dedicated to this task, while the remaining ones focus on whatever problem the processor has been set.
As an accompanying analysis in Nature notes, adding more qubits to these systems is certain to complicate things, and maintaining the same fidelities in larger systems will be tough. Finding ways to connect qubits across large systems will also be a challenge.
However, the promise of being able to build compact quantum computers using the same tried-and-true technology as existing computers suggests these are problems worth trying to solve.
Image Credit: UNSW/Tony Melov
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After First Pig-to-Human Heart Transplant, Scientists Aim to Make It Routine – Singularity Hub
Posted: at 9:55 am
Jan 7, 2022 marked a medical breakthrough. For the first time ever, surgeons transplanted a genetically modified pig heart into a living human. Two weeks later, David Bennett is doing well, with the heart pumping away and sustaining his life.
The surgery brings xenotransplantationtransplanting organs between speciesfrom a wild science fiction dream to reality. Its a milestone that paves the road for more people to receive animal organs, making up for donor organ shortages and potentially saving hundreds of thousands of lives. For now, its just a single case. The technology is still fraught with technical and ethical conundrums. But by carefully monitoring Bennett, scientists are hopeful they can access a trove of unprecedented data to aid future xenotransplants.
Make no mistake: whether youd call this opening a Pandoras box or a medical miracle, xenotransplants are taking off after decades of turmoil. Bennett is far from a one-off. Big players in the field are aiming for clinically controlled trials and have readily begun building clinic-grade facilities to raise pigs that meet the FDAs strict demands.
Heres how the team pulled it off.
Xenotransplantation has had quite the ride. First dreamed up in the 1960s, the idea languished for decades due to its sheer complexity. For one, theres no chance of an animal organ matching a human recipient, as transplants usually require. This generates a severe immune storm, destroying the organ and also damaging the host.
Another concern is animal viruses, which donor pigs can tolerate but wreak havoc on human cells. Some of these are tough to get rid of. Take PERVsporcine endogenous retroviruseswhich are embedded inside pigs DNA and need to be accurately snipped out with gene editing. For years, scientists worked out genetic changes that would transform a pig heart into one more amenable to a human chest. The problem? There was no way to make these changes.
Enter CRISPR. Due to the gene editors precision, xenotransplant enthusiasts finally have a tool to test out those theories. The field took off. In 2015 eGenesis, a life-science company, announced it had edited 62 segments of the pig genome responsible for immune rejection and infections. Genetically engineered pig hearts were soon transplanted into baboons, allowing them to survive for more than six months.
Yet the billion-dollar question remained: will it work for humans? Because non-human primates have different immune systems than ours, theyre less-than-ideal models. In 2021, we got a first answer. A kidney grown in a heavily genetically edited pig was transplanted into two people who were legally dead without brain function. The kidneys functioned normally for more than 50 days while the recipients were on life support. A similar recent case resulted in promisingthough mixedresults.
A leader in xenotransplants, Dr. Muhammad Mohiuddin has worked towards a successful pig-to-human transplant for years. The head surgeon at the University of Maryland Medical Center who pulled off Davids surgery, he had previously asked the FDA for approval for a clinical trial.
He was rejected. The agency was worried about the origin of the genetically edited pigs, requiring that they come from a clinic-grade facility.
Then Mohiuddin met Bennett. At 57 years old, Bennett had been on heart support for almost 2 months. With untreated high blood pressure and other health problems, he was ineligible for a human heart transplant. With his health rapidly declining, Bennett gave the go-ahead for the surgeons team to seek compassionate use authorization from the FDA for a pig heart transplant.
It was either die or do this transplant. I want to live. I know its a shot in the dark, but its my last choice, said Bennett.
The heart was provided by Revivicor, a company based in Virginia that has been engineering pig organs for roughly two decades. In several experiments for pig-to-baboon transplants, the organs survived up to nine months, until the animals passed away due to a lung infection unrelated to the transplant.
Overall, the heart had 10 hefty genetic edits. Three of them wiped out sugar molecules on the outside of cells that provoke an immune response. Six bolstered the chance of the human host accepting the heartamping up an anti-inflammatory response, preventing blood vessel damage, and dampening any antibodies against the organ. Finally, the last edit limited the pig hearts size. Although it generally matched the size of a human heart, the team wanted to prevent the pig organ from overgrowth inside Bennetts chest once it was transplantedsomething they previously noticed happened in baboons.
The next challenge was how to keep the heart healthy once it was removed from the pig. Heart failure occurs rapidly once deprived of blood and oxygen, and keeping the organs healthy and functional has been a major heartache (pun intended). Here, Mohiuddin tapped into a method developed in Sweden by Dr. Stig Steen at Lund University. Once removed, the heart is bathed in a bubbling, circulating bath chock-full of hormones, nutrients, and cocaine (yup, you read that right).
Then came the third part of the trifecta: immunosuppressants. Even with genetic edits, Bennett was kept on a hefty dose of a new antibody drug, dubbed anti-CD40, to dampen his immune system. Compared to previous generations the drug is like a master switch that shuts down antibody production, while also killing communication between different immune cells. This nixes the bodys ability to mount a coordinated attack against the new organ.
The 10 [altered] genes help, but the anti-CD40 antibody, which had been my main focus throughout my career, I think is the game changer, said Mohiuddin.
Bennett is doing well. Scientists dont yet know how long the heart will survive, but theyre carefully monitoring the organs function and Bennetts immune response. Theyre also obsessively keeping him away from any source of infection.
But as the living pioneer of xenotransplants, Bennett has lots to offer. Experts agree that its a remarkable chance to tailor an organ for humans, rather than for baboons as in previous lab experiments. Because we have far more antibodies that may attack the pig organ than baboons do, its critical to nail those responses down.
Another unsolved question is how the pig heart will behave in a human. According to one estimate, a pigs resting heart rate is roughly 90 beats per minute, which is on the high range of a healthy human heart.
The prospect of a future surge in xenotransplants is reigniting a bioethics firestorm. Is it ethical to grow pigs for whats essentially replacement organ parts for humans (cue humans as batteries for robots, la The Matrix)? Although theyre a popular food source, pigs are surprisingly intelligent creatures that, unlike human organ donors, have no say in the process. What if there are alternatives, like 3D printed organs?
For now, the technology remains highly experimental and risky. Failure, as seen in a previously tragic case, could lead to a tortuous death. And Bennett will be the first to experience the risk of porcine viruses, which the team is monitoring closely.
Another burning question is who should be allowed access, or placed at the top of a xenotransplant list? For example, people who need a kidney transplant can generally be put on dialysis as they wait for a human donor organ. Its a grueling process. But does that justify the dangers of an animal transplant?
As Dr. Jeremy Chapman, a retired transplant surgeon at the University of Sydney, told Nature, a long wait by itself isnt sufficient to justify approval. Bennett was granted the procedure and fully informed of the risks because it was his only chance for survivalshould the same guideline apply to others down the road?
We wont wait long for an answer. Revivicor still dominates the game. The company is readily working on a new clinic-grade facility according to FDA standards to increase pig production, with the aim of launching in 2023. Others are on its heels. eGenesis, for example, is tackling the PERV problem, genetically editing pigs that cant pass on those viruses to their human recipients. Nzeno, based in New Zealand, is breeding pigs for kidney transplants.
While many questions remain, the surgery is a landmark. This is truly a historic, monumental step forward, said Dr. Bert W. OMalley, president and CEO of the University of Maryland Medical Center.
Image Credit: Alexandru Acea on Unsplash
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This Week’s Awesome Tech Stories From Around the Web (Through January 22) – Singularity Hub
Posted: at 9:55 am
ROBOTICS
Now You Can Rent a Robotic Workerfor Less Than Paying a HumanWill Knight | WiredLast year, to meet rising demand amid a shortage of workers, Polar hired its firstrobot employee. The robot arm performs a simple, repetitive job: lifting a piece of metal into a press, which then bends the metal into a new shape. And like a person, the robot worker gets paid for the hours it works. Jose Figueroa, who manages Polars production line, says the robot, which is leased from a company calledFormic, costs the equivalent of $8 per hour, compared with a minimum wage of $15 per hour for a human employee.
Going Bald? Lab-Grown Hair Cells Could Be On the WayAntonio Regalado | MIT Technology ReviewWere born with all the hair follicles well ever havebut aging, cancer, testosterone, bad genetic luck, even covid-19 can kill the stem cells inside them that make hair. Once these stem cells are gone, so is your hair. [Ernesto] Lujan says his company can convert any cell directly into a hair stem cell by changing the patterns of genes active in it.
Autonomous Battery-Powered Rail Cars Could Steal Shipments From TruckersTim de Chant | Ars TechnicaParallel Systems isnt just taking an existing freight train andswapping its diesel-electric locomotive for a battery version. Instead, its taking the traction motors and distributing them to every car on the train. Its how many electric passenger trains operate, but its a system that has been slow to migrate to the freight world. Parallel Systems is going a step further, though. Each of its rail vehicles consists of a battery pack, electric motors, four wheels, and a package of sensors that allow it to operate autonomously.
A $3 Billion Bet on Finding the Fountain of YouthStaff | The EconomistThough preparations for the launch of what must surely be a candidate for the title of Best financed startup in history have been rumoured for months, the firm formally announced itself, and its modus operandi, on January 19th. And, even at $3bn, its proposed product might be thought cheap at the price. For the alchemy its founders, Rick Klausner, Hans Bishop and Yuri Milner, hope one day to offer the world is an elixir of life.
Intel Selects Ohio for Largest Silicon Manufacturing Location on the PlanetJon Porter | The VergeAfter helping to establish Silicon Valley, Gelsinger said the new site could become the Silicon Heartland. Intel plans to invest up to $100 billion in the site over the next decade, as well as around $100 million in partnership with Ohio universities, colleges, and the US National Science Foundation to foster new talent.
Machine to Melt Moon Rocks and Derive Metals May Launch in 2024Eric Berger | Ars Technicaa Houston-based company says there is value in the gray, dusty regolith spread across the entire lunar surface. The firm, Lunar Resources, is developing technology to extract iron, aluminum, magnesium, and silicon from the Moons regolith. These materials, in turn, would be used to manufacture goods on the Moon.
Its All Just Wild: Tech Startups Reach a New Peak FrothErin Griffith | The New York TimesHow crazy is the money sloshing around in start-up land right now? Its so crazy thatmore than 900 tech start-upsare each worth more than $1 billion. In 2015, 80seemed like a lot. Investors and founders have adopted a seize-the-day mentality, believing the pandemic created a once-in-a-lifetime opportunity to shake things up. The basic fabric of the world is up for grabs, [entrepreneur Phil Libin] said, calling this time the changiest the world has ever been.i
What Happens If a Space Elevator BreaksRhett Alain | WiredIn the first episode ofFoundation, some people decide to set off explosives that separate the space elevators top station from the rest of the cable. The cable falls to the surface of the planet and does some real damage down there. What would a falling space elevator cable look like in real life? Its not that simple to model, but we can make a rough guess.
Image Credit:Pawel Czerwinski / Unsplash
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Why the EU can’t get its act together on Ukraine – The Japan Times
Posted: at 9:55 am
WASHINGTON Post-1945 attempts to transform Europe from a geographical to a political designation have resulted in a baroque accretion of bureaucracies, but no answer to Henry Kissingers reported question: Who do I call if I want to speak to Europe?
The European Union is the worlds second-largest economic entity, with member nations combined gross domestic products ($15.3 trillion) larger than that of China ($14.7 trillion), and dwarfing Russias ($1.5 trillion), which is less than Italys ($1.9 trillion). Geopolitically, however, it is much less than the sum of its 27 parts, as the Ukraine crisis is demonstrating.
French President Emmanuel Macron would like to be designated to take Kissingers telephone call. This month, when he began a six-month term in the rotating office of EU president, he displeased the febrile portion of the French right by flying the European Union flag alone under the Arc de Triomphe. He then delivered to the European Parliament in Strasbourg, France, a speech that demonstrated why no Kissinger would bother placing that call.
Macrons speech began with some continental chauvinism about Europes supposed democratic singularity, such as the idea of universal human rights which need to be protected from the fervors of history. This idea animated the American Revolution before and better than the French Revolution, but Macron was not under oath. He rhapsodized about Europeans sharing a civility, a way of living in the world, from our cafes to our museums, which is incomparable, and about making Europe a democratic, cultural and educational power. Military power went unmentioned.
Of NATOs 30 members, just 10 are fulfilling the commitment, first announced 16 years ago, to spend at least 2% of GDP on defense. Macron waxed optimistically about better batteries and more women on corporate boards before getting around to mentioning something unpleasant: Ukraine.
He called for the EU to have our own security doctrine, in complementarity with NATO and with a genuine technological independence, industrial and defense strategy. It is, he said, Europes vocation to be a balancing power, particularly in its dialogue with Russia.
This will not happen. Leave aside the priority EU members give to social spending especially pensions and medical care for their aging populations over military spending. Macrons blurry notion of complementarity with NATO would inevitably mean discord with NATO. Eastern Europeans, who live in a dangerous neighborhood and with memories of Russia rampant, know better than to trust their security to Europe balancing its cafes and museums against Russian President Vladimir Putins tanks and missiles. The farther Europeans are from the Atlantic Ocean, the more trans-Atlanticist they are.
It is fanciful to talk, as Macron is merely the latest European leader to do, about Europe speaking with a single, powerful voice on behalf of principles and rules established not against or without Russia, but with Russia. These principles, he said, include rejection of the use of force, of threats and of coercion; the free choice for states to take part in the organizations, alliances and security arrangements they wish; the inviolability of borders, the territorial integrity of states and the rejection of spheres of influence.
Macron noted that European nations and Russia signed such principles 30 years ago. As he spoke, Russia was violating all of them.
An irony of 2022 is that Ukraine yearns to affirm and buttress its nationality primarily by associating not with NATO but with the EU, which many nationalists throughout Europe disparage as inimical to national sovereignty and a solvent of national cultures. Ukraine is wiser than the EUs despisers for reasons that illuminate Americans stake in todays clash of civilizations: Universal human rights protected by sovereign nations commitments to the rule of law is a trans-Atlantic ideal.
In The Abandonment of the West: The History of an Idea in America Foreign Policy, Michael Kimmage, who served on the State Departments policy planning staff from 2014 to 2016, reminds us that for our Founders, the United States was more vividly European before it was ever palpably American. There has been a Euro-American path to liberty.
The United States, Kimmage insists, is a country carved from the stone of Enlightenment thought, which migrated west from England, Scotland, France and Germany, from Konigsberg Immanuel Kants home in Europes East to Philadelphia in the American colonies. Ukraine is looking to the West, away from Putins ethnoreligious, blood-and-soil notion of nationhood, toward the community of nations of shared Enlightenment values. For the West to look away from Ukraine would be an apostasy foreshadowing a dark future.
George F. Will writes on politics and domestic and foreign affairs. He began his column with The Post in 1974, and he received the Pulitzer Prize for commentary in 1977. 2022, The Washington Post Writers Group
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The Beatles song that uses just one chord – Far Out Magazine
Posted: at 9:55 am
The Beatles sought to be innovators in any area they could. Whether it was through samples, eight track recording, the integration of classical Indian music, or the extension of songs beyond three minutes in length, the Fab Four simply did things that no other major artist did.
But one of the more strange preoccupations that the members of the band obsessed over was more minimalist: they wanted to create a song with just one chord. John and I would like to do songs with just one note like Long Tall Sally. We get near it in The Word. Indeed, The Word represents The Beatles employing a fair amount of restraint, but there were other songs that took the bands desire for harmonic singularity to a greater height.
When it comes to Beatles songs largely revolving around a single chord, the band loved to gravitate towards the key of C. George Harrison especially, with his deep love of Indian classical music, used the sitars common tuning of C as a basis for a large number of songs with more experimental tendencies. Blue Jay Way, for example, has a C drone as the chords alternate between different suspensions and diminished variations on the central C Major chord.
Love You To does the same, although it prominently features a Bb Major chord in the songs chorus. Harrisons most explicit Indian-infused song, Within You Without You, goes to Ravi Shankars preferred tuning of C# and stays there with a few chord variations that follow the central melody. But when it comes to truly only using a single, unchanging chord, no song in the bands catalogue can top Tomorrow Never Knows.
Devised by John Lennon and specifically inspired by the psychedelic experience, Tomorrow Never Knows isnt written like any conventional pop song that came before. Its a song based on tape loops, including a drum loop from Ringo Starr, different lines from Harrison playing sitar and tambura, and Lennon mixing in recorded Mellotron parts. Paul McCartneys bass line is the only standard part of the arrangement.
For almost the entirety of the track, the song stays on the C Major chord. No variations, so suspensions, no additional notes. But the complication comes when Lennon sings it is not dying. Thats because one of the loops, that of a Hammond organ, is playing a Bb Major chord. The rest of the song continues to play C Major, but Lennons vocal lines highlights the Bb Major to the extent that chord has to be considered a Bb Major/C chord, thereby ruining the pipe dream of recording a song with only one chord.
Its likely for the best that The Beatles never achieved their one-chord goal. Tomorrow Never Knows is the ultimate example of making a harmonically static song vibrant and audibly entertaining. If someone were to simply strum a C chord on a guitar and sing the songs melody, it would be a fairly limp performance. Songs need different chords to keep the listeners attention, and unless youre Muddy Waters barking out Mannish Boy or Howlin Wolf singing Smokestack Lighting, chances are youre not going to have a very good song on your hands.
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URL Media is turning one. Here’s what it accomplished in supporting Black and Brown newsrooms Poynter – Poynter
Posted: at 9:55 am
S. Mitra Kalita and Sara Lomax-Reese had this moment when they knew they had to build something with existing newsrooms, not remake them or start new.
There was yet another piece about a mainstream news outlet and racism it was contending with in its top ranks, Kalitatold Poynters Mel Grau last October. I called Sara. We had seen enough of that at that point. I remember one of us said, We have to do something. And the moment is now.
That was July 2020. By January 2021, the former senior vice president for news, opinion and programming for CNN Digital (Kalita), and the CEO/president of WURD Radio in Philadelphia (Lomax-Reese) launchedURL Media. URL stands for uplift, respect and love, and URLs homepage describes their work as a decentralized, multi-platform network of high-performing Black and Brown media organizations. Well share content, distribution, and other resources to enhance reach, expand revenue and build long-term sustainability.
URL Media launched one year ago today. Via email, I asked the founders about the last year, starting with whats changed since they first gathered eight network member newsrooms.
In the world: we are seeing deeper, more sophisticated ways of dividing the country along racial lines, Lomax-Reese said. The Virginia governors race was a blueprint for how to mobilize white voters around the issue of critical race theory. Dog whistles are real. We are seeing increased restrictions on voting rights as we head into the 2022 midterm elections. And COVID fatigue seems to be numbing out the country just when we need to be energized to fight for reproductive rights, voting, health care, education and everything. This is why URL and the work of all of our BIPOC media partners is absolutely critical right now. We need diverse, trusted voices to chronicle the truth of our present reality.
In URL Medias first year, it:
Held a monthly roundtable, Meet the BIPOC Press, on The Laura Flanders Show, which airs on 280 public television stations
Grew to help its members with coaching and talent development
Added two more newsrooms,Sahan JournalandNative News Online
Got the networks newsrooms on Apple News, which is something mainstream newsrooms have taken for granted for years to reach masses, Kalita said. Our BIPOC newsrooms dont always have the developers or audience managers to enable this so this felt like a real feat.
Among URLs 10 newsrooms, theres also a common thread of generosity and openness, Lomax-Reese said. Kalita, who is the founder and publisher ofEpicenter NYC, agreed.
I often joke that our members are the same because we all grew up with extra relatives living in our basement and strangers showing up at the dinner table, Kalita said. I say this because a spirit of generosity runs through every single one of our newsrooms. When I think about what we represent to our communities in this deadly pandemic that has disproportionately sickened us, killed us even, I get choked up. Theres a sameness there but also a singularity and customization by community and platform.
In its second year, URL Media ishiring, working to grow advertising and sponsorship revenue and to add members. I asked the two founders what we should all learn from the newsrooms URL Media works with.
I think all of our partners center and prioritize service to their audiences, Lomax-Reese said. This is a relatively new trend in mainstream journalism right now, but this is fundamental and foundational for our BIPOC media organizations. And this has been at the center of Black media throughout history, starting as early as 1827 when the first Black newspaper, Freedoms Journal, was launched to advocate for the humanity of enslaved Africans. Our business models are intimately connected to service, filling gaps that exist not just in the media but in society.
This piece originally appeared in Local Edition, our newsletter devoted to the telling stories of local journalists
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A Complex Test of the Genome, Right Here at Home – UPMC & Pitt Health Sciences News Blog – UPMC
Posted: at 9:54 am
The traditional route to test for a possible genetic disease involves a physician determining what they believe their patient might have. Then, the individual genes for those diseases are tested one by one to discover whether the patient has that condition. When each gene is tested individually, it is called a diagnostic odyssey. The process is expensive and can take years to complete because, at birth, a child might not present any signs of a genetic disease.
Some genetic diseases, like down syndrome, cystic fibrosis, and sickle cell anemia, are easily recognizable, so specific genetic tests can be ordered to diagnose patients. Yet, when young patients show signs of less recognizable genetic disease usually genetic diseases present in the pediatric population there are two avenues to diagnose them.
Its a roller coaster for families, said Ed Smith, M.S., M.B.A., director of UPMC Clinical Genomics Laboratory within UPMC Magee-Womens Hospital, as well as three other UPMC labs at Magee that perform the genetics and genomics testing. With 20,000 genes in the human genome, the variety of potential abnormalities is endless. Some genetic diseases arent curable but having certainty can still bring peace.
By looking at the coding region in the DNA, which contains the genetic material where diseases sometimes manifest, whole exome sequencing tests the entire human genome. The human genome includes every single one of a patients genes, allowing the care team to find a diagnosis for a genetic disease without having to isolate the gene in advance. As of 2020, exome sequencing is offered through the labs at UPMC Magee, which reduces the costs of sending samples to external labs and keeps the entire process within the same system.
Before a patient consents to whole exome sequencing, a UPMC genetic counselor must review the ramifications of the test with their family. Since the test requires a DNA sample, a family could discover non-paternity or end up learning that their child has another disease or unrelated condition that will appear later in their adult life.
You might get valuable information, but the timing isnt always good, said Smith. You could find out that a 3-year-old patient will be at an increased risk for breast cancer in her thirties, so you find clinically important things unrelated to why the child was referred for testing in the first place.
Alex Yatsenko, M.D., Ph.D., director of Clinical Genomics at UPMC, looks forward to improving the costs and efficiency of whole exome sequencing as the field grows. Although sequencing the whole exome can be costly, its worthwhile when its needed and, with prior authorization, covered by many insurers, including UPMC Health Plan.
Even for physicians, whole exome sequencing has required new processes. Physicians must describe their patients symptoms to the UPMC genetics and genomics team using a number system called Human Phenotype Ontology (HPO) terms when referring patients for genetic testing. HPO terms standardize symptom explanations, instead of doctors writing their own descriptions, and the software that the genetics lab uses takes HPO terms and associates genetic changes to the diseases.
Were bringing a digital revolution to UPMC, too, said Yatsenko.
To learn more about genetic sequencing available at UPMC Magee-Womens Hospital, click here.
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One of Google’s earliest genetic experiments, 23andMe, paid off here’s what will make or break its future – CNBC
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A reporter examines a 23andMe DNA genetic testing kit in Oakland, California.
Cayce Clifford | Bloomberg | Getty Images
In this weekly series, CNBC takes a look at companies that made the inaugural Disruptor 50 list, 10 years later.
In 2006, the estimated cost of sequencing a single human genome was about $14 million. That same year, Anne Wojcicki, along with co-founders Linda Avey and Paul Cuszena, started a company that promised to provide direct-to-consumer genetic sequencing for as little as $99.
23andMe stands out as an example of many of the traits we've seen in the most disruptive companies over the last decade: It built a strong consumer brand that has become synonymous with a new business model (personal genetics); it fought off a regulatory challenge that threatened to sink the company in its early years; it partnered with a larger incumbent to expand its business and find a path to profitability; and it rode the wave of popularity of special purpose acquisition companies (SPACs) to reach the public markets. In all, it's a great company for our year-long look back at the inaugural Disruptor 50 list.
By the time the first Disruptor 50 list was published in 2013, and 23andMe earned a spot on the list, the company had raised more than $50 million from investors including biotech firm Genentech, venture capital firm New Enterprise Associates, and Google (Wojcicki's sister, Susan, was an early Google employee and is the CEO of YouTube, and, at the time, Anne Wojcicki was married to Google founder Sergey Brin). Consumers were finding their way to the product, showing both an interest in knowing more about their ancestry and health, and a willingness to pay for it.
Then came the regulators. The FDA stopped 23andMe from making any health-related claims in October 2013, severely slowing its growth and putting it in direct competition with other companies that were more focused on genealogy. The FDA put 23andMe through a two-year review process before finally giving its health data the green light in October 2015. That cleared the way for a period of hypergrowth.
It also cleared the way, following a two year absence, for another appearance on the Disruptor 50 list. The new, regulator-approved 23andMe ranked fifth on the 2016 list, the first of four consecutive appearances from 2016-2019. During that time, it achieved "unicorn" status, announced a critical partnership with pharmaceutical company GlaxoSmithKline to use its genetic data to design new drugs, and the popularity of personal DNA testing soared, becoming somewhat of a cultural phenomenon. The number of people who took 23andMe's test nearly quadrupled from 2017 to 2019, thanks in part to some clever marketing efforts including a commercial voiced by billionaire investor Warren Buffett.
As of last September, the company says, nearly 12 million people have had their DNA sequenced by 23andMe, with 80% of them opting in to research that could lead to new drug discoveries and more. This is its promise as a publicly traded company. In June, 23andMe completed a merger with VG Acquisition Corp, a SPAC backed by Sir Richard Branson. It's been a bumpy road since the stock has lost more than half its value since it began trading under the ticker symbol "ME."
Anne Wojcicki, 23andMe co-founder & CEO (right) celebrates with 23andMe employees after remotely ringing the NASDAQ opening bell at the headquarters of DNA tech company 23andMe in Sunnyvale, California, U.S., June 17, 2021.
Peter DaSilva | Reuters
23andMe now has another thing in common with many Disruptor 50 companies it has to convince investors to believe in the next act. It's thanks in part to 23andMe's initial disruption that the cost of genomic sequencing has fallen by 99.99% in 16 years, but 23andMe's future lies in its ability to power the drug discovery that will help it find a way to sustained profitability as the novelty of sequencing one's own DNA wears off.
The deal with GlaxoSmithKline was extended for another year, the companies announced earlier this month. GSK noted in a release that genetically validated drug targets have "at least double the probability of success" in becoming medicines.
"We want them to truly have a personalized health-care experience and ... benefit the human genome from seeing all of this aggregated data turned into therapeutic programs," Wojcicki said in a CNBC interview on the stock's first day of trading. "When I think about the future of therapeutics, in the next five years it is really about moving these programs forward and getting them into the clinic."
CNBC is now accepting nominations for the 2022 Disruptor 50 list, our annual look at private innovators using breakthrough technology to transform industries and become the next generation of great public companies. Submit your nomination by Friday, Feb. 4, at 3 pm Eastern time.
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Psychology and Genetics: How Are They Connected? – The Great Courses Daily News
Posted: at 9:54 am
By Catherine A. Sanderson, Amherst College Genes and Psychological Behavior
One of the newest methods used to examine questions in psychology is behavioral genetics. How are genes linked with psychological behaviors? From roughly 1960 to 1990, research in the genetics of behavior was based almost entirely on twin studies, adoption studies, and extended-family studies.
It focussed on questions such as how similar are identical twins when raised in different homes? Are adopted children more similar to their biological parents or adoptive parents? Do particular conditions, such as depression or Alzheimers disease, run in families?
These studies did provide some evidence that genes matter, but typically couldnt tell exactly how or why.
This article comes directly from content in the video series Introduction to Psychology. Watch it now, on Wondrium.
Interestingly, genetic factors predict how kind we are to other people, whom we vote for in elections, and how likely we are to get divorced. A 2018 study found that some people seem to be genetically predisposed to getting divorced. Adopted childrens rate of divorce was similar to that of their biological parents, even if they were separated from these parents very early in life. There was no correlation between adopted childrens likelihood of divorce and that of their adoptive parents.
Yet, this genetic predisposition is relatively limited in its impact. Genetic factors only predicted 13% of a persons likelihood of getting a divorce. So, this tells us that genes do play a role, but a relatively small role in predicting something like getting divorced.
Moreover, most complex behaviors are influenced by multiple genes, each gene interacting with other genes, and with environmental factors. Contrary to what was commonly touted back around 2000, its not as simple as finding the gene thats responsible for depression, or alcoholism, or your IQ, or whether you will get divorced.
Instead, its how genes and the environment interact that predicts behavior. For example, even among people with the same genetic predisposition to obesity,such as siblings, environmental factors may influence whether the gene that triggers obesity is turned on or off.
This finding helps explain why, even with identical twins, one twin may be obese and the other not.
This finding, that environmental factors can cause changes in gene expression, is known as epigenetics. Moreover, these environmental changes in gene expression can be passed on through generations. Heres a powerful example from women who were pregnant and near the World Trade Centers on the day of the 9/11 terrorist attacks.
Researchers measured these womens levels of cortisol, a hormone that helps the body respond effectively to stress, shortly after the attack, and about a year later tested symptoms of post-traumatic stress disorder, or PTSD. Women who developed PTSD in the year after the attack had abnormally low levels of initial cortisol compared to those who did not develop this disorder, perhaps exacerbating the longer-term harm of stress for these women.
But heres how epigenetics makes it even more interesting. The children who gestated inside women who developed PTSD also had abnormally low levels of cortisol, especially if their mothers were in the third trimester of pregnancy at the time of the 9/11 attack.
These babies were basically programmed in the womb to have a lower level of cortisol, as a result of their mothers traumatic experience, and that likely increased their risk of developing a stress disorder themselves.
These advances in genetics have also led to challenging legal questions, such as whether we should be able to use our genes to excuse bad or criminal behavior. In a 2009 murder trial, a defense attorney provided evidence to a jury that his client was not guilty of premeditated murder because he had the so-called warrior gene which has been shown to predispose people to aggressive behavior and difficulty controlling their impulses.
The jury agreed, convicting on charges of manslaughter instead of first- or second-degree murder. As one jury member noted, Some people without this would react totally different than he would. A bad gene is a bad gene.
Yes, genetic predisposition is relatively limited in its impact. For example, in a study it was found that genetic factors only predicted 13% of a persons likelihood of getting a divorce. So, genes do play a role, but a relatively small role in predicting something like getting divorced.
The finding that environmental factors can cause changes in gene expression is known as epigenetics. Interestingly, these environmental changes in gene expression can be passed on through generations.
Most complex behaviors are influenced by multiple genes, each gene interacting with other genes, and with environmental factors. So, it is how genes and the environment interact that predicts behavior. For example, even among people with the same genetic predisposition to obesity, environmental factors may influence whether the gene that triggers obesity is turned on or off.
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Alexis Battle and Sarah Hrst receive President’s Frontier Awards – The Hub at Johns Hopkins
Posted: at 9:54 am
BySaralyn Cruickshank
Two Johns Hopkins faculty members have received the university's prestigious President's Frontier Award, which recognizes exceptional scholars who are on the cusp of transforming their respective fields.
In a surprise virtual presentation Monday, JHU President Ron Daniels presented the award to Alexis Battle, an associate professor in the Department of Biomedical Engineering, and Sarah Hrst, an associate professor in the Department of Earth and Planetary Sciences. Both researchers will receive $250,000 to pursue new lines of research, expand their laboratories, or support their lab members.
"Let me take this moment to say how dazzled we were, Alexis and Sarah, by the ambitions and scope of your research and how highly your colleagues, mentors, and students regard each of you," said Daniels in the virtual presentation. "Having a way to honor those qualities in our faculty was a reason why we created this amazing award eight years ago. You both join a cadre of truly remarkable people from across all our divisions whose work truly stands apart."
The President's Frontier Award was originally launched with a commitment of $2.5 million from trustee Louis J. Forster, A&S '82, SAIS '83, and is now paired with a $1 million donation from alumnus David Smilow, A&S '84. Winners have spanned the university's divisions and included molecular biologist Andrew Holland (2021), mathematician Emily Riehl (2020), astrophysicist Brice Mnard (2019), nephrologist and epidemiologist Deidra Crews (2018), composer Michael Hersch (2017), molecular biologist Scott Bailey (2016), and stem cell research Sharon Gerecht (2015).
The award typically recognizes one winner and one finalist each year, but Battle and Hrst were both selected this year based on the strength of their applications and the demonstrated impact and continued potential of their work.
"The two of you embody in some sense the incredible breadth of research that goes on at JHU," said Ed Schlesinger, dean of the Whiting School of Engineering. "From the very smallest genetic materials that define what life is all about to the planets, space, the cosmos, and the search for life beyond our own worldthere is something particularly poetic about the juxtaposition of both of [your work]."
During the presentation, both Battle and Hrst discussed the transformative impact the award would have on their research teams.
"Last night and today, I was thinking, What do I really want to do if I get this award? And I was really laying out some of the exciting things that I'm hoping will happen over the next few years," Battle said. "So that makes me even more excited now, to know those things are going to be possible. I'm so thrilled, and I'm thrilled to see my students thrive even more."
Image caption: Alexis Battle
Image credit: Will Kirk / Johns Hopkins University
Battle is an internationally recognized leader in the field of biomedical engineering whose work has vital implications in the fields of human genetics, computational genomics, and precision medicine. Her research focuses on how genetic variation between individuals leads to changes in gene expression, and how these changes then lead to disease risk and progression. Using machine learning and probabilistic modeling, Battle and her lab create computational models capable of interpreting vast sets of genomics and health data to identify variations in gene expression and follow trends in disease progression caused by these changes in DNA. She has pioneered the use of time-series data to understand the impact of genetic variation at critical time points relevant to disease development.
Her breakthrough computational system, Watershed, holds great promise in the field of personalized genomics. Watershed's advanced modeling system combines personal genetic data and diverse cellular measurements to improve predictions of which genetic sequence differences found in a specific individual will affect that person's health. Applying this system across ancestries, families, and new data types has the potential to improve the diagnosis and treatment of rare diseases.
"There is increasing need for creative computational methods in genomics," wrote Michael Miller, director of the Department of Biomedical Engineering, in a letter nominating Battle for the President's Frontier Award. "Seeing the full impact of genomic data on biological and medical research therefore relies on the type of creative and careful methods development Alexis does."
Battle was a senior leader on the GTEx Consortium Project, a massive multi-institution effort that collected and analyzed thousands of human tissue samples to better understand gene expression. With dozens of principal investigators on studies related to the project, Battle's lab played a central role and she served as a senior author on the project's flagship papers.
Educated at Stanford University, Battle received her BS in symbolics systems and her MS and PhD in computer science. She completed a postdoctoral research specialization in genetics at the Howard Hughes Medical Institute at Stanford. She joined the faculty at Johns Hopkins in 2014 after working as a staff software engineer and engineering manager at Google. She has previously won a Johns Hopkins Catalyst Award (2017), which recognizes early career researchers with a $75,000 grant for their research and creative endeavors, and a Johns Hopkins Discovery Award (2019), which provide grants to cross-divisional teams. She was named a 2016 Searle Scholar and received a 2019 Microsoft Investigator Fellowship. She currently mentors four postdoctoral fellows, one medical fellow, 11 PhD students, and serves as an adviser for three undergraduates in the Department of Biomedical Engineering.
Hrst, a planetary scientist, studies the composition and characteristics of aerosols in the atmospheres of early Earth and other planets. Using laboratory experiments, modeling, and remote sensing and in situ measurements of atmospheric chemistry, Hrst and her lab work to understand how small molecules transition to become aerosols and the resulting physical and chemical properties of those particles.
Image caption: Sarah Hrst
The work has implications for assessing the habitability of other planets and for the search for life beyond our solar system. Under the right conditions, adding energy to simple mixtures of common gases can produce much more complex molecules like amino acids, which form the building blocks of living organisms.
Essential to her work is her groundbreaking approach to laboratory science. Using a custom-built Planetary Haze Research laba one-of-its-kind experimental labHrst and her group simulate the chemical reactions that contribute to the formation of aerosols in planetary atmospheres. With this approach, she can experiment with a vast range of temperatures (90-800 degrees Kelvin, or -297-980 degrees Fahrenheit) and can use different energy sources to initiate chemical reactions across a variety of atmospheric gases and conditions. Her lab is the first in the world to be dedicated to studying photochemical haze production in exoplanet environments, and she has published research on Saturn, Saturn's moon Titan, and early Earth.
Hrst's work is directly relevant to important space missions, including two upcoming NASA missions: Dragonfly, which will investigate prebiotic organic chemistry and habitability on Saturn's largest moon, Titan; and DAVINCI+, which will probe the chemical composition of the atmosphere of Venus.
"Particularly impressive is her ingenuity and creativity in developing and leading a new scientific field essentially from scratch: extrasolar planet atmosphere laboratory studies," wrote Sabine Stanley, a Bloomberg Distinguished Professor and chair of the Department of Earth and Planetary Sciences, in a letter nominating Hrst for the award. "Her work has already had major impact on the global effort to observe and characterize exoplanet atmospheres."
She received the 2020 LAD Early Career Award from the American Astronomical Society's Laboratory Astrophysics Division and the prestigious 2020 James B. Macelwane Medal from the American Geophysical Union, widely considered the highest honor for early career scientists in the field of geological and planetary sciences. She received a Johns Hopkins Catalyst Award in 2017 and was a co-investigator on a Discovery Award led by Maya Gomes in 2020.
Hrst received two bachelor of science degreesone in planetary science and one in literaturefrom the California Institute of Technology. She received her PhD in planetary sciences from the University of Arizona, Tucson. She joined Johns Hopkins in 2014 and currently mentors three graduate students, two postdoctoral research fellows, and an associate research scientist.
Chris Celenza, dean of the Krieger School of Arts and Sciences, gave Hrst particular praise for her emphasis on mentorship and collegiality.
"I often think that we are at our best in the arts and sciences when we're reciprocally reinforcing conversations among faculty, postdocs, graduate students, and undergraduates," Celenza said during the award presentation. "I know in your lab, you've cultivated that very type of engagement, so I want to thank you, deeply, for all you have done for this wonderful Department of Earth and Planetary Sciences and for Johns Hopkins and for the Krieger School."
Hrst's dedication to her lab members was evident from the moment they "Zoom bombed" the meeting, joining in on the coordinated surprise. "When I saw the names popping up on the screen, all I could think was how much more great science the people who are already working with me are going to get to do," Hrst said through tears. "And that means the absolute world to me."
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Alexis Battle and Sarah Hrst receive President's Frontier Awards - The Hub at Johns Hopkins
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