Alphabet’s DeepMind AI has solved “the protein folding problem” that could aid medicine research

TL;DR: DeepMind Technologies, a research lab in the UK owned by Alphabet, has developed an AI that can determine the folded shape of a protein in a matter of hours, which would typically require months or years of lab research. Depending on how Alphabet distributes this technology to the science community, this development has the potential to affect a huge array of medical and biological research.

Computer scientists at DeepMind, a lab owned by Alphabet, Google’s parent company, have developed an AI that has made a monumental leap in solving “the protein folding problem.” This conundrum has plagued biologists for decades, and solving it can accelerate countless other studies in medicine, agriculture, and conservation, to name a few.

Proteins are crucial “macromolecules” built from strings of molecules called amino acids. These strings of molecules are built inside of each cell by reading an organism’s DNA and blocking together long chains of amino acids. Of the 20 amino acids that make up proteins, each one chosen depends on the DNA sequence being read, and each amino acid has special properties that cause the long chain of molecules to fold over itself into a very specific, highly complicated shape, which gives the protein its function.

Understanding the shape and how it relates to the function of proteins is so important because they are responsible for most biological functions in the body, including immune response, digestion, energy production, muscle contraction, blood clotting, and countless more.

The interest of many research groups revolves around synthetic proteins used in medicines. Knowing the order of amino acids in a protein is easy enough for researchers if they know the DNA sequence that is used as its template, but knowing its shape can dramatically expedite the process of determining how it will function in people, bacteria or viruses. Among other mysteries this can unravel, think of vaccine research, a topic on everyone’s mind presently.

DeepMind’s neural network can quickly and reliably determine a protein’s shape, given the string of amino acids that comprise the protein.

Scientists have been working hard to crack this nut for over 50 years. A competition called the Critical Assessment of Structure Prediction (CASP) was formed 25 years ago to bring together this research, compare results and spur on investigation.

No one has really come close to solving this problem until DeepMind came onto the scene. Tested on a variety of proteins, DeepMind’s neural network was able to accurately assume the folded structure of a protein with the precision of lab-based experiments that typically take months or years to solve.

It should be noted that experts say solving the protein folding problem speeds up just the initial stage of the long process of safely developing a medication.

This has also apparently emerged too late to affect vaccine research into the coronavirus but could be used down the line to stem future pandemics, determine whether existing medications can be used on novel infections, and research genetic diseases such as Alzheimer’s.

John Moult, a University

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AI-based earlier medicine development leveraging TWCC HPC to aid cancer prediction research

AI-based earlier medicine development leveraging TWCC HPC to aid cancer prediction research

Artificial Intelligence (AI) is shaping the future of global medical industries. The practice of medicine is changing with the development of AI methods of machine learning. As the increasing accuracy of predictive medicine, AI technology, based on analyzing patient’s medical records, is entailing predicting the probability of disease in order to either further diagnosis of disease allowing for the estimation of disease risks or significantly decrease the cost to deal with its impact upon the patient. The AI based prediction medicine is a new type of earlier medicine

Hsuan-Chia Yang, assistant professor of the Graduate Institute of Biomedical Informatics, Taipei Medical University, explains Prediction of Principle Health Threat (PROPHET) project. Led by Dr. Li Yu-Chuan, a pioneer of AI in Medicine and Medical Informatics Research, earlier medicine for fatal diseases is leveraging AI technology and data mining systems to provide a personal, real-time, accurate and manageable healthcare program. The PROPHET project provides the prediction of cancer risks and boosts the new business opportunity of start-ups. Taiwan Ministry of Science and Technology provides the funding support for this kind of projects.

Taking breast cancer detection as an example, there are 5 persons confirmed as positive out of every 1000 people screening. Applying the AI earlier medicine perdition method, the effective rate will be reduced to 5 confirmed out of 233 people check. There are 77% saving of breast cancer earlier diagnosis. The saved cost is obvious.

The basic of PROPHET project is making AI Bio-maker model using AI technology to screen cancer and provide the prediction. Transforming the patient medical records to time matrix data diagrams, the skill is setting to predict 10 kinds of cancer risks after one year time frame based on sequential medical records to develop a prediction model. Each prediction of various cancers could reach 85% AUROC (Area under the receiver operating characteristic) curves. Taiwan Healthcare insurance program preserves every citizen’s healthcare digital records of treatments and medicine usage. PROPHET takes this strength to analyze three-year personal data records to predict the cancer risks of next 12-month. These lower cost AI-based cancer predictions allow healthcare professions to participate in the decision about whether or not it is appropriate testing or detection priority for patients.

From the technical point of view, the dynamic prediction value of personal diseases is a time-dependent scenario. The time matrix combined with personal medicine usage records and various diseases could make a two dimensional health diagram. The vertical axis is thousands of variables including medicine usage, set of medical signs and symptoms. The horizontal axis is time listings based on week or month. There are about 250 thousand health diagrams to use in the AI training process to get effective prediction AI models. After requiring repeat fine-tuning in training new AI models of each cancer, it can be derived effective prediction models based on above AI Bio-marker.

However, the huge compute power to perform these AI training tasks requires huge support

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Philadelphia Fitness Coalition Forms to Protest Shutdown Without Aid

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The group, made up of 30-plus fitness studios and gyms in the region, is petitioning the city to change its latest coronavirus restrictions.


Philadelphia Fitness coalition logo

The Philadelphia Fitness Coalition has launched to protest the recent city shutdown with a petition and a workout outside City Hall. | Photograph courtesy of Philadelphia Fitness Coalition

Last week, the City of Philadelphia launched new “Safer At Home” restrictions to curb the spread of the coronavirus amid rising cases that have led to a current high risk of community transmission. The new rules put many local gym and studio owners, who have received limited government aid, in a position of facing down mounting bills and further reduced revenue over the holidays. Without action from officials, it may be impossible for Philly’s gyms to keep their doors open through the winter.

Many small gym and studio owners have made dramatic changes to their business models in order to keep patrons and members as safe as possible during the COVID-19 crisis. Some, however, have flouted the safety restrictions, hurting the case of the fitness centers who were complying with the previous rules. Despite best efforts by some, it’s hard to know where cases are being contracted and spread, which is why many small businesses are looking for a government lifeline to get them through the winter while they keep their doors shut.

Others want to stay open and be declared essential businesses, in addition to calling for increased grants from the state and federal government. On Sunday, November 23rd, a group called the Philadelphia Fitness Coalition, comprised of 30-plus local gyms and fitness studios, launched with an appeal to officials regarding the recent shutdown. The coalition was spearheaded by Gavin McKay, founder of Unite Fitness, with leadership partnership from Osayi Osunde, founder of Fit Academy; Shoshana Katz, founder of BPM Fitness; and Stephanie Luongo, founder of Sculpt 360, among others. The group has started a Change.org petition (a previous petition from a different source already exists) under the heading “Reopen Fitness Providers As Essential Health Services and Provide Funding To Sustain Them.”

In the petition they explain that the gyms and studios in their coalition have collected data on over 260,000-plus indoor visits from July to November 2020, and that “only 30 reported cases walked into our locations,” citing a “0% transmission rate traced from person to person” among reported, known cases. It’s important to note that this claim derives from self-reported and self-collected data from the gyms. And, unfortunately in a city and state where contact tracing has been conducted poorly or not at all (and where citizens are not complying with tracing), it’s impossible to know the reality of where cases are originating and spreading.

Nonetheless, McKay argues that in small studios particularly “the communities are tight” — that people know one another and communicate if there’s been potential exposure. “We’ve been put in the wrong

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Pittman Expands Financial Aid For Coronavirus Patients, Families

MILLERSVILLE, MD — Anne Arundel County Executive Steuart Pittman launched three initiatives Thursday to help locals weather the coronavirus fallout. The programs will help residents pay bills, find resources and cope with virus-related deaths.

Water Shutoffs

The first initiative looks to help struggling families pay their water bills. Pittman announced the relief effort at a press conference in front of a Millersville water tower.

About 20,000 county residents are behind on their water payements, Pittman said. That’s up 19,000 from this time last year, the county executive added.

“If we don’t help these people, they could not only have their water cut off, but the liens that we are required to put on their homes, and the subsequent foreclosure proceedings could leave them homeless,” Pittman said in a press release after the conference. “Helping to pay their bills is essential.”

Pittman recently bought time for these families by signing Executive Order 30. The mandate prohibited water shutoffs for nonpayment until Nov. 16.

The county will mail applications for the Water Bill Relief Program to residents who qualify. Interested applicants may also dial (410) 222-1144 or email [email protected] TTY users should call Maryland Relay at 7-1-1.

Family Resources

Pittman also announced the COVID Care Coordination Program, an extension of the Department of Health’s contract tracing. The program’s case managers will reach out to people who test positive for coronavirus. The bilingual workers can help find food, shelter, housing, commodities and financial assistance.

The final initiative addresses the pandemic’s effects on mental health. This COVID Recovery and Grief Support Program will offer counseling to families who lost a loved one to coronavirus.

The extra money will bolster the mental health warm line, which has answered more calls during the pandemic. Residents can reach the line at (410) 768-5522.

“What we are experiencing is an increase in the number of individuals who are seeking additional mental health support, many of whom have financial barriers,” said Adrienne Mickler, the executive director of the Anne Arundel County Mental Health Agency. “These funds will support urgent care appointments and follow up treatment.”

CARES Act Check-In

Pittman will fund his $2 million plan with money from the Coronavirus, Aid, Relief, and Economic Security Act, better known as the CARES Act. Anne Arundel County got $101.1 million in CARES Act funding after Congress passed the stimulus package in March.

The county executive’s announcement came hours before Gov. Larry Hogan announced his $250 million plan to keep Maryland’s small businesses afloat. Hogan stressed the importance of spending CARES Act money soon, noting that it expires at the end of the year.

Pittman said that Anne Arundel County has about $25 million to $30 million left in its CARES Act account. Residents can track the county’s coronavirus spending and find resources at this link. The website shows that Anne Arundel has about $52.2 million of CARES Act money remaining, but Pittman noted that the portal needs to be updated with the county’s latest expenditures.

“Water bill

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A deadline, then a viral surge and Florida hospitals miss out on pandemic aid

Florida’s caseload surged around the June cutoff date for the high-impact distribution. Between March and June 10, 2,801 people in the state had died from Covid-19 and 67,371 had tested positive for the virus, according to data from the Florida Department of Health.

Two months after the cutoff date, deaths had nearly tripled and the state was coping with an eightfold increase in cases.

Jackson and Shands are among 30 safety net hospitals designated to treat Florida’s poorest and typically uninsured residents. Combined, the hospitals have treated 60 percent of the state’s 46,693 hospitalized Covid-19 patients, but have received a sliver of the funding given to some states that saw fewer infections.

Gainesville-based Shands Hospital lost $160 million in revenue because of the pandemic and has received only $31.4 million in CARES Act aid. The shortfall forced Shands CEO Ed Jimenez to freeze employee raises indefinitely.

“Imagine you’re a nurse, and you take care of Covid patients, and your boss just said you don’t get a raise,” Jimenez said in an interview. “If Florida had gotten its fair share, if the safety nets had gotten their fair share, if my hospital had not been overlooked in the safety net tranche, things would be better.”

“They wouldn’t be great but they’d be better,” Jimenez said.

While Shands received $31.4 million from the Provider Relief Fund’s first phase of general distribution, it received no high-impact aid.

Jackson, which lost more than $78 million in revenue from the pandemic, said it received a combined $108 million from high-impact and general distributions. HHS data shows Jackson received $83.1 million from the high-impact fund.

And both Shands and Jackson got nothing from $14.4 billion set aside for safety net providers because, under HHS rules, both hospitals made too much money.

In Jackson’s case, the federal agency counted revenue from a tax levied by Miami-Dade County that funds the hospital. At Shands, Jimenez was unable to write off $68 million tied to the teaching hospital’s partnership with the University of Florida.

“After that, not a dime,” Jimenez said of the first phase of cash. Sens. Marco Rubio and Rick Scott heard his complaints, he said, but the Republican lawmakers told him there was little they could do.

“At the end of the day, it’s HHS, which is not subject to the will of the Congress or Senate,” JImenez said.

Talks with HHS Deputy Secretary Eric Hargan about updating the distribution rules went nowhere, Migoya said.

“Deputy Secretary Hargan was talking to me about it, and trying to figure out how to help us,” Migoya said. “It still didn’t happen.

“Obviously that was never the intent of the CARES money — that was to make up for lost revenues, but we’re not even close to that,” Migoya said.

When asked about the complaints from Jimenez and Migoya, a HHS spokesperson who would speak only on the condition of anonymity pointed to $20 billion set aside for Phase 3 of the general distribution, which opened for applications Oct.

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