A Look Back at Science’s 2022 Breakthroughs
Posted on by Lawrence Tabak, D.D.S., Ph.D.
Happy New Year! I hope everyone finished 2022 with plenty to celebrate, whether it was completing a degree or certification, earning a promotion, attaining a physical fitness goal, or publishing a hard-fought scientific discovery.
If the latter, you are in good company. Last year produced some dazzling discoveries, and the news and editorial staff at the journal Science kept a watchful eye on the most high-impact advances of 2022. In December, the journal released its list of the top 10 advances across the sciences, from astronomy to zoology. In case you missed it, Science selected NASA’s James Webb Space Telescope (JWST) as the 2022 Breakthrough of the Year .
This unique space telescope took 20 years to complete, but it has turned out to be time well spent. Positioned 1.5-million-kilometers from Earth, the JWST and its unprecedented high-resolution images of space have unveiled the universe anew for astronomers and wowed millions across the globe checking in online. The telescope’s image stream, beyond its sheer beauty, will advance study of the early Universe, allowing astronomers to discover distant galaxies, explore the early formation of stars, and investigate the possibility of life on other planets.
While the biomedical sciences didn’t take home the top prize, they were well represented among Science’s runner-up breakthroughs. Some of these biomedical top contenders also have benefited, directly or indirectly, from NIH efforts and support. Let’s take a look:
RSV vaccines nearing the finish line: It’s been one of those challenging research marathons. But scientists last year started down the homestretch with the first safe-and-effective vaccine for respiratory syncytial virus (RSV), a leading cause of severe respiratory illness in the very young and the old.
In August, the company Pfizer presented evidence that its experimental RSV vaccine candidate offered protection for those age 60 and up. Later, they showed that the same vaccine, when administered to pregnant women, helped to protect their infants against RSV for six months after birth. Meanwhile, in October, the company GSK announced encouraging results from its late-stage phase III trial of an RSV vaccine in older adults.
As Science noted, the latest clinical progress also shows the power of basic science. For example, researchers have been working with chemically inactivated versions of the virus to develop the vaccine. But these versions have a key viral surface protein that changes its shape after fusing with a cell to start an infection. In this configuration, the protein elicits only weak levels of needed protective antibodies.
Back in 2013, Barney Graham, then with NIH’s National Institute of Allergy and Infectious Diseases (NIAID), and colleagues, solved the problem . Graham’s NIH team discovered a way to lock the protein into its original prefusion state, which the immune system can better detect. This triggers higher levels of potent antibodies, and the discovery kept the science—and the marathon—moving forward.
These latest clinical advances come as RSV and other respiratory viruses, including SARS-CoV-2, the cause of COVID-19, are sending an alarming number of young children to the hospital. The hope is that researchers will cross the finish line this year or next, and we’ll have the first approved RSV vaccine.
Virus fingered as cause of multiple sclerosis: Researchers have long thought that multiple sclerosis, or MS, has a viral cause. Pointing to the right virus with the required high degree of certainty has been the challenge, slowing progress on the treatment front for those in need. As published in Science last January, Alberto Ascherio, Harvard T.H. Chan School of Public Health, Boston, and colleagues produced the strongest evidence yet that MS is caused by the Epstein-Barr virus (EBV), a herpesvirus also known for causing infectious mononucleosis .
The link between EBV and MS had long been suspected. But it was difficult to confirm because EBV infections are so widespread, and MS is so disproportionately rare. In the recent study, the NIH-supported researchers collected blood samples every other year from more than 10 million young adults in the U.S. military, including nearly 1,000 who were diagnosed with MS during their service. The evidence showed that the risk of an MS diagnosis increased 32-fold after EBV infection, but it held steady following infection with any other virus. Levels in blood serum of a biomarker for MS neurodegeneration also went up only after an EBV infection, suggesting that the viral illness is a leading cause for MS.
Further evidence came last year from a discovery published in the journal Nature by William Robinson, Stanford University School of Medicine, Stanford, CA, and colleagues. The NIH-supported team found a close resemblance between an EBV protein and one made in the healthy brain and spinal cord . The findings suggest an EBV infection may produce antibodies that mistakenly attack the protective sheath surrounding our nerve cells. Indeed, the study showed that up to one in four people with MS had antibodies that bind both proteins.
This groundbreaking research suggests that an EBV vaccine and/or antiviral drugs that thwart this infection might ultimately prevent or perhaps even cure MS. Of note, NIAID launched last May an early-stage clinical trial for an experimental EBV vaccine at the NIH Clinical Center, Bethesda, MD.
AI Gets Creative: Science’s 2021 Breakthrough of the Year was AI-powered predictions of protein structure. In 2022, AI returned to take another well-deserved bow. This time, Science singled out AI’s now rapidly accelerating entry into once uniquely human attributes, such as artistic expression and scientific discovery.
On the scientific discovery side, Science singled out AI’s continued progress in getting creative with the design of novel proteins for vaccines and myriad other uses. One technique, called “hallucination,” generates new proteins from scratch. Researchers input random amino acid sequences into the computer, and it randomly and continuously mutates them into sequences that other AI tools are confident will fold into stable proteins. This greatly simplifies the process of protein design and frees researchers to focus their efforts on creating a protein with a desired function.
AI research now engages scientists around world, including hundreds of NIH grantees. Taking a broader view of AI, NIH recently launched the Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity (AIM-AHEAD) Program. It will help to create greater diversity within the field, which is a must. A lack of diversity could perpetuate harmful biases in how AI is used, how algorithms are developed and trained, and how findings are interpreted to avoid health disparities and inequities for underrepresented communities.
And there you have it, some of the 2022 breakthroughs from Science‘s news and editorial staff. Of course, the highlighted biomedical breakthroughs don’t capture the full picture of research progress. There were many other milestone papers published in 2022 that researchers worldwide will build upon in the months and years ahead to make further progress in their disciplines and, for some, draw the attention of Science’s news and editorial staff. Here’s to another productive year in biomedical research, which the blog will continue to feature and share with you as it unfolds in 2023.
 2022 Breakthrough of the Year. Science. Dec 15, 2022.
 Structure of RSV fusion glycoprotein trimer bound to a prefusion-specific neutralizing antibody. McLellan JS, Chen M, Leung S, Kwong PD, Graham BS, et al. Science. 2013 May 31;340(6136):1113-1117.
 Longitudinal analysis reveals high prevalence of Epstein-Barr virus associated with multiple sclerosis. Bjornevik K, Cortese M, Healy BC, Kuhle J, Mina MJ, Leng Y, Elledge SJ, Niebuhr DW, Scher AI, Munger KL, Ascherio A. Science. 2022 Jan 21;375(6578):296-301.
 Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM. Lanz TV, Brewer RC, Steinman L, Robinson WH, et al. Nature. 2022 Mar;603(7900):321-327.
Respiratory Syncytial Virus (RSV) (National Institute of Allergy and Infectious Diseases/NIH)
Multiple Sclerosis (National Institute of Neurological Disorders and Stroke/NIH)
Barney Graham (Morehouse School of Medicine, Atlanta)
Alberto Ascherio (Harvard T.H. Chan School of Public Health, Boston)
Robinson Lab (Stanford Medicine, Stanford, CA)
Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity (AIM-AHEAD) Program (NIH)
James Webb Space Telescope (Goddard Space Flight Center/NASA, Greenbelt, MD)
From Brain Waves to Real-Time Text Messaging
Posted on by Lawrence Tabak, D.D.S., Ph.D.
For people who have lost the ability to speak due to a severe disability, they want to get the words out. They just can’t physically do it. But in our digital age, there is now a fascinating way to overcome such profound physical limitations. Computers are being taught to decode brain waves as a person tries to speak and then interactively translate them onto a computer screen in real time.
The latest progress, demonstrated in the video above, establishes that it’s quite possible for computers trained with the help of current artificial intelligence (AI) methods to restore a vocabulary of more than a 1,000 words for people with the mental but not physical ability to speak. That covers more than 85 percent of most day-to-day communication in English. With further refinements, the researchers say a 9,000-word vocabulary is well within reach.
The findings published in the journal Nature Communications come from a team led by Edward Chang, University of California, San Francisco . Earlier, Chang and colleagues established that this AI-enabled system could directly decode 50 full words in real time from brain waves alone in a person with paralysis trying to speak . The study is known as BRAVO, short for Brain-computer interface Restoration Of Arm and Voice.
In the latest BRAVO study, the team wanted to figure out how to condense the English language into compact units for easier decoding and expand that 50-word vocabulary. They did it in the same way we all do: by focusing not on complete words, but on the 26-letter alphabet.
The study involved a 36-year-old male with severe limb and vocal paralysis. The team designed a sentence-spelling pipeline for this individual, which enabled him to silently spell out messages using code words corresponding to each of the 26 letters in his head. As he did so, a high-density array of electrodes implanted over the brain’s sensorimotor cortex, part of the cerebral cortex, recorded his brain waves.
A sophisticated system including signal processing, speech detection, word classification, and language modeling then translated those thoughts into coherent words and complete sentences on a computer screen. This so-called speech neuroprosthesis system allows those who have lost their speech to perform roughly the equivalent of text messaging.
Chang’s team put their spelling system to the test first by asking the participant to silently reproduce a sentence displayed on a screen. They then moved on to conversations, in which the participant was asked a question and could answer freely. For instance, as in the video above, when the computer asked, “How are you today?” he responded, “I am very good.” When asked about his favorite time of year, he answered, “summertime.” An attempted hand movement signaled the computer when he was done speaking.
The computer didn’t get it exactly right every time. For instance, in the initial trials with the target sentence, “good morning,” the computer got it exactly right in one case and in another came up with “good for legs.” But, overall, their tests show that their AI device could decode with a high degree of accuracy silently spoken letters to produce sentences from a 1,152-word vocabulary at a speed of about 29 characters per minute.
On average, the spelling system got it wrong 6 percent of the time. That’s really good when you consider how common it is for errors to arise with dictation software or in any text message conversation.
Of course, much more work is needed to test this approach in many more people. They don’t yet know how individual differences or specific medical conditions might affect the outcomes. They suspect that this general approach will work for anyone so long as they remain mentally capable of thinking through and attempting to speak.
They also envision future improvements as part of their BRAVO study. For instance, it may be possible to develop a system capable of more rapid decoding of many commonly used words or phrases. Such a system could then reserve the slower spelling method for other, less common words.
But, as these results clearly demonstrate, this combination of artificial intelligence and silently controlled speech neuroprostheses to restore not just speech but meaningful communication and authentic connection between individuals who’ve lost the ability to speak and their loved ones holds fantastic potential. For that, I say BRAVO.
 Generalizable spelling using a speech neuroprosthesis in an individual with severe limb and vocal paralysis. Metzger SL, Liu JR, Moses DA, Dougherty ME, Seaton MP, Littlejohn KT, Chartier J, Anumanchipalli GK, Tu-CHan A, Gangly K, Chang, EF. Nature Communications (2022) 13: 6510.
 Neuroprosthesis for decoding speech in a paralyzed person with anarthria. Moses DA, Metzger SL, Liu JR, Tu-Chan A, Ganguly K, Chang EF, et al. N Engl J Med. 2021 Jul 15;385(3):217-227.
Voice, Speech, and Language (National Institute on Deafness and Other Communication Disorders/NIH)
ECoG BMI for Motor and Speech Control (BRAVO) (ClinicalTrials.gov)
Chang Lab (University of California, San Francisco)
NIH Support: National Institute on Deafness and Other Communication Disorders
National Library of Medicine Helps Lead the Way in AI Research
Posted on by Patricia Flatley Brennan, R.N., Ph.D., National Library of Medicine
Did you know that the NIH’s National Library of Medicine (NLM) has been serving science and society since 1836? From its humble beginning as a small collection of books in the library of the U.S. Army Surgeon General’s office, NLM has grown not only to become the world’s largest biomedical library, but a leader in biomedical informatics and computational health data science research.
Think of NLM as a door through which you pass to connect with health data, literature, medical and scientific information, expertise, and sophisticated mathematical models or images that describe a clinical problem. This intersection of information, people, and technology allows NLM to foster discovery. NLM does so by ensuring that scientists, clinicians, librarians, patients, and the public have access to biomedical information 24 hours a day, 7 days a week.
The NLM also supports two research efforts: the Division of Extramural Programs (EP) and Intramural Research Program (IRP). Both programs are accelerating advances in biomedical informatics, data science, computational biology, and computational health. One of EP’s notable investments is focused on advancing artificial intelligence (AI) methods and reimagining how health care is delivered with the power of AI.
With support from NLM, Corey Lester and his colleagues at the University of Michigan College of Pharmacy, Ann Arbor, MI, are using AI to assist in pill verification, a standard procedure in pharmacies across the land. They want to help pharmacists avoid dangerous and costly dispensing errors. To do so, Lester is using AI to develop a real-time computer vision model. It views pills inside of a medication bottle, accurately identifies them, and determines that they are the correct or incorrect contents.
The IRP develops and applies computational methods and approaches to a broad range of information problems in biology, biomedicine, and human health. The IRP also offers intramural training opportunities and supports other training aimed at pre-baccalaureate to postdoctoral students and professionals.
The NLM principal investigators use biological data to advance computer algorithms and connect relationships between any level of biological organization and health conditions. They also use computational health sciences to focus on clinical information processing and analyze clinical data, assess clinical outcomes, and set health data standards.
NLM investigator Sameer Antani is collaborating with researchers in other NIH institutes to explore how AI can help us understand oral cancer, echocardiography, and pediatric tuberculosis. His research also is examining how images can be mined for data to predict the causes and outcomes of conditions. Examples of Antani’s work can be found in mobile radiology vehicles, which allow professionals to take chest X-rays (right) and screen for HIV and tuberculosis using software containing algorithms developed in his lab.
For AI to have its full impact, more algorithms and approaches that harness the power of data are needed. That’s why NLM supports hundreds of other intramural and extramural scientists who are addressing challenging health and biomedical problems. The NLM-funded research is focused on how AI can help people stay healthy through early disease detection, disease management, and clinical and treatment decision-making—all leading to the ultimate goal of helping people live healthier and happier lives.
The NLM is proud to lead the way in the use of AI to accelerate discovery and transform health care. Want to learn more? Follow me on Twitter. Or, you can follow my blog, NLM Musings from the Mezzanine and receive periodic NLM research updates.
I would like to thank Valerie Florance, Acting Scientific Director of NLM IRP, and Richard Palmer, Acting Director of NLM Division of EP, for their assistance with this post.
National Library of Medicine (National Library of Medicine/NIH)
Video: Using Machine Intelligence to Prevent Medication Dispensing Errors (NLM Funding Spotlight)
Video: Sameer Antani and Artificial Intelligence (NLM)
NLM Division of Extramural Programs (NLM)
NLM Intramural Research Program (NLM)
NLM Intramural Training Opportunities (NLM)
Principal Investigators (NLM)
NLM Musings from the Mezzanine (NLM)
Note: Dr. Lawrence Tabak, who performs the duties of the NIH Director, has asked the heads of NIH’s Institutes and Centers (ICs) to contribute occasional guest posts to the blog to highlight some of the interesting science that they support and conduct. This is the 20th in the series of NIH IC guest posts that will run until a new permanent NIH director is in place.
Using AI to Find New Antibiotics Still a Work in Progress
Posted on by Lawrence Tabak, D.D.S., Ph.D.
Each year, more than 2.8 million people in the United States develop bacterial infections that don’t respond to treatment and sometimes turn life-threatening . Their infections are antibiotic-resistant, meaning the bacteria have changed in ways that allow them to withstand our current widely used arsenal of antibiotics. It’s a serious and growing health-care problem here and around the world. To fight back, doctors desperately need new antibiotics, including novel classes of drugs that bacteria haven’t seen and developed ways to resist.
Developing new antibiotics, however, involves much time, research, and expense. It’s also fraught with false leads. That’s why some researchers have turned to harnessing the predictive power of artificial intelligence (AI) in hopes of selecting the most promising leads faster and with greater precision.
It’s a potentially paradigm-shifting development in drug discovery, and a recent NIH-funded study, published in the journal Molecular Systems Biology, demonstrates AI’s potential to streamline the process of selecting future antibiotics . The results are also a bit sobering. They highlight the current limitations of one promising AI approach, showing that further refinement will still be needed to maximize its predictive capabilities.
These findings come from the lab of James Collins, Massachusetts Institute of Technology (MIT), Cambridge, and his recently launched Antibiotics-AI Project. His audacious goal is to develop seven new classes of antibiotics to treat seven of the world’s deadliest bacterial pathogens in just seven years. What makes this project so bold is that only two new classes of antibiotics have reached the market in the last 50 years!
In the latest study, Collins and his team looked to an AI program called AlphaFold2 . The name might ring a bell. AlphaFold’s AI-powered ability to predict protein structures was a finalist in Science Magazine’s 2020 Breakthrough of the Year. In fact, AlphaFold has been used already to predict the structures of more than 200 million proteins, or almost every known protein on the planet .
AlphaFold employs a deep learning approach that can predict most protein structures from their amino acid sequences about as well as more costly and time-consuming protein-mapping techniques.
In the deep learning models used to predict protein structure, computers are “trained” on existing data. As computers “learn” to understand complex relationships within the training material, they develop a model that can then be applied for making predictions of 3D protein structures from linear amino acid sequences without relying on new experiments in the lab.
Collins and his team hoped to combine AlphaFold with computer simulations commonly used in drug discovery as a way to predict interactions between essential bacterial proteins and antibacterial compounds. If it worked, researchers could then conduct virtual rapid screens of millions of new synthetic drug compounds targeting key bacterial proteins that existing antibiotics don’t. It would also enable the rapid development of antibiotics that work in novel ways, exactly what doctors need to treat antibiotic-resistant infections.
To test the strategy, Collins and his team focused first on the predicted structures of 296 essential proteins from the Escherichia coli bacterium as well as 218 antibacterial compounds. Their computer simulations then predicted how strongly any two molecules (essential protein and antibacterial) would bind together based on their shapes and physical properties.
It turned out that screening many antibacterial compounds against many potential targets in E. coli led to inaccurate predictions. For example, when comparing their computational predictions with actual interactions for 12 essential proteins measured in the lab, they found that their simulated model had about a 50:50 chance of being right. In other words, it couldn’t identify true interactions between drugs and proteins any better than random guessing.
They suspect one reason for their model’s poor performance is that the protein structures used to train the computer are fixed, not flexible and shifting physical configurations as happens in real life. To improve their success rate, they ran their predictions through additional machine-learning models that had been trained on data to help them “learn” how proteins and other molecules reconfigure themselves and interact. While this souped-up model got somewhat better results, the researchers report that they still aren’t good enough to identify promising new drugs and their protein targets.
What now? In future studies, the Collins lab will continue to incorporate and train the computers on even more biochemical and biophysical data to help with the predictive process. That’s why this study should be interpreted as an interim progress report on an area of science that will only get better with time.
But it’s also a sobering reminder that the quest to find new classes of antibiotics won’t be easy—even when aided by powerful AI approaches. We certainly aren’t there yet, but I’m confident that we will get there to give doctors new therapeutic weapons and turn back the rise in antibiotic-resistant infections.
 2019 Antibiotic resistance threats report. Centers for Disease Control and Prevention.
 Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery. Wong F, Krishnan A, Zheng EJ, Stark H, Manson AL, Earl AM, Jaakkola T, Collins JJ. Molecular Systems Biology. 2022 Sept 6. 18: e11081.
 Highly accurate protein structure prediction with AlphaFold. Jumper J, Evans R, Pritzel A, Kavukcuoglu K, Kohli P, Hassabis D., et al. Nature. 2021 Aug;596(7873):583-589.
 ‘The entire protein universe’: AI predicts shape of nearly every known protein. Callaway E. Nature. 2022 Aug;608(7921):15-16.
Antimicrobial (Drug) Resistance (National Institute of Allergy and Infectious Diseases/NIH)
Collins Lab (Massachusetts Institute of Technology, Cambridge)
The Antibiotics-AI Project, The Audacious Project (TED)
AlphaFold (Deep Mind, London, United Kingdom)
NIH Support: National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences