Wednesday, January 17, 2024

 

We need a staph vaccine: here’s why we don’t have one


Research from UC San Diego explains the clinical failure of dozens of candidate vaccines for one of the most common human infections; it also suggests a way to fix the problem

Peer-Reviewed Publication

UNIVERSITY OF CALIFORNIA - SAN DIEGO

Bacteria virus illustration 

IMAGE: 

THIS ILLUSTRATION SHOWS SA (GOLDEN SPHERES) AND VARIOUS ANTIGENS AND ANTIBODIES. DOMINANT ANTIGENS (PURPLE) CAUSE SA TO PRODUCE NON-PROTECTIVE ANTIBODIES (RED WITH PURPLE TIPS). THESE NONPROTECTIVE ANTIBODIES OUTCOMPETE ANTIBODIES DERIVED FROM VACCINATION (GREEN WITH PURPLE TIPS). VACCINES TARGETING SUBDOMINANT ANTIGENS (BLUE) COULD HELP YIELD MORE PROTECTIVE ANTIBODIES (GREEN WITH BLUE TIPS), MAKING THE VACCINE MORE EFFECTIVE.

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CREDIT: JR CALDERA/ UC SAN DIEGO HEALTH SCIENCES





Staphylococcus aureus (SA) is an extremely common bacterial infection; about 30% of people have colonies of SA living in their nose. SA is often harmless, but it is also a leading cause of hospital-acquired and community-associated infections. A vaccine for SA would be a game-changer for public health, but for decades, all vaccine candidates for SA have failed in clinical trials despite successful preclinical studies in mice. Researchers at University of California San Diego School of Medicine have finally explained why.

In a new study, published January 16, 2024 in Cell Reports Medicine, they tested a new hypothesis that SA bacteria can trick the body into releasing non-protective antibodies when they first colonize or infect humans. When the individual is later vaccinated, these non-protective antibodies are preferentially recalled, making the vaccine ineffective.

SA has a unique relationship with humans. While it causes many dangerous health complications, including wound and bloodstream infections, the bacterium is also a normal part of the healthy human microbiome, where it lives peacefully in the nose and on the skin.

“SA has been with humans a long time, so it’s learned how to be part-time symbiont, part-time deadly pathogen,” said senior author George Liu MD, PhD, professor in the Department of Pediatrics at UC San Diego School of Medicine. “If we’re going to develop effective vaccines against SA, we need to understand and overcome the strategies it uses to maintain this lifestyle.”

The immune system releases protective antibodies in response to molecules it suspects are foreign, called antigens. These antibodies are then saved in the immune system’s memory, so the next time the immune system encounters that same antigen, it will generally recall its earlier immune response rather than mount a brand-new attack.

“This is an effective system for conferring long-term protection against pathogens, but it only works when the initial immune response to that pathogen was actually protective,” said co-lead author JR Caldera, PhD, who completed his doctoral research in the Liu Lab. “What sets SA apart is that the bacteria themselves have ways of evading the immune system from the moment they encounter us, and these evasive strategies are only reinforced by vaccination.”

While SA vaccines have unilaterally failed in clinical trials, they generally do well in preclinical studies of mice. In order to figure out why this is, the researchers collected blood serum from healthy volunteers, quantifying and purifying the anti-SA antibodies present in the samples. They then transferred these antibodies to mice to explore how protective they were against SA on their own, as well as how they influenced the efficacy of several clinically-tested SA vaccine candidates.

The researchers found that the vaccines were ineffective in mice that had been given human anti-SA antibodies, as well as mice that had been previously exposed to SA. However, in mice that had never been exposed to either SA or human antibodies, the vaccines worked. Unlike previous mouse studies of SA vaccines, the researchers’ results were consistent with those of failed clinical trials, suggesting that their experimental model could help predict the clinical success of SA vaccines while they are still being tested in preclinical mouse studies.

Further, they found that specific antibodies were to blame for the effect they observed. The antibodies that attack the cell walls of SA bacteria, which are the basis for most current SA vaccines, didn’t protect the mice against SA. By contrast, antibodies that target the toxins produced by SA were able to successfully neutralize them.

“One pathogen can have many different antigens that the immune system responds to, but there is a hierarchy as far as which antigen is dominant,” said co-lead author Chih Ming Tsai, PhD, a project scientist in the Liu Lab.  “Most vaccines are based on the dominant antigen to trigger the strongest possible immune response. But our findings suggest that for SA, the rules are different, and it is more beneficial to target so-called subdominant antigens, which triggered a weak immune response in the first place.”

In addition to exploring the possibility of targeting new antigens with future SA vaccines, the researchers are also interested in exploring the deeper question at play here: why is the natural human immune response to this bacterium so ineffective to begin with?

“Somehow, SA is able to trick our immune system, and figuring out how will help us improve existing SA vaccines and develop new ones,” said Liu. “More broadly, these findings suggest a whole new way of reevaluating failed vaccines, which could have implications well beyond this one bacterium.”

Co-authors of the study include: Desmond Trieu, Cesia Gonzalez, Irshad A. Hajam, Xin Du and Brian Lin at UC San Diego.

This study was funded, in part, by the National Institute of Health (grants R01AI127406, R01AI144694 and R01AI181321).

This graphical abstract shows the experimental approach used by the researchers to study immune responses to SA vaccination. Vaccines targeting subdominant antigens, such as toxins produced by the bacteria, conferred more protection than vaccines targeting dominant antigens.

CREDIT

UC San Diego Health Sciences

Disclaimer: AAAS and Eure

 JAMA

Analysis of breast cancer mortality in the US


Peer-Reviewed Publication

JAMA NETWORK



About The Study: Based on four simulation models, breast cancer screening, treatment of stage I to III breast cancer, and treatment of metastatic breast cancer were each associated with reduced breast cancer mortality between 1975 and 2019 in the U.S. 

Authors: Sylvia K. Plevritis, Ph.D., of the Stanford University School of Medicine in Stanford, California, is the corresponding author.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(doi:10.1001/jama.2023.25881)

Editor’s Note: Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding and support.

Embed this link to provide your readers free access to the full-text article This link will be live at the embargo time https://jamanetwork.com/journals/jama/fullarticle/10.1001/jama.2023.25881?guestAccessKey=a28ac933-5836-47a6-94f1-7a04ea2310c9&utm_source=For_The_Media&utm_medium=referral&utm_campaign=ftm_links&utm_content=tfl&utm_term=011624

JOURNAL

Consumption of 100% fruit juice and body weight in children and adults

JAMA Pediatrics

Peer-Reviewed Publication

JAMA NETWORK



About The Study: This systematic review and meta-analysis of 42 eligible studies, including 17 among children (n = 45,851) and 25 among adults (n = 268,095), found a positive association between intake of 100% fruit juice and weight gain in children. Analysis of cohort studies in adults found a significant positive association among studies unadjusted for total energy, suggesting potential mediation by calories; an analysis of trials in adults found no significant association between 100% fruit juice consumption and body weight. The findings support guidance to limit consumption of fruit juice to prevent the intake of excess calories and weight gain.

Authors: Vasanti S. Malik, M.Sc., Sc.D., of the University of Toronto, is the corresponding author.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(doi:10.1001/jamapediatrics.2023.6124)

Editor’s Note: Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding and support.

Embed this link to provide your readers free access to the full-text article This link will be live at the embargo time https://jamanetwork.com/journals/jamapediatrics/fullarticle/10.1001/jamapediatrics.2023.6124?guestAccessKey=872103a6-f1eb-4ab3-82cb-f7336d108823&utm_source=For_The_Media&utm_medium=referral&utm_campaign=ftm_links&utm_content=tfl&utm_term=011624

COACHING IS ABUSE

Experiences of interpersonal violence in sport and perceived coaching style among college athletes


JAMA Network Open

Peer-Reviewed Publication

JAMA NETWORK




About The Study: The results of this survey study involving 4,119 currently competing U.S. college athletes suggest that interpersonal violence is associated with marked changes in the psychosocial health and emotional well-being of college athletes, particularly those who identify as female and with non-heterosexual sexual orientations. Variations in coaching style have the potential to alter these associations. Ongoing efforts are needed to leverage the unique position that coaches hold to help reduce interpersonal violence and create safe places where all college athletes can thrive. 

Authors: Yetsa A. Tuakli-Wosornu, M.D., M.P.H., of the Yale School of Public Health in New Haven, Connecticut, is the corresponding author. 

 To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(doi:10.1001/jamanetworkopen.2023.50248)

Editor’s Note: Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding and support.

Embed this link to provide your readers free access to the full-text article This link will be live at the embargo time http://jamanetwork.com/journals/jamanetworkopen/fullarticle/10.1001/jamanetworkopen.2023.50248?utm_source=For_The_Media&utm_medium=referral&utm_campaign=ftm_links&utm_term=011624

 

Palliative telecare significantly improves quality of life for those with chronic illnesses, and results last for months


When working with nurse and social worker virtually, trial participants with chronic heart and lung diseases report long-lasting improvements


Peer-Reviewed Publication

UNIVERSITY OF COLORADO ANSCHUTZ MEDICAL CAMPUS

Study: How a Palliative Telecare Program Improves Quality of Life with Long-Lasting Results 

VIDEO: 

RESEARCHERS FROM THE UNIVERSITY OF COLORADO ANSCHUTZ MEDICAL CAMPUS HAVE FOUND THAT A TEAM INTERVENTION, PROVIDED BY PHONE, LEADS TO PERSISTENT IMPROVEMENTS IN DEPRESSION, ANXIETY, AND QUALITY OF LIFE FOR PEOPLE MANAGING CHRONIC ILLNESSES. ADDITIONALLY, RESEARCHERS FOUND THAT THE IMPROVEMENT IN QUALITY OF LIFE RESULTS LAST MONTHS AFTER INTERVENTION CONCLUDES.

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CREDIT: UNIVERSITY OF COLORADO ANSCHUTZ MEDICAL CAMPUS





AURORA, Colo. (January 16, 2024) – Researchers from the University of Colorado Anschutz Medical Campus have found that a team intervention, provided by phone, leads to persistent improvements in depression, anxiety, and quality of life for people managing chronic illnesses. Additionally, researchers found that the improvement in quality of life results last months after intervention concludes.

In a study, published today in JAMA, researchers observe the impact a telecare intervention program, called ADAPT, has on veterans suffering from poor quality of life as a result of existing chronic illnesses, such as chronic obstructive pulmonary disease (COPD), heart failure (HF) and interstitial lung disease (ILD). This program provides palliative care that is not widely available and tackles health concerns that may be missed in standard appointments. Nurses and social workers reach out to study participants with structured questions and assistance, then discuss responses with a team of doctors, including specialists, to determine how best to address concerns with follow-up calls to track progress.

“While we do a great job caring for these patients’ illnesses, we can do more for quality of life. Many have persistent symptoms, such as depression, anxiety, shortness of breath, and sleep problems that can make living with these illnesses very difficult and have been associated with earlier death” says David Bekelman, MD, MPH, professor at the University of Colorado School of Medicine and study lead author. “Palliative care can help.  However, access to outpatient palliative care specialists is limited to non-existent, and new, scalable ways to provide early palliative care are needed.”

For adults with COPD, HF or ILD at high risk of hospitalization and death and poor quality of life, this program demonstrated early, persistent and clinically meaningful improvements in depression, anxiety, and quality of life. Additionally, while ADAPT lasted for 4 months, Bekelman and researchers saw positive results early that lasted for many months after the program ended.  

“There are people who endure persistent symptoms and poor quality of life despite great treatments. We need to fill in the gaps and provide more for these patients,” says Bekelman who worked with the VA of Eastern Colorado  Puget Sound Health Care Systems to conduct this research to conduct this research. “This innovative team care model is adaptable, scalable and can help make life better for people living with these illnesses. This program demonstrates that even a short amount of time providing structured telecare results in increased quality of life months after the calls end.”

About the University of Colorado Anschutz Medical Campus

The University of Colorado Anschutz Medical Campus is a world-class medical destination at the forefront of transformative science, medicine, education and patient care. The campus encompasses the University of Colorado health professional schools, more than 60 centers and institutes, and two nationally ranked independent hospitals - UCHealth University of Colorado Hospital and Children's Hospital Colorado - that treat more than two million adult and pediatric patients each year. Innovative, interconnected and highly collaborative, the University of Colorado Anschutz Medical Campus delivers life-changing treatments, patient care and professional training and conducts world-renowned research fueled by over $704 million in research grants. For more information, visit www.cuanschutz.edu.

Quantum computing and machine learning are effective tools in fluid dynamics


Quantum support vector machines classify flow separation better than classical counterparts


Peer-Reviewed Publication

INTELLIGENT COMPUTING

Flow separation and pressure distribution on an airfoil. 

IMAGE: 

A. FLOW WITHOUT FLOW SEPARATION AND WITH FLOW SEPARATION. B. PRESSURE DISTRIBUTION TREND WITHOUT FLOW SEPARATION AND WITH FLOW SEPARATION.

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CREDIT: XI-JUN YUAN ET AL.





To prevent aircraft stalls, engineers have long studied the flow of air over airfoils such as airplane wings to detect the angles when flow separation occurs. Recently, a team of researchers at Shanghai Jiao Tong University including Xi-Jun Yuan and Zi-Qiao Chen investigated the use of quantum computing in connection with machine learning as a more accurate way of solving such problems. Their research was published Nov. 21 in Intelligent Computing, a Science Partner Journal.

The use of a quantum support vector machine rather than a classical support vector machine increased the accuracy of classification of flow separation from 81.8% to 90.9% and increased the accuracy of classification of the angle of attack from 67.0% to 79.0%. These results help show that using quantum computing methods for fluid dynamics problems could be faster and more accurate than using classical computing methods, especially because the datasets in such contexts are large. Potential applications of quantum support vector machines in addition to aircraft design include underwater navigation and target tracking.

The researchers performed two classification tasks. The first was a binary classification on a small dataset to detect whether or not flow separation had occurred. A small dataset was chosen because it is difficult to achieve high-accuracy classification for small datasets. Data for this task were collected from pressure sensors on an airfoil in a wind tunnel with different airspeeds and angles of attack. The dataset consists of 45 multidimensional points: 27 cases without flow separation and 18 cases with flow separation. This dataset was divided into 34 points for training and 11 points for testing.

The second task was more complex. It classified the angle of attack of the airfoil after flow separation into one of four classes. To achieve this, the problem was broken into four one-against-all classification problems, with a binary in-or-out classifier for each of the four classes. Data for this task were created by simulation. The dataset consists of 63 multidimensional points obtained by sampling. This dataset was divided into 43 points for training and 20 for testing. The training and testing process was repeated 10 times with different combinations of training and test data, and the average accuracy of 10 tests was obtained.

The particular type of classification algorithm chosen by the researchers is a quantum-annealing-based supervised machine learning algorithm called a support vector machine. The quantum annealer they used was the D-Wave Advantage 4.1 system, a physical quantum computing device.

Quantum annealing implementations of support vector machines have demonstrated better performance than their classical counterparts, which are structurally simple and robust, but have high storage and computation costs and thus do not scale up easily.

Quantum annealing is an optimization process that uses quantum fluctuations to look for a global minimum among a set of solutions. Because the process generates multiple good candidates for the global minimum, it can achieve more accurate results than other optimization algorithms, which are more likely to get stuck at a local minimum.


Results of the flow classification problem. 


Experiment could test quantum nature of large masses for the first time


An experiment outlined by a UCL-led team could test whether relatively large masses have a quantum nature, resolving the question of whether quantum mechanical description works at a much larger scale than that of particles and atoms.


Peer-Reviewed Publication

UNIVERSITY COLLEGE LONDON

LIGO mirrors 

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TECHNICIANS INSPECT THE "FIRST CONTACT" COATING ON ONE OF LIGO'S INPUT TEST MASSES (MIRRORS). HTTPS://WWW.LIGO.CALTECH.EDU/PAGE/OPTICS

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CREDIT: CALTECH/MIT/LIGO LAB





An experiment outlined by a UCL (University College London)-led team of scientists from the UK and India could test whether relatively large masses have a quantum nature, resolving the question of whether quantum mechanical description works at a much larger scale than that of particles and atoms.

Quantum theory is typically seen as describing nature at the tiniest scales and quantum effects have not been observed in a laboratory for objects more massive than about a quintillionth of a gram, or more precisely 10^(-20)g.

The new experiment, described in a paper published in Physical Review Letters and involving researchers at UCL, the University of Southampton and the Bose Institute in Kolkata, India, could in principle test the quantumness of an object regardless of its mass or energy.

The proposed experiment exploits the principle in quantum mechanics that the act of measurement of an object can change its nature. (The term measurement encompasses any interaction of the object with a probe – for instance, if light shines on it, or if it emits light or heat).

The experiment focuses on a pendulum-like object oscillating like a ball on a string. A light is shone on one half of the area of oscillation, revealing information about the location of the object (i.e., if scattered light is not observed, then it can be concluded that the object is not in that half). A second light is shone, showing the location of the object further along on its swing.

If the object is quantum, the first measurement (the first flash of light) will disturb its path (by measurement induced collapse -- a property inherent to quantum mechanics), changing the likelihood of where it will be at the second flash of light, whereas if it is classical then the act of observation will make no difference. Researchers can then compare scenarios in which they shine a light twice to ones where only the second flash of light occurs to see if there is a difference in the final distributions of the object.

Lead author Dr Debarshi Das (UCL Physics & Astronomy and the Royal Society) said: “A crowd at a football match cannot affect the result of the game simply by staring strongly. But with quantum mechanics, the act of observation or measurement itself changes the system.

“Our proposed experiment can test if an object is classical or quantum by seeing if an act of observation can lead to a change in its motion.”

The proposal, the researchers say, could be implemented with current technologies using nanocrystals or, in principle, even using mirrors at LIGO (Laser Interferometer Gravitational-Wave Observatory) in the United States which have an effective mass of 10kg.

The four LIGO mirrors, which each weigh 40kg but together vibrate as if they were a single 10kg object, have already been cooled to the minimum-energy state (a fraction above absolute zero) that would be required in any experiment seeking to detect quantum behaviour.

Senior author Professor Sougato Bose (UCL Physics & Astronomy) said: “Our scheme has wide conceptual implications. It could test whether relatively large objects have definite properties, i.e., their properties are real, even when we are not measuring them. It could extend the domain of quantum mechanics and probe whether this fundamental theory of nature is valid only at certain scales or if it holds true for larger masses too.

“If we do not encounter a mass limit to quantum mechanics, this makes ever more acute the problem of trying to reconcile quantum theory with reality as we experience it.”

In quantum mechanics, objects do not have definite properties until they are observed or interact with their environment. Prior to observation they do not exist in a definite location but may be in two places at once (a state of superposition). This led to Einstein’s remark: “Is the moon there when no one is looking at it?”

Quantum mechanics may seem at odds with our experience of reality but its insights have helped the development of computers, smartphones, broadband, GPS, and magnetic resonance imaging.

Most physicists believe quantum mechanics holds true at larger scales, but is merely harder to observe due to the isolation required to preserve a quantum state. To detect quantum behaviour in an object, its temperature or vibrations must be reduced to its lowest possible level (its ground state) and it must be in a vacuum so that nearly no atoms are interacting with it. That is because a quantum state will collapse, a process called decoherence, if the object interacts with its environment. 

The new proposed experiment is a development of an earlier quantum test devised by Professor Bose and colleagues in 2018. A project to conduct an experiment using this methodology, which will test the quantum nature of a nanocrystal numbering a billion atoms, is already underway, funded by the Engineering and Physical Sciences Research Council (EPSRC) and led by the University of Southampton.

That project already aims for a jump in terms of mass, with previous attempts to test the quantum nature of a macroscopic object limited to hundreds of thousands of atoms. The newly published scheme, meanwhile, could be achieved with current technologies using a nanocrystal with trillions of atoms.

The new paper was co-authored by Dr Das and Professor Bose at UCL along with Professor Dipankar Home of India’s Bose Institute (who also co-authored the 2018 paper) and Professor Hendrik Ulbricht of the University of Southampton.