Category Archives: Molecular Medicine

Colorized scanning electron micrograph of a cell (pink) infected with a variant strain of SARS-CoV-2 virus particles (UK B.1.1.7; gold), isolated from a patient sample. Courtesy NIAID

UC San Diego researchers have found that a post-COVID lung disease shares origins with other scarring lung diseases, which may offer a path to effective therapies, according to a study released Wednesday.

Although most people recover relatively quickly from COVID-19, around one-third of survivors experience symptoms weeks and months after the initial infection. However, in the study published in Wednesdays online issue of eBioMedicine, UCSD scientists studied interstitial lung disease, a form of long COVID that consists of a group of chronic pulmonary disorders characterized by inflammation and scarring of the lung.

The researchers said little is currently known about ILD which can be fatal without a lung transplant in its most severe form. But they found insights into the causes and paths the disease may take.

Using an artificial intelligence approach, we found that lung fibrosis caused by COVID-19 resembles idiopathic pulmonary fibrosis, the most common and the deadliest form of ILD, said co-senior study author Dr. Pradipta Ghosh, professor in the departments of Medicine and Cellular and Molecular Medicine at UCSD School of Medicine. At a fundamental level, both conditions display similar gene expression patterns in the lungs and blood, and dysfunctional processes within alveolar type II cells.

Those AT2 cells play several roles in pulmonary function, including the production of lung surfactant that keeps lung cells from collapsing after exhalation and regeneration of lung cells after injury.

The findings are insightful because AT2 cells are known to contain an elegant quality control network that responds to stress, internal or external, Ghosh said. Failure of quality control leads to broader organ dysfunction and, in this case, fibrotic remodeling of the lung.

To conduct the study, Ghosh collaborated with co-author Debashis Sahoo, associate professor in the departments of Computer Science, Engineering and Pediatrics at UCSD for the AI assisted analysis among other aspects.

Ghosh and Sahoo said the approach would help them stay unbiased in navigating the unknowns of an emerging, post-pandemic disease. They analyzed more than 1,000 human lung datasets associated with various lung conditions, specifically looking for gene expression patterns, inflammation signaling and cellular changes. The disease with the closest match: IPF.

IPF affects around 100,000 people in the United States, with 30,000 to 40,000 new cases annually. The condition has a poor prognosis, with an estimated mean survival of 2 to 5 years from time of diagnosis.

City News Service contributed to this article.

Continued here:
UCSD Post-COVID Lung Disease Study May Unlock Path to Therapies - Times of San Diego

As the latest COVID-19 vaccine, Novavax, jumps the final regulatory hurdle onto the US market, the US Food and Drug Administration has its eyes set on the COVID-19 vaccine plan for this fall and winter, when we're likely to see another wave of cases.

The FDA last month made arecommendationthat vaccine manufacturers should make a booster dose of COVID-19 vaccine that targets the omicron variant -- specifically, theBA.4 and BA.5 subvariants. BA.5, the most contagious version of the virus to date, now makes upthe majorityof COVID-19 cases in the US and seemslikely to leadto another summer surge of COVID-19 cases ahead of the anticipated fall or winter booster rollout.

The current advice for this summer is the same: Get the booster shots you're eligible for. (For everyone 50 and older, that means two boosters.) But the question at hand for health regulators was whether vaccine-makers should continue to use their original primary vaccine formulas (which will probably stay the same for the time being) for boosters, or if they should create a vaccine that targets omicron, which has been dominant worldwide for months and keeps mutating into more-contagious versions of itself.

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While there's still the chance we could be dealing with a whole new variant come fall or winter (you can never underestimate COVID-19), the FDA decided boosters targeting BA.5 should be the way forward.

The US government is expected to roll out vaccine boosters based on need: People most at risk will be eligible for a new booster first. And the vaccines based on earlier strains of the virus that causes COVID-19 (also called "ancestral" strains) are still protective against severe disease and death from omicron -- the most important function of vaccination in general.

While the details are being tested and ironed out, here's what we know about the fall COVID-19 vaccine strategy.

Both BA.4 and BA.5 are considered part of the "original" omicron variant (BA.1) family. They're newer versions of the virus that causes COVID-19. BA.5 quickly overtook the conversation on BA.4/BA.5 because of its extreme contagiousness, and it's now the dominant variant in the US. In a late June post, Dr. Eric Topol, professor of molecular medicine, called BA.5 "the worst version of the virus that we've seen."

While more time and research is needed to see what effect they have in the US (which has already experienced a high number of cases this late spring and summer), BA.5 is thought to whittle away much of the infection protection people got prior sickness, even with other omicron variants.

Omicron caused such a huge number of cases last winter because it was the most contagious variant to date, evading some infection protection from prior illness and effectiveness of the vaccines. The fact that newer versions of omicron are proving to be even more contagious isn't a big surprise, as this is the path COVID-19 has taken over the last two and half years.

Read more abouteverything we know about BA.5.

Specifically, the FDA is asking for abivalent(two-component) vaccine booster, which will include the BA.4/BA.5 spike protein in addition to an older strain. The FDA doesn't make vaccines, so the agency will likely authorize individual vaccine types as companies create and test them, as it did for the original COVID-19 vaccines and booster doses.

The vaccines currently authorized or approved only use older or "ancestral" strains of the virus. These vaccines still provide good protection against severe disease and death, but the effectiveness against infection is becoming more limited as the virus keeps mutating.

At a White House COVID-19 Response Teambriefing Tuesday, Dr. Ashish Jha said that if the timeline goes accordingly, he expects the first people to be eligible will start getting vaccinated in October, with other people becoming eligible in November or December.

But there is no authorized booster yet, so an exact timeline isn't available right now.

Moderna and Pfizer had both been working on boosters that target the general omicron variant. With the FDA's request to target omicron's newest strains, they will need to switch lanes to meet their target, hopefully in time for fall.

Novavax which justreceived CDC recommendationfor its primary two-dose vaccine also said it'sspeeding up workon a formula specifically targeting the new versions of omicron.

Pfizer announced last month that it struck a deal with the US government to provide more doses including ones that are adapted for omicron, pending FDA authorization.

The information contained in this article is for educational and informational purposes only and is not intended as health or medical advice. Always consult a physician or other qualified health provider regarding any questions you may have about a medical condition or health objectives.

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Here's What We Know About COVID Vaccine Plans for the Fall - CNET

Researchers used data from the American Heart Associations COVID-19 CVD Registry to determine the impact of smoking or vaping among people hospitalized with COVID-19

DALLAS, July 26, 2022 People who reported smoking or vaping prior to their hospitalization for COVID-19 were more likely than their counterparts who did not smoke or vape to experience severe complications, including death, from the SARS-CoV-2 infection. The findings are from a new study based on data from the American Heart Associations COVID-19 CVD Registry and published in PLOS ONE, a peer-reviewed, open access scientific journal published by the Public Library of Science.

Researchers examined data on people over 18 years of age who were hospitalized with COVID-19 in 107 registry-participating hospitals across the nation between January 2020 to March 2021. Smoking status was self-reported and people were classified as smoking if they reported currently using either traditional, combustible cigarettes or e-cigarette products, with no distinction between the two and no information on duration of smoking or former smoking status. For the final analysis, records were selected for 4,086 people with a 1:2 ratio of people who smoked (1,362) to people who did not smoke (2,724), with the two groups matched for no statistically significant difference in age, sex, race, medical history or medication.

The study findings indicate smoking or vaping are associated with more severe COVID-19 independent of age, sex, race or medical history:

In general, people who smoke or vape tend to have a higher prevalence of other health conditions and risk factors that could play a role in how they are impacted by COVID-19. However, the robust and significant increase in the risk of severe COVID-19 seen in our study, independent of medical history and medication use and particularly among young individuals, underscores the urgent need for extensive public health interventions such as anti-smoking campaigns and increased access to cessation therapy, especially in the age of COVID, said the studys senior author, Aruni Bhatnagar, Ph.D., FAHA, a professor of medicine, biochemistry and molecular biology at the University of Louisville in Louisville, Kentucky. These findings provide the clearest evidence to date that people who smoke or vape have a higher risk of developing severe COVID-19 and dying as a result of SARS-CoV-2 infection.

Bhatnagar is co-director of the American Heart Associations Tobacco Center for Regulatory Science which supported the study in part with funding from the U. S. National Institutes of Health and the Food and Drug Administration research grants.

We established the COVID-19 CVD Registry early on in the pandemic to better understand the link between COVID-19 and cardiovascular disease, specifically, to identify increased risk to help inform the diagnosis and care of people who are at highest risk for complications, said Sandeep R. Das, M.D., M.P.H., M.B.A., FAHA, co-chair of the steering committee for the American Heart Association COVID-19 CVD Registry Powered by Get With The Guidelines and director for Quality and Value in the Cardiology Division at UT Southwestern Medical Center in Dallas, Texas. The findings of this study deliver on that goal and provide invaluable information individuals and their health care teams.

The American Heart Association launched the registry in 2020 to gather data specific to all patients hospitalized with COVID-19 as part of the Get With The Guidelines quality improvement program. Registry participation was offered at no cost to all U.S. hospitals caring for adults with active COVID-19 and with the infrastructure to support accurate data collection. More than 160 hospitals provided data on more than 79,000 patient records between 2020 and June 2022.

The American Heart Association receives funding primarily from individuals; foundations and corporations (including pharmaceutical, device manufacturers and other companies) also make donations and fund specific Association programs and events. The Association has strict policies to prevent these relationships from influencing the science content. Revenues from pharmaceutical and biotech companies, device manufacturers and health insurance providers and the Associations overall financial information are available here.

Additional Resources:

About the American Heart Association

The American Heart Association is a relentless force for a world of longer, healthier lives.We are dedicated to ensuring equitable health in all communities.Through collaboration with numerous organizations, and powered by millions of volunteers, we fund innovative research, advocate for the public's health and share lifesaving resources.The Dallas-based organization has been a leading source of health information for nearly a century.Connect with us onheart.org,Facebook,Twitteror by calling 1-800-AHA-USA1.

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For Media Inquiries: 214-706-1173

Cathy Lewis: cathy.lewis@heart.org; 214-706-1324

Michelle Rosenfeld: michelle.rosenfeld@heart.org; 214-706-1099

For Public Inquiries: 1-800-AHA-USA1 (242-8721)

heart.org and stroke.org

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Smoking, vaping linked to higher risk of severe COVID-19 complications, including death - American Heart Association

In January 2022, the U.S. Food and Drug Administration (FDA) cautioned the public against a peculiar method for testing oneself COVID-19 tests.

"FACT: When it comes to at-home rapid antigen #COVID19 tests, those swabs are for your nose and not your throat," the agency said Friday.

The anti-throat-swabbing warning came amid the first omicron surge in the United States. The reason? Anecdotal reports surfaced about people who were testing positive for COVID-19 only after they swabbed their throats. (A typical COVID-19 at-home test involves swabbing one's nose exclusively.)

Nearly seven months later, as the country faces yet another surge due to omicron subvariant BA.5, the FDA warning has yet to put an end to this off-label collection method. Anecdotal reports continue to surface on social media regarding symptomatic people who received negative results on an at-home test with nasal swabs, followed by a positive test only after they poked the back of their throat with the long swab instead.

Other countries' health agencies do call for testing one's throat for viral residue. Canadian provinces, including Ontario and Nova Scotia, have updated their recommendations for at-home testing to include swabs of both throat and nose.

"To collect a sample for a rapid antigen test (RATs), users should follow the instructions described in the kit insert," Ontario Health, a government health agency, advises in an information sheet updated in February 2022. "In addition to the collection method option approved by Health Canada (as described in the kit insert), users may choose to perform combined oral and nasal sampling as it may increase test sensitivity." The health agency proceeds to instruct people how to properly collect a sample from one's throat.

The collection method of throat swabbing remains a divisive issue among experts in infectious disease.

Despite the FDA's warning, many Americans are apt to wonder who to believe. Is this a collection method that does indeed "increase test sensitivity," as Ontario Health claims?

The answer depends on who's asked as the collection method of throat swabbing remains a divisive issue among experts in infectious disease.

Nathaniel Hafer, an assistant professor in molecular medicine at University of Massachusetts' Chan Medical School who has researched both at-home antigen tests and polymerase chain reaction (PCR) tests, told Salon he believes it is best for people to follow the instructions of their specific test. In other words, if the test calls for throat swabbing, do it; if not, avoid it.

"I come down on the side that people should really do what's indicated in the test kit itself, which for all kits that are authorized in the U.S., the collection should be from the nose only," Hafer. "I think people should be following the instructions in the kits."

Yet Dr. Amesh Adalja, a senior scholar at the Johns Hopkins Center, disagreed. He told Salon via email he's been "recommending this for months" as in, swabbing one's throat when using an at-home tests "especially when sore throat is a prominent symptom."

As for lab-based PCR tests, Dr. Adalja said he doesn't recommend that physicians swab throats unless the instructions call for that method, which some do. For example, the Rheonix COVID-19 test does involve throat swabs. In other parts of the world, it is more common for PCR tests to be performed using throat swabs.

Going off-instructions could lead to some weird gray areas that raise new questions. For instance, say an individual swabs one's throat when doing an at-home test that doesn't call for throat swabbing and then tests positive. Does that imply the result would be inaccurate?

Hafer said there is some "anecdotal evidence" that the location of the tropisms of SARS-CoV-2 have changed over time with different variants.

"People are speculating that there's just more virus in the throat. I mean, that might be true, but the kits have not been tested for that kind of collection method, and so people might be getting actually true results," Hafer said. "But when people don't use the kids according to the instructions, they're opening the door to not get accurate results and that's both in the positive direction and the negative direction."

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William Schaffner, a professor of infectious diseases at the Vanderbilt University Medical Center, told Salon he believes when a person swabs their throat with an at-home antigen test and they're positive, that means definitively that they are indeed positive no question.

"They've been infected with the virus," Schaffner said. He noted that he thinks people should be following the test's instructions, but he's not surprised that people are swabbing their throats and getting positive test results.

"If you swab the throat, which is way in the back and you can consider that the back of the nose also, we call that the nasopharynx, way back there in the throat this is a virus that does cause sore throats, and indeed it gets down into your chest."

Indeed, as Schaffner pointed out, if the virus is lingering in the cavity where the nose and throat meet that is likely why positive results are appearing after throat swabs.

Notably, most of this adviceis based anecdotal reports. There have not been any scientific papers with peer-reviewed evidence that confirm or deny the efficacy of throat swabbing with at-home tests that don't call for it. One study,published on medRxiv by researchers in Cape Town, South Africa, concluded that saliva swabs were the preferred sample-collection method for detecting omicron infections.

In the meantime, everyday people may take it upon themselves to swab their throats when self-testing. If that yields a positive result, it's time to contact a doctor and isolate from people.

In that scenario, "they should obviously contact their healthcare provider, particularly if they're in a high risk group," Schaffner said.

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Experts still torn on whether you should swab your throat when taking COVID tests - Salon

Engineering | Health and medicine | Science | UW News blog

July 15, 2022

Another beautiful day on the University of Washingtons Seattle campus.University of Washington

Seven professors at the University of Washington are among 25 new members of the Washington State Academy of Sciences, according to a July 15 announcement. Joining the academy is a recognition of their outstanding record of scientific and technical achievement, and their willingness to work on behalf of the Academy to bring the best available science to bear on issues within the State of Washington.

Twenty of the incoming members for 2022 were selected by current WSAS members, while the other five were chosen by virtue of recently joining one of the National Academies.

UW faculty selected by current Academy members are:

In addition, Dr. Jay Shendure, UW professor of genome sciences, investigator with the Howard Hughes Medical Institute and faculty member in the Molecular Engineering & Sciences Institute, was selected by virtue of his election to the National Academy of Sciences for pioneering a variety of genome sequencing and analysis methods, including exome sequencing and its earliest applications to gene discovery for Mendelian disorders and autism; cell-free DNA diagnostics for cancer and reproductive medicine; massively parallel reporter assays; saturation genome editing; whole organism lineage tracing; and massively parallel molecular profiling of single cells.

New members to the Washington State Academy of Sciences will be formally inducted in September.

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Seven UW faculty members elected to the Washington State Academy of Sciences - University of Washington

Precision medicine is changing the treatment landscape for countless patients, but with the transformational advances come a host of intellectual property (IP) issues that must be overcome to ensure the continued evolution of these life changing technologies. With a focus on digital health, we will discuss what precision medicine is and the IP hurdles it faces, such as patent subject matter eligibility, proving infringement, and software licensing.

What Is Precision Medicine?

Precision medicine is a term used to refer to treatment and prevention strategies tailored to groups of people based on genetic, environmental, and lifestyle factors, instead of using a one-size-fits-all approach. Precision medicine is often used interchangeably with the older term, personalized medicine, but is preferred by some because personalized medicine was often misconstrued as individualized treatments, not those developed for a group of people.

Targeted therapies are the foundation of precision medicine. They include cancer treatments that target proteins controlling cell growth. Many targeted therapies are small molecule drugs or monoclonal antibodies, which have targets inside and on the outside of cancer cells. Using these targets, the drugs can mark cells for destruction by the immune system, stop cancer cell growth signals, stop blood vessel growth, cause cancer cell death, prevent access to hormones necessary for cell growth, or carry toxins to the cancer cells. Targeted therapies differ from chemotherapy in that they act on specific molecular targets associated with cancer cells instead of targeting all rapidly dividing cells, and they often prevent cell growth (cytostatic) where chemotherapies kill cells (cytotoxic).

Along with targeted therapies, precision medicine may also utilize diagnostics. Diagnostics can perform a variety of functions, including identifying potential for disease, diagnosing disease, and identifying patients who may or may not benefit from a particular therapy. In precision medicine, diagnostics may be used to analyze a patients genome for mutations or measure protein expression or metabolites to guide treatment decisions.

What Are the Benefits of Precision Medicine?

While precision medicine is still in its early days, its development and use is increasing because of its therapeutic and cost saving benefits. Ineffective medications are a concern for health care, from both a patient and cost perspective. As of 2015, for every patient that was helped by the 10 highest grossing medications, between 3 and 24 patients received no benefit.[1] In 2001, a study showed that the available cancer drugs were ineffective for 75% of patients.[2] Taking an ineffective drug subjects the patient to side effects without a therapeutic benefit, and prolongs the time to receiving an effective treatment, time during which their disease could irreversibly progress. Spending money on ineffective treatments is problematic, with an estimated $2.5 billion per year wasted on ineffective rheumatoid arthritis treatments alone.[3] It was estimated that US pharmaceutical spending was over $575 billion in 2021, and given the high level of ineffective treatments, the overall waste could amount to billions of dollars each year.

Precision medicines and new diagnostic tools hope to provide prevention strategies and treatments more tailored to each individual. Targeted research is increasing, with 61% of clinical trials for cancer treatments conducted in 2019 using biomarkers, compared to only 18% in 2000. Precision medicine approvals have also been on the rise, accounting for over 25% of drug approvals each year since 2015, and with over 42% of new drug approvals in 2018 being precision medicines.[4]

As of 2020, there were 286 precision medicines on the market in the US. In addition, 24 new or expanded indications for in vitro diagnostic testing systems have been FDA-approved over the last 3 years that can inform targeted therapeutic decisions. The cost for sequencing a human genome has dropped from $100 million in 2001 to approximately $1000 in 2019, allowing for more frequent use of this technology and the potential to compile large databases of genetic information for analysis.

What Is the Role of Digital Health in Advancing Precision Medicine?

Digital health is facilitating advances in precision medicine by helping patients manage their diseases and collecting and analyzing data that leads to the development of new treatments and indications. Digital health includes technologies such as medical mobile apps and software, wearable devices, artificial intelligence (AI), and machine learning. Software and devices can be used by patients to collect data and manage their treatments.

For example, a patient with multiple sclerosis may be able to use a wearable device to track their steps and speed, and using a mobile app, compare their data to other patients and track their own data over time to monitor the progression of their disease.

In addition to benefiting the individual patient, the data collected can also be compiled and analyzed to optimize treatment or to develop new and more effective diagnostics and therapeutics. AI and machine learning can be used to analyze large data sets, such as patient genomes, to determine correlations between genetic mutations and drug efficacy, or determine which drugs may or may not work for a particular patient based on their individual characteristics.

IP Issues for Digital Health Inventions

With the advances in digital health come a variety of patenting and licensing opportunities, as well as legal challenges that must be considered. Patenting opportunities exist throughout the process of discovery, testing, and administration of precision medicines. In the area of digital health, patents may potentially cover tools for building databases, analyzing, and sharing medical data, computer programs, and ways of storing data like electronic health records. Patenting opportunities may also exist for discovery platforms for designing and engineering precision antibodies, methods of screening genomes to identify disease targets, modeling tools, and wearable devices. Patenting challenges will vary depending on the technology, but some of the particular pitfalls for precision medicine come from 35 U.S.C. 101 patentable subject matter challenges, divided infringement issues, and open source software (OSS) licensing.

101 Subject Matter Eligibility

The Supreme Court issued a series of cases from 2012 to 2014 that form the basis for applying 101 patentable subject matter, including Mayo v. Prometheus, 132 S. Ct. 1289 (2012), Assn for Molecular Pathology v. Myriad Genetics, 132 S. Ct. 1794 (2013), and Alice Corp. Pty. Ltd. v. CLS Bank Intl, 134 S. Ct. 2347 (2014).

In Mayo, the Court found diagnostic testing claims to be unpatentable laws of nature, explaining that claims that include laws of nature can be patentable if the claims apply the law of nature. The claims cannot preempt the entire use of the law of nature, and the additional elements added to the claim have to be significant. They cannot simply add steps that are well understood, routine, or conventional.

In Myriad, the Court found claims covering isolated gene sequences unpatentable because isolating naturally occurring DNA is not patentable subject matter, where creating DNA that is not naturally occurring is eligible.

In Alice, the Court found a computer system implementing intermediated settlement of financial obligations to be unpatentable, creating a 2-part test for subject matter eligibility. In Step 1, the court determines whether the claim is directed to a patent-ineligible concept (law of nature, natural phenomena, or abstract idea). If the answer is yes, then the court proceeds to Step 2. In Step 2, the court considers the elements of each claim both individually and as an ordered combination to determine whether the claim contains an inventive concept that transforms the claim into a patent-eligible application that is sufficient to ensure that the patent in practice amounts to significantly more than a patent upon the [ineligible concept] itself. Id. at 2355.

The cases since this trio have shown that obtaining patents on digital health inventions can be challenging, particularly given the inconsistent application of case law, but they give some guidance on the types of claims that may survive a 101 challenge and should be considered when drafting claims covering computerized methods.

Smartgene Inc. v. Advanced Biological Laboratories, 555 F. App'x 950 (Fed. Cir. 2014) held that adding a computer to perform steps of a mental process routinely engaged in by doctors is not enough to transform an abstract mental process into patentable subject matter, finding that systems and methods for guiding the selection of a therapeutic treatment regimen for a patient with a known disease or condition using a computer to be ineligible as abstract. Claims directed to the abstract ideas of mathematical calculations and statistical modeling that included generic steps of implementing and processing calculations and storing the data without any practical application were found unpatentable despite claims of improved accuracy, because different use of a mathematical calculation, even one that yields different or better results, does not render patent eligible subject matter.

In re: Board of Trustees of the Leland Stanford Junior Univ., 991 F.3d 1245, 1251 (Fed. Cir. 2021). Combining 2 abstract ideas, such as machine learning technology using support vector machines (SVM) and recursive feature elimination (RFE) to process large sets of data (like human genomes), is still an abstract idea and not patent eligible, particularly if a non-abstract application is not identified. See Health Discovery Corp. v. Intel Corp., 2021 WL 6116891 (W.D. Tex. Dec. 27, 2021).

As an example of how courts distinguish between patentable and unpatentable subject matter, its interesting to look at a pair of related cases between CardioNet and InfoBionic. These cases suggest that if an actual device is developed using the abstract mathematical concepts as opposed to using a generic computer, the claims are more likely to be found patent eligible. See CardioNet, LLC v. InfoBionic, Inc., 955 F.3d 1358 (Fed. Cir. 2020) CardioNet, LLC v. InfoBionic, Inc., 2021 WL 5024388 (Fed. Cir. Oct. 29, 2021).

The courts analysis hinged on whether the claims were directed to the computer/device or the mathematical concept that the computer/device was performing. Providing proof of using the device in a real world context was also helpful in conferring patent eligibility, as was describing the advantages offered by the claimed system or device in the specification. See CardioNet, 955 F.3d 1358.

Finally, in the CardioNet case finding patent eligibility, there was nothing in the record suggesting doctors were previously employing the techniques at issue. See id.

However, in the case finding ineligibility, the claims did not describe how a doctor decided when to turn on the claimed T wave filter, suggesting that doctors using conventional techniques, and automating known techniques using a computer would not be patent eligible. See CardioNet, 2021 WL 5024388.

Although employing AI as part of precision medicine may be part of a patented process, so far it has not been feasible to list that AI as an inventor on patents in the United States. See Thaler v. Hirshfeld, 558 F. Supp. 3d 238 (E.D. Va. 2021).

This is consistent with the findings of courts in the United Kingdom, the European Union, and recently Australia (which had previously found that AI could be listed as an inventor). South Africa has allowed AI inventors, but lacks substantive prosecution, so it is unclear if it will be upheld if challenged.

Since performing a mathematical concept on a generic computer and automating known techniques have been found ineligible, drafting claims for computerized methods and software related to precision medicine that are directed to discrete devices, and include specific process and operation steps, will give the best chances of patent eligibility under 101. Describing the improvements over the prior technology and providing evidence of actual application in the specification will also be helpful in avoiding a 101 challenge.

Trade secrets should also be considered to protect aspects of inventions that may be considered ineligible subject matter. For example, an isolated nucleotide sequence may be unpatentable under Myriad, but could possibly be protected as a trade secret if the company takes the necessary steps to keep the information secure.

Until 2016, trade secret misappropriation was governed by state law, with varying statutes of limitation, remedies, and definitions of what a trade secret is. In 2016, the Defend Trade Secrets Act (DTSA) was passed, creating a civil cause of action for trade secret owners to sue in federal court. The DTSA does not preempt state trade secret law, but provides an additional option of filing a case in federal court. It also provides uniform definitions of trade secret and misappropriation and remedies including civil seizure, injunction, payment of a reasonable royalty, and damages.

Divided Infringement

Another potential concern for precision medicine patents is enforcement. Because patents for precision medicine often require steps to be performed by more than one party, without a single party controlling the actions of all the parties, divided infringement can be an issue. In particular, this can be an issue for claims involving a diagnostic method followed by a treatment based on the outcome of the diagnostic test. This type of claim has shown to be subject matter eligible under 101, but the diagnostic testing is often done by one party followed by a treatment decision made by a doctor, dividing the infringement between multiple unrelated parties. For digital health, this could be an issue if, for example, claims were directed to diagnostic testing through patients collecting data via a wearable device, followed by their doctor providing treatment based on the data collected.

Under the precedent of Akami Techs., Inc. v. Limelight Networks, Inc., 797 F.3d 1020, (Fed. Cir. 2015) (en banc), a party can be held responsible for the infringement of other partiesperforming the steps of a method claim to 2 situations:

Direction or control can be found when an alleged infringer conditions participation in an activity or receipt of a benefit upon performance of a step or steps of a patented method and establishes the manner or timing of that performance. Id. The level of cooperation or control necessary to prove divided infringement should be considered broadly, and conditioning participation is not limited to legal obligations or technical prerequisites, and does not require penalties for non-compliance. See Travel Sentry, Inc. v. Tropp, 877 F.3d 1370 (Fed. Cir. 2017).

Proving direct infringement when there are multiple actors may be easier in the generic drug context than for diagnostic testing methods followed by treatment decisions, because instructions in the Physician Prescribing Information and Patient Information can establish the necessary level of direction or control to prove treatment was conditioned on performance of other method steps, and can show specific intent to induce infringement. See Eli Lilly and Co. v. Teva Parenteral Medicines, Inc., 845 F.3d 1357 (Fed. Cir. 2017).

A laboratory report provided to a doctor by a diagnostic testing company has not been shown to provide the necessary specific intent to induce infringement of method steps requiring the performance of an assay followed by administering a drug. See Cleveland Clinic Found. v. True Health Diagnostics LLC, 859 F.3d 1352 (Fed. Cir. 2017). The Court here also noted that a party that provides a service, but no material or apparatus, cannot be liable for contributory infringement.Id.

While the case law indicates that proving infringement of certain digital health patent claims may be challenging, it does leave open the possibility of proving infringement in some situations, such as if a doctor conditions a patients treatment on their collection of data using a device or mobile app, or if a diagnostic laboratory is affiliated with a doctor or hospital and their contracts provide the necessary level of direction or control to prove infringement.

Open-Source Software (OSS) Licensing

Precision Medicine may employ the use of computer programs and mobile device apps. Many of these programs and apps may be built on open-source software (OSS), which is a type of software that has source code that is open to anyone to review, modify, and improve.

This software can be used instead of closed source (also known as proprietary) software which has code that can only be modified by the company that owns it. While there are some types of free OSS, many are available pursuant to an OSS license that may have restrictions on distribution, particularly if a company is considering white labeling software (rebranding to appear as though it is a companys own software) for its precision medicine process. Depending on the license, code modifications may need to be provided to others for free.

OSS comes with many advantages, such as being less expensive than proprietary software and being interoperable with various systems. However, OSS does have issues that precision medicine companies will need to consider when developing their software and applications. Since patient health data is often collected in precision medicine, privacy is important and is directly impacted by software security. This is a concern for both OSS and proprietary software, with some feeling that OSS may be safer because so many people are reviewing the code.

However, support for technical issues can be unreliable for OSS since it typically relies on the open source community and not a particular vendor. Enterprise grade OSS could be used to avoid this issue and remain HIPPA compliant because it requires enhanced testing, performance tuning, and is proactively examined for security flaws. Unlike other OSS that relies only on the open source community to fix technical issues, enterprise grade OSS typically has a security team that reviews the code and has processes for responding to issues and notifying users about the issues and how to fix them. OSS rarely comes with any warranty, liability, or infringement indemnity protection should there be any issues.

Depending on the technology, certification of the software may be necessary, for example to comply with FDA regulations or interoperability standards set by the CMS and the Office of the National Coordinator for Health Information Technology. While it is possible to have OSS certified, it may be more challenging than for closed source alternatives.

Conclusion

While precision medicine has the potential to change the lives of many patients and save our health care system significant costs by better avoiding ineffective treatments, companies developing these technologies have many issues to consider when developing, patenting, and licensing their technologies. Because of the complex and often inconsistent application of case law to precision medicine and digital health inventions, IP counsel should be consulted on how to best protect these discoveries.

References

[1] Schork, NJ. Personalized medicine: Time for one-person trials. Nature. 2015;520:609-611. doi:10.1038/520609a

[2] The personalized medicine report: 2020 - Opportunity, challenges, and the future. Personalized Medicine Coalition. Published 2020. https://www.personalizedmedicinecoalition.org/Userfiles/PMC-Corporate/file/PMC_The_Personalized_Medicine_Report_Opportunity_Challenges_and_the_Future.pdf

[3] Lagasse, J. Precision medicine has potential to reduce wasteful ineffective treatments, study says. Healthcare Finance. Published May 22, 2018. https://www.healthcarefinancenews.com/news/precision-medicine-has-potential-reduce-wasteful-ineffective-treatments-study-says

[4] Personalized medicine at FDA: The scope & significance of progress in 2021. Personalized Medicine Coalition. Published 2021. https://www.personalizedmedicinecoalition.org/Userfiles/PMC-Corporate/file/Personalized_Medicine_at_FDA_The_Scope_Significance_of_Progress_in_2021.pdf

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Watch the AMA's COVID-19 Update, with insights from AMA leaders and experts about the pandemic.

Featured topic and speakers

In todays COVID-19 Update,the latest on Omicron subvariants, delays in state-by-state COVID-19 case reporting and more with AMA Director of Science, Medicine and Public Health Andrea Garcia, JD, MPH. American Medical Association Chief Experience Officer Todd Unger hosts.

Learn more at the AMA COVID-19 resource center.

Unger: Hello. This is the American Medical Association's COVID-19 Update video and podcast. Today, we have our weekly look at the numbers, trends and latest news about COVID-19 with the AMA's Director of Science, Medicine, and Public Health Andrea Garcia in Chicago. I'm Todd Unger, AMA's chief experience officer, also in Chicago. Andrea, before we get started, let's talk about one important number. This is the 400th episode of the COVID-19 Update. How do you like that?

Garcia: I don't think we realized we would be doing 400 of these when we started.

Unger: I don't either. It's been longer than anticipated, but still a lot of news. So, let's start with the other numbers. What are we looking at in terms of cases?

Garcia: Well, if we look at The New York Times to give the virus report, I think that number of new known cases of COVID continues to look relatively stable. We're averaging around 100 and 117,000 cases per day. Of course, we talk about this pretty much every week.

The key word is known. Our numbers have always been an undercount, and that's low this week, of course, as we've talked about before due to the reporting delays from the holiday. I think the keys here really are the test positivity rate in the U.S. is rising. It's at about 18%. And then, of course, the new dominant BA.5 subvariant that is really growing and in places around the country and, of course, leading to new outbreaks. And so, even with that delayed reporting, more than half of states are seeing slightly higher cases now than two weeks ago.

Unger: And we're going to talk in more detail about subvariants here in a minute. You mentioned the word delay. Are we seeing delays in reporting?

Garcia: So yes, but I think the key here is more states have actually stopped giving daily data updates, and that's created a blurrier view of where we stand with cases overall. And as we see states report less frequency, changes in the trajectory of the virus become less apparent. Nearly every state, when earlier in the pandemic, reported new COVID cases, hospitalizations and deaths five days a week or more. And now, we have about 23 states that are releasing that data only once a week.

Unger: Wow. So between that change in reporting and between, let's say, underreporting for home testing, that's got to have a pretty significant impact at this point on tracking where we stand, correct?

Garcia: It does, for sure.

Unger: Well, finally, other numbers. Any kind of issues on the hospitalization and deaths front?

Garcia: So hospitalizations have increased steadily in recent weeks. We're at about 37,000 people in the U.S. hospitalized with COVID on a given day. That's an increase of about 17% over the last two weeks, and it's the highest national average since early March. Deaths continue to remain stable. For now, that data, of course, is also in flux due to the holiday, but we really are seeing fewer than 400 deaths reported each day. That's, of course, down from the peak of 2,600 a day at the height of the surge.

Unger: Well, let's talk a little bit about what's driving that uptick. Reading a lot about different kinds of sub variants out there, let's first talk about the latest Omicron variant. What do we know about this newest one?

Garcia: The latest subvariant of possible concern is the BA.275. Time reported earlier this week that there are three cases of this subvariant reported in the U.S. so far, they're all in the west coast two in California and one in Washington state. On the global level, we know this this subvariant has been gaining some traction in India, and it's also been detected in 10 other countries.

It has a large number of mutations in areas of the spike protein, and that makes it concerning. And it could potentially be more adept at spreading quickly and evading antibody protection. Of course, we hear this concern about it being even more transmissible than the new BA.5 variant we discussed last week. It's something that we're keeping an eye on for sure, but it's really too soon to draw some conclusions around whether or not it will outpace BA.5 here in the U.S.

Unger: It's almost like a subvariant per week. Just last week, you said, we were talking about BA.5. Any change on that particular variant?

Garcia: Last week, we talked about BA.5 now being dominant. According to federal estimates this week, it is now making up 65% of cases together with BA.4, which is making up about 16% of cases. So over 80% between the two of them, this is really fueling the current outbreak of cases and hospitalizations that we're seeing.

We heard Eric Topol, who's a professor of molecular medicine at Scripps Research, say in a recent New York Times article, I think there's an under-appreciation of what it's going to do in the country, and it's already exerting its effect. And while we know these subvariants can evade immunity from previous infections and vaccines, so far, the relatively low number of deaths suggests that the vaccines are still working to prevent the worst outcomes.

Unger: And there's been a lot of data just recently, again, talking about the effectiveness of vaccines. Tell us a little bit more about the newest research.

Garcia: So a modeling study that was conducted by the CDC and published in JAMA last week really highlights that life-saving power that the vaccines have had. And that study looked at the period between December 1 of 2020 and September 30 of 2021 and estimated that COVID-19 vaccination prevented 27 million infections, 1.6 million COVID-associated hospitalizations, and 235,000 COVID-19 associated deaths. That's among vaccinated people 18 years and older.

We know that by September 30 of 2021, vaccination prevented an estimated 52% of expected infections, 56% of expected hospitalizations, and 58% of expected deaths. And so, these findings indicate that the COVID vaccination program prevented substantial morbidity and mortality through direct protection of vaccinated individuals, I would just note that. We, of course, still have a significant proportion of the population that has not been vaccinated. So there's still work to do to build that trust and confidence in these vaccines.

Unger: Well, those are big numbers. And I think off the extent of the impact is not, let's say, fully appreciated. But vaccines aren't the only tool that we've had, of course, that have saved lives. We've also had treatments that have helped bring those numbers down. And just last week, we heard about a drug that was originally developed to treat cancer that may be helpful against COVID. What do we know about that?

Garcia: Yeah, so there was a study published last Wednesday in the New England Journal, and it was on an experimental drug that was developed initially to fight cancer, but it ended up cutting the relative risk of death for people hospitalized with COVID by more than half. So it was a phase three clinical trial conducted in hospitalized patients with moderate to severe COVID, they were at high-risk for acute respiratory distress syndrome and death.

And so, the drug known as Sabizabulin, and the hope here is really that this is going to be a safe and effective treatment for severely ill COVID patients who are hospitalized. And while we have oral antivirals that are effective when administered early in the course of illness, we know that those options currently for hospitalized patients with severe COVID are limited.

So Veru is the company that developed this drug. They've applied for an EUA from the FDA. And if authorized, this is going to give physicians another option for this patient population. But the one caveat here is that the trial was relatively small, with just 134 patients receiving the drug.

Unger: Thats potentially exciting news. A couple of other key pieces of news in the last week from the AMA. Why don't we start by talking first about Paxlovid.

Garcia: Yeah, so we have a number of press releases this week, and the Paxlovid one came out in reaction to an FDA regulatory decision last Wednesday. It gave U.S.-based pharmacists the authority with certain limitations to prescribe Paxlovid, and we know that's Pfizer's oral antiviral COVID treatment. Prior to this, only doctors, nurses and TAs were allowed to prescribe Paxlovid.

While this move is aimed at making it easier for patients to get the drug, the AMA statement points out that prescribing it requires knowledge of a patient's medical history, requires clinical monitoring for side effects and follow-up care to determine whether a patient's improving, and those requirements are beyond pharmacists scope and training.

It goes on to explain that patients will get the best, most comprehensive care from physician-led teams, teams that include pharmacists. And to ensure the best possible care for COVID-19 patients, we urge people who test positive to discuss treatment options with their physicians if they have one.

Unger: Second press release has to do with vaccinations for young children. Let's talk a little bit about that.

Garcia: So that was an open letter from the AMA, the American Academy of Pediatrics and the American Academy of Family Physicians, encouraging all parents and caregivers to talk with their physician about getting their children vaccinated against COVID. The letter says that doing so will help ensure your family is protected before this fall, when we know there may be another surge, as schools resume and people spend more time indoors.

It also explains how COVID is unpredictable, and we do not know which children will suffer severe, long term, or debilitating symptoms. And we know that children can become severely ill from COVID-19, be hospitalized, or even die. In addition to talking to a physician, the letter provides parents with helpful resources to answer their questions. Those include getvaccineanswers.org, healthychildren.org, and familydoctor.org/vaccines.

Unger: Andrea, thank you so much for the updates this week. We'll be back with another COVID-19 update next week. In the meantime, you can visit ama-assn.org/COVID-19 for all our resources on COVID. Thanks for joining us today, and please take care.

Disclaimer: The viewpoints expressed in this video are those of the participants and/or do not necessarily reflect the views and policies of the AMA.

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CDC study shows power of COVID-19 vaccines with Andrea Garcia, JD, MPH - American Medical Association

When the pandemic first began, COVID-19 seemed to lurk around every corner, so it came as a big relief when scientists established that the virus doesnt easily spread outdoors. This summer, however, that feeling of relative safety has come into question. Now that the BA.5 subvariant is driving a new wave in the U.S., can people count on the open air to keep them safe?

The truth is that being outside has never been a sure way to avoid COVID-19 transmissionespecially at crowded events, like music festivals, which have been linked to outbreaks in the past. We certainly hear, in our study, of people who pretty clearly were infected outdoors, so it happens, says Dr. Donald Milton, professor of environmental health at the University of Maryland School of Public Health, who is principal investigator of an ongoing study on COVID-19 transmission. Of course, its still a lower risk than indoors, but Milton does not feel comfortable in every outdoor situation. I didnt go to the fireworks on July 4, and I have not been in any crowds, he says. My outdoor activities mostly consist of exercising, riding a bike, walking, and jogging.

BA.5 seems to evade immunity from vaccines and past infections more easily than past subvariants, which experts say increases risk no matter where you are. Were more susceptible hosts, and were more susceptible whether were inside or outside, says Dr. Duane Wesemann, an associate professor at Harvard Medical School and an immunologist at Brigham and Womens Hospital.

While scientists are still learning about BA.5, its increasingly clear that compared to past variants, it has advantages that help it bypass the immune systems defenses. Like other Omicron subvariants, BA.5 has developed new mutationsin this case, in the spike protein, the part of the virus that binds to cellswhich may help it to evade immunity, explains Bing Chen, an associate professor of medicine at Harvard Medical School and Boston Childrens Hospital who studies molecular medicine. Our antibodies are a little less effective against BA.5 compared to BA.1 and Delta, he says.

BA.5s increased transmission and our diminished immune defenses mean that COVID-19 transmission outdoors has become more likely. But that doesnt mean that being outdoors isnt going to provide some protectionespecially if you also take other precautions. As always, context matters. Being in the open air and away from other people is safer than being in a crowd with worse air circulationlike in a packed baseball stadium without a breeze, says Milton. Outdoors remains a much lower-risk setting than indoors, says Linsey Marr, professor of civil and environmental engineering at Virginia Tech. Transmission outdoors is most likely to occur in close, face-to-face conversation. Theres also the possibility of transmission if you happen to be close enough and downwind of someone who is infected.

The same precautions that keep you safe indoors can also help outside, including avoiding crowds and wearing a mask when youre with other people. Being up to date on COVID-19 vaccinations can also make you safer, since the shots trigger the immune system to develop multiple types of defenses against COVID-19, says Wesemann. While the virus is increasingly good at getting around the neutralizing antibodieswhich help prevent people from getting infected in the first placevaccines also trigger longer-lasting types of immune responses. In the end, that means that vaccinated people who get infected with COVID-19 are less likely to become very sick or die from the diseaseno matter where they were infected.

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BA.5 Outdoor Transmission: The Risk of Catching COVID-19 - TIME

Early in 2020, Austria began decoding the Sars-CoV-2 genome from wastewater samples from wastewater treatment plants. These analyzes are now part of the National Epidemic Surveillance. They reflect the diverse dynamics in astonishing detail and precision, according to a report by a team led by Andreas Bergthaler of CeMM, Med-Uni Vienna and Innsbruck researchers in the Nature Biotechnology journal. At the moment, with the exception of BA.5, fairly little happens with variants.

In Austria, researchers from the University of Innsbruck, the Technical University of Vienna and the Medical University of Innsbruck have developed analyzes of viruses in wastewater in the early stage of the epidemic. As a result, the ministries of education and health established a national monitoring system for the sewage treatment plant. Samples were taken from about 100 wastewater treatment plants across Austria regularly in order to have an overview of the local infection process and circulating variables. But at the end of the school year, the so-called school website monitoring was gradually abolished. At the moment, the monitoring of the 24 largest sewage treatment plants in Austria, funded by the Ministry of Health, is still in place their catchment area covers about half of the population.

For the current study, the scientists used sequencing and analysis data from a total of 3,413 wastewater samples from more than 90 municipal catchment areas and wastewater treatment plants, which were taken between December 2020 and February 2022. Using specially developed software, the first authors, Fabian Oman From the Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences (AW) and Rudolf Markt from the Institute of Microbiology at the University of Innsbruck, from the spatio-temporal frequency determination of virus variants from wastewater samples. This data was then compared to records of more than 311,000 individual cases, that is, confirmed infections, along with infection epidemiologists at the Agency for Health and Food Safety (AGES).

The results will confirm for the first time worldwide that wastewater analyzes provide a highly accurate overview of the pandemic situation in an entire country and reflect the spread of virus variants in the population. For every week and every gathering area where a particular variant has occurred at least once, according to the Epidemiological Reporting System, we see a corresponding signal in wastewater in 86 percent of samples from the same week. Conversely, in about three percent of wastewater samples we see escaped variants of the existing system, Oman says.

The researchers emphasize that the data obtained from wastewater analyzes will provide a basis for prediction of newly emerging variables and facilitate the calculation of reproductive advantage for questionable variables. Another advantage is that the infection process can be recorded in people who do not have symptoms or who do not use the test presentation. Overall, the study shows that wastewater-based epidemiology can support public health at the national level and specifically benefit countries without extensive individual surveillance, the researchers wrote. In addition, it also shows the potential of wastewater analytics in order to improve global surveillance of other infectious diseases in the future.

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According to the study: Wastewater analyzes provide an accurate overview of the variables of Covid 19 - Socialpost

The US Food and Drug Administration made arecommendationlast week that vaccine manufacturers should make a booster dose of COVID-19 vaccine that targets the omicron variant -- specifically, BA.4 and BA.5 subvariants. BA.5, the most contagious version of the virus to date, now makes upthe majorityof COVID-19 cases in the US and seemslikely to leadto another summer surge of COVID-19 cases ahead of the anticipated fall or winter booster rollout.

The current advice for this summer is the same: Get the booster shots you're eligible for. (For everyone 50 and older, that means two boosters.) But the question at hand for health regulators was whether vaccine-makers should continue to use their original primary vaccine formulas (which will probably stay the same for the time being) for boosters, or if they should create a vaccine that targets omicron, which has been dominant worldwide for months and keeps mutating into more contagious versions of itself.

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While there's still the chance we could be dealing with a whole new variant come fall or winter (you can never underestimate COVID-19), the FDA decided boosters targeting BA.5 should be the way forward.

The US government is expected to roll out vaccine boosters based on need: the most at-risk will be eligible for a new booster first. And the vaccines based on earlier strains of the virus that causes COVID-19 (also called "ancestral" strains) are still protective against severe disease and death from omicron the most important function of vaccination in general. On Tuesday, the FDA authorized another primary vaccine based on an ancestral strain of COVID,called Novavax.

While the details are being tested and ironed out, here's what we know about the fall COVID-19 vaccine strategy.

Both BA.4 and BA.5 are considered part of the "original" omicron variant (BA.1) family. They're newer versions of the virus that causes COVID-19. BA.5 quickly overtook the conversation on BA.4/BA.5 because of its extreme contagiousness, and it's now the dominant variant in the US. In a late June post, Dr. Eric Topol, professor of molecular medicine, called BA.5 "the worst version of the virus that we've seen."

While more time and research is needed to see what effect they have in the US (which has already experienced a high number of cases this late spring and summer), BA.5 is thought to whittle away much of the infection protection people got prior sickness, even with other omicron variants.

Omicron caused such a huge number of cases last winter because it was the most contagious variant to date, evading some infection protection from prior illness and effectiveness of the vaccines. The fact that newer versions of omicron are proving to be even more contagious isn't a big surprise, as this is the path COVID-19 has taken over the last two and half years.

Read more abouteverything we know about BA.5.

Specifically, the FDA is asking for abivalent(two-component) vaccine booster, which will include the BA.4/BA.5 spike protein in addition to an older strain. The FDA doesn't make vaccines, so the agency will likely authorize individual vaccine types as companies create and test them, as it did for the original COVID-19 vaccines and booster doses.

The vaccines currently authorized or approved only use older or "ancestral" strains of the virus. These vaccines still provide good protection against severe disease and death, but the effectiveness against infection is becoming more limited as the virus keeps mutating.

At a White House COVID-19 Response Teambriefing Tuesday, Dr. Ashish Jha said that if the timeline goes accordingly, he expects the first people to be eligible will start getting vaccinated in October, with other people becoming eligible in November or December.

But there is no authorized booster yet, so an exact timeline isn't available right now.

Moderna and Pfizer had both been working on boosters that target the general omicron variant. With the FDA's request to target omicron's newest strains, they will need to switch lanes to meet their target, hopefully in time for fall.

Novavax which justreceived FDA authorization for its primary two-dose vaccine also said it'sspeeding up workon a formula specifically targeting the new versions of omicron.

Pfizer announced last month that it struck a deal with the US government to provide more doses including ones that are adapted for omicron, pending FDA authorization.

The information contained in this article is for educational and informational purposes only and is not intended as health or medical advice. Always consult a physician or other qualified health provider regarding any questions you may have about a medical condition or health objectives.

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New COVID Vaccine for Fall? What to Know About the FDA's Plans - CNET