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Tweets & Retweets 2020 World Medical Innovation Forum – COVID-19, AI and the Future of Medicine, Featuring Harvard and Industry Leader Insights – MGH & BWH, Virtual Event: Monday, May 11, 8:15 a.m. – 5:15 p.m. ET

From: “Partners Innovation (via Twitter)” <notify@twitter.com>

Date: Tuesday, May 12, 2020 at 2:24 PM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>

Subject: Partners Innovation (@PHSInnovation) has sent you a Direct Message on Twitter!

 

Thanks for tweeting about the live event Aviva! We appreciate the support!

 

e-Proceedings 2020 World Medical Innovation Forum – COVID-19, AI and the Future of Medicine, Featuring Harvard and Industry Leader Insights – MGH & BWH, Virtual Event: Monday, May 11, 8:15 a.m. – 5:15 p.m. ET

https://pharmaceuticalintelligence.com/2020/04/22/world-medical-innovation-forum-covid-19-ai-and-the-future-of-medicine-featuring-harvard-and-industry-leader-insights-mgh-bwh-virtual-event-monday-may-11-815-a-m-515-p-m-et/

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Aviva Lev-Ari
@AVIVA1950

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Michel Vounatsos, CEO, Biogen Venture community supportive to be on the safe side  employees tested every evenings to prevent rebound of the pandemic Pandemic is acceleration progress technologies new drugs Biogen will lead new model

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#WMIF2020 @PHSInnovation @pharma_BI @AVIVA1950 Michael Mina, MD, PhD @BH Antigen test for home administration consumerization of the Testing  Walmart can be positioned for blood tests Not only Physicians can order tests @Microsoft @Amazon can interpretation of Test using Alexa

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#WMIF2020 @PHSInnovation @pharma_BI @AVIVA1950 Michael Mina, MD, PhD @BH Antigen test for home administration consumerization of the Testing  Walmart can be positioned for blood tests Not only Physicians can order tests @Microsoft @Amazon can interpretation of Test using Alexa

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Aviva Lev-Ari
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#WMIF2020 @PHSInnovation @pharma_BI @AVIVA1950 Ross Zafonte, DO, SVP, Research Education and Medical Affairs, SRN; Earle P. and Ida S. Charlton Professor of Physical Medicine and Rehabilitation, HMS @MGH is family, the unattainable is attainable

Stephen J Williams
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#WMIF2020 #Telemedicine so important for #COVID19 pandemic. Platforms developed years ago. Who would have known?

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#WMIF2020 @PHSInnovation @pharma_BI @AVIVA1950 Jan Garfinkle, Founder & Manager Partner, Arboretum Ventures Can you close a deal with out meeting management team Known funds will prevail vs new funds Parma adjacencies vs medical devices Telehealth is of interest GI Cardiovascular

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#WMIF2020 @PHSInnovation @pharma_BI @AVIVA1950 Ravi Thadhani, MD, CAO, Mass General Brigham; Professor of Medicine and Faculty Dean for Academic Programs, HMS Great Broadcasting services, expertise on the top Management of the Event 100% no room to improve Recovery COVID Patients

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2020 World Medical Innovation Forum – COVID-19, AI and the Future of Medicine, Featuring Harvard and Industry Leader Insights – #MGH & #BWH Virtual Event: Monday, May 11, 8:15 a.m. – 5:15 p.m. ET #WMIF

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2020 World Medical Innovation Forum – COVID-19, AI and the Future of Medicine, Featuring Harvard…
2020 World Medical Innovation Forum – COVID-19, AI and the Future of Medicine, Featuring Harvard and Industry Leader Insights – MGH & BWH, Virtual Event: Monday, May 11, 8:15 a.m. –…
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#WMIF20 @pharma_BI @AVIVA1950 covering event in #realtime +9,500 Global Attendees for lnkd.in/ePwTDxm about worldmedicalinnovation.org/2020-disruptiv 2020 #Virtual #World #Medical #Innovation #Forum#COVID-19 #AI #Future #Medicine @MGH & @BWH, Monday, May 11, 8:15 a.m. – 5:15 p.m. ET

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#WMIF20 @pharma_BI @AVIVA1950 covering event in #realtime +9,500 Global Attendees for lnkd.in/ePwTDxm about worldmedicalinnovation.org/2020-disruptiv 2020 #Virtual #World #Medical #Innovation #Forum#COVID-19 #AI #Future #Medicine @MGH & @BWH, Monday, May 11, 8:15 a.m. – 5:15 p.m. ET

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Reporter: Gail S. Thornton, M.A.

The following article is reprinted from the Anchorage Daily News.

https://www.adn.com/alaska-news/2020/03/18/one-of-alaskas-first-confirmed-coronavirus-patients-tells-his-story/

One of Alaska’s first confirmed coronavirus patients tells his story

March 19, 2020

A Ketchikan man who contracted the illness caused by the new coronavirus is speaking out about his experience.

In a social media post and an interview with the Ketchikan Daily News, he described his symptoms, how he was tested and his experience communicating with Alaska public health officials.

As of Wednesday morning, Glenn Brown, the attorney for the Ketchikan Gateway Borough, is one of nine people statewide who have confirmed cases of the virus. Officials have not said any of the people with confirmed cases have been hospitalized.

Brown said in a Facebook post that he was feeling better and was notified by public health officials that he’d tested positive for COVID-19 on Tuesday afternoon.

“I became sick Saturday morning with fever, headache, general achiness and chills,” Brown wrote.

Brown said he has “no idea” how he contracted the illness.

“I interacted with no one in recent weeks who was exhibiting obvious symptoms,” he wrote.

According to a statement Tuesday from the Ketchikan Emergency Operations Center saying one of its employees tested positive for the virus, the employee had a history of travel to the Lower 48. The Ketchikan Emergency Operations Center on Wednesday confirmed Brown is the employee.

The Ketchikan Daily News reported that Brown had recently traveled to Oregon and Juneau before returning to Ketchikan on March 9.

After public health officials told Brown his diagnosis, he said that he went through more than an hour of questions with them, he told the Ketchikan Daily News.

“I used everything from cellphone records to work calendars to debit card bills, to recall everybody that I may have had contact with,” Brown told the Ketchikan Daily News. “I wanted to provide that information to public health, (so) that they could alert those people and really hope to kind of arrest this thing.”

Brown told the paper that public health officials focused on two days before he developed symptoms of the illness. Brown had been “working closely with borough staff and upper management” in those days as part of his job, the paper reported.

“I apologize for causing undue concern for anyone, especially my co-workers at the Borough,” Brown said in the Facebook post.

Ketchikan Gateway Borough employees in direct contact with Brown were instructed to self-quarantine for two weeks, according to the Ketchikan Emergency Operations Center statement.

The statement also said that the borough had hired a service to disinfect the now-closed White Cliff Building, which houses the Ketchikan Borough offices.

According to the Ketchikan Daily News, the last time Brown was at the borough’s White Cliff Building was Friday.

The paper reported that as of Tuesday night, there were no plans to test people who had been in direct contact with Brown.

A public information officer for Ketchikan’s Emergency Operations Center told the Ketchikan Daily News that she understood that to be tested, people would need to have “several” symptoms of the virus.

“I would also ask that you join me and all of Ketchikan to actively minimize community transmission so that we can protect our seniors or other medically vulnerable folks in Ketchikan,” Brown wrote. “I pray that we all make it through this largely unharmed, and together.”

The first person in Alaska to test positive for COVID-19 was an air cargo pilot who arrived at Ted Stevens Anchorage International Airport on March 11, officials announced last week. He went through the airport’s North Terminal, which is separate from the domestic terminal.

Alaska’s chief medical officer, Dr. Anne Zink, said last week the man had self-isolated and was “stable.”

On Monday, officials said two older men in Fairbanks were diagnosed with the illness. Both had recently traveled to the Lower 48, Zink said, but were not traveling together.

In addition to the Anchorage case, the case in Ketchikan and the two in Fairbanks, officials on Tuesday announced that two more people had become sick with the virus — one in Fairbanks and one in Anchorage — bringing the total number of confirmed cases as of Wednesday morning to six.

Zink said that both of those cases were also travel-related. None of the three people who tested positive for COVID-19 on Tuesday were hospitalized, Zink said.

Fairbanks Memorial Hospital released a statement Tuesday saying a woman with a history of recent travel had tested positive for COVID-19.

“She self-isolated prior to testing,” the statement said. “This patient has been notified and is in stable condition and does not require hospitalization.”

A University of Alaska Fairbanks employee was one of the people who had recently tested positive for the virus in Alaska, university officials said Tuesday.

An internal email advised anyone who had used the O’Neill Building, which houses the College of Fisheries and Ocean Sciences, to stay home and monitor themselves for two weeks.

State and local officials have taken a series of steps to stem the spread of COVID-19 in Alaska, including closing schools, calling on hospitals to halt elective surgeries and shutting down dine-in service at all restaurants, bars, breweries, cafes and similar businesses.

About this Author

Morgan Krakow

Morgan Krakow is a general assignment reporter for the Anchorage Daily News. She is a 2019 graduate of the University of Oregon and spent the past summer as a reporting intern on the general assignment desk of The Washington Post. Contact her at mkrakow@adn.com.

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Ethics Behind Genetic Testing in Breast Cancer: A Webinar by Laura Carfang of survivingbreastcancer.org

Reporter: Stephen J. Williams, PhD

The following are Notes from a Webinar sponsored by survivingbreastcancer.org  on March 12,2020.

The webinar started with a brief introduction of attendees , most who are breast cancer survivors.  Survivingbreastcancer.org is an organization committed to supplying women affected with breast cancer up to date information, including podcasts, webinars, and information for treatment, care, and finding support and support groups.

Some of the comments of survivors:

  • being strong
  • making sure to not feel overwhelmed on initial diagnosis
  • get good information
  • sometimes patients have to know to ask for genetic testing as physicians may not offer it

Laura Carfang discussed her study results presented at  a bioethics conference in Clearwater, FL   on issues driving breast cancer patient’s  as well as at-risk women’s decision making process for genetic testing.  The study was a phenomenological study in order to determine, through personal lived experiences, what are pivotal choices to make genetic testing decisions in order to improve clinical practice.

The research involved in depth interviews with 6 breast cancer patients (all women) who had undergone breast cancer genetic testing.

Main themes coming from the interviews

  • information informing decisions before diagnosis:  they did not have an in depth knowledge of cancer or genetics or their inherent risk before the diagnosis.
  • these are my genes and I should own it: another common theme among women who were just diagnosed and contemplating whether or not to have genetic testing
  • information contributing to decision making after diagnosis: women wanted the option, and they wanted to know if they carry certain genetic mutations and how it would guide their own personal decision to choose the therapy they are most comfortable with and gives them the best chance to treat their cancer (the decision and choice is very personal)
  • communicating to family members and children was difficult for the individual affected;  women found that there were so many ramifications about talking with family members (how do I tell children, do family members really empathize with what I am going through).  Once women were tested they felt a great strain because they now were more concerned with who in their family (daughters) were at risk versus when they first get the diagnosis the bigger concern was obtaining information.
  • Decision making to undergo genetic testing not always linear but a nonlinear process where women went from wanting to get tested for the information to not wanting to get tested for reasons surrounding negative concerns surrounding knowing results (discrimination based on results, fear of telling family members)
  • Complex decision making involves a shift or alteration in emotion
  • The Mayo Clinic has come out with full support of genetic testing and offer to any patient.

Additional resources discussed was a book by Leslie Ferris Yerger “Probably Benign” which discusses misdiagnoses especially when a test comes back as “probably benign” and how she found it was not.

 

for more information on further Podcasts and to sign up for newsletters please go to https://www.survivingbreastcancer.org/

and @SBC_org

More articles on this Online Open Access Journal on Cancer and Bioethics Include:

Ethical Concerns in Personalized Medicine: BRCA1/2 Testing in Minors and Communication of Breast Cancer Risk

Tweets and Re-Tweets by @Pharma_BI ‏and @AVIVA1950 at 2019 Petrie-Flom Center Annual Conference: Consuming Genetics: Ethical and Legal Considerations of New Technologies, Friday, May 17, 2019 from 8:00 AM to 5:00 PM EDT @Harvard_Law

Genomics & Ethics: DNA Fragments are Products of Nature or Patentable Genes?

Study Finds that Both Women and their Primary Care Physicians Confusion over Ovarian Cancer Symptoms May Lead to Misdiagnosis

 

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Reporter and Curator: Dr. Sudipta Saha, Ph.D.

 

Early menopause, defined as the cessation of ovarian function before the age of 45 years, affects approximately 10% of women in Western populations. Current research suggests that women who experience early menopause are at increased risk of premature mortality, cognitive decline, osteoporosis, and cardiovascular disease.

 

The reproductive aging process is characterized by the gradual decrease in both quantity and quality of oocytes within ovarian follicles. The number of oocytes a woman is born with, the rate of loss of those oocytes during the life span because of the process of atresia, and the threshold number of oocytes needed to produce sufficient hormones to maintain menstrual cyclicity have been identified as determinants of age at menopause.

 

Women who breastfed their infants exclusively for seven to 12 months may have a significantly lower risk of early menopause than their peers who breastfed their infants for less than a month, according to an analysis funded by the National Institutes of Health. The study was conducted at University of Massachusetts provide the strongest evidence to date that exclusive breastfeeding may reduce the risk of early menopause. The study also suggests that pregnancy can reduce the risk of early menopause.

 

Previous studies have suggested that menopause before age 45 (early menopause) increases the risk of early death, cognitive decline, osteoporosis and cardiovascular disease. Smaller studies have found evidence linking pregnancy and breastfeeding with later menopause, but because of their size and other limitations, the results are inconclusive. Moreover, the earlier studies focused on timing of menopause and not on the risk of early menopause.

 

In the present study, researchers analyzed data from more than 100,000 women ages 25 to 42 years. Every two years, from 1989 to 2015, the participants responded to detailed questionnaires, providing health information and medical history, including pregnancy history. Compared to women who had never been pregnant or who had been pregnant for less than six months, women who had one full-term pregnancy had an 8% lower risk of early menopause. Those who had two pregnancies had a 16% lower risk, and those who had three pregnancies had a 22% lower risk.

 

Women who breastfed had an even smaller risk for early menopause. Those who breastfed for a total of 25 months or more during their premenopausal years had a 26% lower risk than women who breastfed for less than a month. Similarly, women who breastfed exclusively seven to 12 months had a 28% lower risk of early menopause, compared to those who breastfed for less than a month.

 

It is yet to be determined why pregnancy and breastfeeding lower the risk of early menopause. However, researchers theorize that because pregnancy and breastfeeding halt ovulation, the slowing of the egg loss may delay menopause. This study population is fairly homogeneous with respect to race and ethnicity, but it is expected that the physiological association between the reproductive factors of parity, breastfeeding, and early menopause would not differ substantially by race/ethnicity. Additional evaluation of these associations in more diverse populations as well as further study of the association with anti-Müllerian hormone levels are important.

 

References:

 

https://www.nih.gov/news-events/news-releases/pregnancy-breastfeeding-may-lower-risk-early-menopause-nih-study-suggests

 

https://www.ncbi.nlm.nih.gov/pubmed/31968114

 

https://www.ncbi.nlm.nih.gov/pubmed/19733988

 

https://www.ncbi.nlm.nih.gov/pubmed/18192670

 

https://www.ncbi.nlm.nih.gov/pubmed/7856687

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615483/

 

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What's The Big Data?

Terence Parr: “I am a computer scientist retooling as a machine learning droid and have found the nomenclature used by statisticians to be peculiar to say the least, so I thought I’d put this document together. It’s meant as good-natured teasing of my friends who are statisticians, but it might actually be useful to other computer scientists. I look forward to a corresponding document written by the statisticians about computer science terms!” (Statisticians say the darndest things)

I know of at least one corresponding document, published in 1994 with the rise of Neural Networks or what I have called Statistics on Steroids (SOS), which are responsible, to a large extent, to the success of today’s “AI” or Deep Learning, an advanced version of machine learning.

In Neural Networks and Statistical Models (1994), Warren Sarle explained to his worried and confused fellow statisticians that the ominous-sounding artificial neural…

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Healing traumatic brain injuries with self-assembling peptide hydrogels

Reporter : Irina Robu, PhD

In 2014, TBIs resulted in about 2.53 million emergency department visits in the U.S., according to the Centers for Disease Control and Prevention. A traumatic brain injury (TBI) can range from a mild concussion to a severe head injury. It is caused by a blow to the head or body, a wound that breaks through the skull or another injury that jars or shakes the brain. Individuals with traumatic brain injuries can develop secondary disorders after the initial blow. Researchers, Biplab Sarkar and Vivek Kumar from New Jersey Institute of Technology are hoping to prevent secondary disorders by injecting a self-assembling peptide hydrogel into the brains of rats with traumatic brain injury and see what happens. They observed that the hydrogel helped blood vessels regrow in addition to neuronal survival.

The researchers explained that after traumatic brain injury, the brain can amass glutamate which kills some neurons which is marked by overactive oxygen-containing molecules (oxidative stress), inflammation and disruption of the blood-brain barrier. Furthermore, TBI survivors can experience impaired motor control and depression. Within the experiment, the researchers showed that a week after injecting the gel in rats, the neurons have twice as many neurons at the injury site than the control animals did.

The NJIT researchers distinguished that they needed to inject the hydrogel directly in a rat’s brain just seconds after a TBI, which is not ideal, because it would be impossible to give a patient the treatment within that short period of time. The next step in showing that the self-assembling peptide hydrogel works is to combine their previous blood vessel-growing peptide and the new version to see whether it could enhance recovery. And the researchers plan to inspect whether the hydrogels work for more diffuse brain injuries such as concussions.

SOURCE

https://www.fiercebiotech.com/research/healing-traumatic-brain-injuries-self-assembling-peptide-hydrogels

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Using A.I. to Detect Lung Cancer gets an A!

Reporter: Irina Robu, PhD

Google researchers hypothesized that computers are as good or better than doctors at detecting tiny lung cancers on CT scans, since CT scan combines data from several X-rays to produce a detailed image of a structure inside the body. CT scans produce 2-dimensional images of a slice of the body and the data can also be used to construct 3-D images.

However, the technology published in Nature Medicine offers input in the future of artificial intelligence in medicine. By feeding vast amounts of data from medical imaging into systems called artificial neural networks, scientists can teach computers to identify patterns linked to a specific condition, like pneumonia, cancer or a wrist fracture that would be hard for a person to see. The system trails an algorithm, or set of instructions, and learns as it goes. The more data it receives, the better it becomes at interpretation.

The process, known as deep learning enables computers to identify objects and understand speech but it also created systems to help pathologists read microscope slides to diagnose cancer, and to help ophthalmologists detect eye disease in people with diabetes. In their recent study, the scientist used artificial intelligence to CT scans used to screen people for lung cancer, which caused 160,000 deaths in the United States last year, and 1.7 million worldwide. The scans are recommended for people at high risk because of a long history of smoking.

Screening studies showed that it can reduce the risk of dying from lung cancer and can also identify spots that might later become cancer, so that radiologists can categorize patients into risk groups and decide whether they need biopsies or more frequent follow-up scans to keep track of the suspect regions.

However, the test has errors. It can miss tumors or mistake benign spots for malignancies and shove patients into invasive, risky procedures like lung biopsies or surgery.

SOURCE

https://www.nytimes.com/2019/05/20/health/cancer-artificial-intelligence-ct-scans.html

Other related articles were published in this Online Scientific Open Access Journal including the following:

https://pharmaceuticalintelligence.com/2019/07/21/multiple-barriers-identified-which-may-hamper-use-of-artificial-intelligence-in-the-clinical-setting/

https://pharmaceuticalintelligence.com/2019/06/28/ai-system-used-to-detect-lung-cancer/

 

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Artificial throat may give voice to the voiceless

Reporter
Irina Robu, PhD

Flexible sensors have fascinated more and more attention as a fundamental part of anthropomorphic robot research, medical diagnosis and physical health monitoring. The fundamental mechanism of the sensor is based on triboelectric effect inducing electrostatic charges on the surfaces between two different materials. Just like a plate capacitor, current is produced while the size of the parallel capacitor fluctuations caused by the small mechanical disturbances and therefore the output current/voltage is produced.

Chinese scientists combine ultra sensitive motion detectors with thermal sound-emitting technology invented an “artificial throat” that could enable speech in people with damaged or non-functioning vocal cords. Team members from University in Beijing, fabricated a homemade circuit board on which to build out their dual-mode system combining detection and emitting technologies.

Graphene is a wonder material because it is thinnest material in the universe and the strongest ever measured. And graphene is only a one-atom thick layer of graphite and possess a high Young’s modulus as well as superior thermal and electrical conductivities. Graphene-based sensors have attracted much attention in recent years due to their variety of structures, unique sensing performances, room-temperature working conditions, and tremendous application prospects.

The skin like device, wearable artificial graphene throat (WAGT) is as similar as a temporary tattoo, at least as perceived by the wearer. In order to make the device functional and flexible, scientists designed a laser-scribed graphene on a thin sheet of polyvinyl alcohol film. The device is the size of two thumbnails side by side and can use water to attach the film to the skin over the volunteer’s throat and connected to electrodes to a small armband that contained a circuit board, microcomputer, power amplifier and decoder. At the development phase, the system transformed subtle throat movements into simple sounds like “OK” and “No.” During the trial of the device, volunteers imitated throat motions of speech and the device converted these movements into single-syllable words.

It is believed that this device, would be able to train mute people to generate signals with their throats and the device would translate signals into speech.

SOURCE
https://www.aiin.healthcare/topics/robotics/artificial-throat-may-give-voice-voiceless?utm_source=newsletter

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Merck KGaA-owned Sigma-Aldrich has petitioned the US Patent and Trademark Office (USPTO) to open an interference proceeding between its own pending CRISPR-Cas9 patents and patents awarded to the University of California, Berkeley (UC Berkeley).

On Friday, July 19, Sigma-Aldrich submitted the request, available on blog PatentDocs, asking for a parallel interference to the one declared by the USPTO in June between UC Berkeley and the Broad Institute of MIT and Harvard.

Sigma-Aldrich recognizes, of course, that its pending applications’ claims have not yet been allowed, and thus declaring a patent interference now would – in ordinary U.S. Serial Nos. 15/188,911; 15/188,924; & 15/456,204 -2- circumstances – be premature. However, the facts here are truly extraordinary, and Sigma-Aldrich feels compelled to apprise the Director and the CAPJ of the current situation and to briefly explain why the PTAB’s declaration of a parallel interference in this instance would be in the long-term best interests of everyone, including the USPTO, the parties, and the public. Indeed, the sole issue raised by this Petition has already been effectively decided by both the PTAB and the Federal Circuit, and those decisions completely support Sigma-Aldrich’s request here; namely, does UC’s disclosure of CRISPR-Cas9 in in vitro cell-free and nucleus-free test tube environments (hereinafter, “prokaryotic environment”) render obvious claims directed to CRISPR-Cas9 in eukaryotic cells? The controlling answer to this question is decidedly “no.” SigmaAldrich respectfully submits that the PTAB’s and the Federal Circuit’s “no” answer compels the grant of this Petition. The following timeline – which shows the 2012 and early-2013 provisional applications of Sigma-Aldrich, UC, and Broad Inst. – is relevant to the issues presented.

https://patentdocs.typepad.com/files/181_petition.pdf

 

In June, the office revived the dispute between the Broad Institute and UC Berkeley over which first invented the CRISPR gene-editing technology by announcing that it would conduct an interference proceeding between 13 patents and one application to the Broad Institute and ten patent applications filed by UC Berkeley.

All of the Broad Institute and UC Berkeley patents and applications cover the use of CRISPR/Cas9 in eukaryotic cells.

Sigma-Aldrich’s pending patent applications (serial numbers 15/188,911, 15/456,204, and 15/188,924) are also directed to CRISPR-Cas9-based methods in eukaryotic cells.

“Of critical importance here, Sigma-Aldrich’s benefit applications pre-date the earliest possible benefit applications involved in the UC Berkeley v Broad Institute interference with respect to their respective disclosures of CRISPR-Cas9 in eukaryotic cells,” said Sigma-Aldrich in its petition.

The Merck-owned unit said that it “feels compelled to apprise the director and the chief administrative patent judge (CAPJ) of the current situation and to briefly explain why the Patent Trial and Appeal Board’s (PTAB) declaration of a parallel interference in this instance would be in the long-term best interests of everyone, including the USPTO, the parties, and the public”.

Sigma-Aldrich went on to claim that the sole issue raised by the petition has already been effectively decided by both the PTAB and the US Court of Appeals for the Federal Circuit.

‘Treated unfairly’

In February 2017, the PTAB held that the Broad Institute’s patents—which are all limited to CRISPR/Cas9 systems in a eukaryotic environment—do not interfere with patent claims (which are not restricted to any environment) filed by UC Berkeley and the University of Vienna.

UC Berkeley and the University of Vienna appealed against the decision, asking the Federal Circuit to determine whether the PTAB committed error in “ignoring overwhelming evidence” that the Broad Institute’s claims are obvious in light of UC Berkeley’s.

The PTAB’s finding was affirmed by the Federal Circuit in September 2018.

“Sigma-Aldrich respectfully submits that the PTAB’s and the Federal Circuit’s ‘no’ answer compels the grant of this petition,” said the Merck subsidiary.

Sigma-Aldrich has claimed that the USPTO is treating it “very differently and unfairly” when compared to the agency’s treatment of the Broad Institute and UC Berkeley.

It said: “Indeed, the USPTO has now granted Broad Inst over a dozen issued patents. In direct contrast, the USPTO continues to reject Sigma-Aldrich’s CRISPR-Cas9 eukaryotic claims as not patentable over those same UC CRISPR-Cas9 prokaryotic provisional applications that the USPTO has repeatedly found have been successfully overcome by Broad Inst’s eukaryotic claims.”

The petition claimed that this “blatant inconsistency” and the unfairness to Sigma-Aldrich could not be “more palpable”.

“In today’s highly charged political environment, certainly the director and CAPJ are sensitive to criticism levelled at the agency regarding issues of fairness and equity, eg whether the USPTO provides ‘a level playing field’,” added the petition.

A spokesperson for the Broad Institute said: “It is time for certainty around CRISPR and for the parties to come together to resolve these disputes and to simplify access to this important technology.”

Sigma-Aldrich is part of Merck’s life science business and, in combination with Merck’s other acquisition Millipore, operates as MilliporeSigma in North America.

A spokesperson for UC Berkeley said: “We remain confident that the USPTO will ultimately recognise that the Doudna and Charpentier team hold the priority of invention specific to the CRISPR-Cas9 gene-editing technology in eukaryotic cells, as well as other settings covered by the Doudna-Charpentier team’s previous patents.”

 

Keywords

Sigma-Aldrich, Merck KGaA, USPTO, CRISPR, Broad Institute, UC Berkeley, MIT, Harvard, Cas9, patent, genome editing

 

SOURCE

https://www.lifesciencesipreview.com/news/sigma-aldrich-submits-crispr-petition-at-uspto-3615

 

Other related articles published in these Open Access Online Scientific Journal include the following:

Multiple UPDATES for original article of April 13, 2017

UPDATED – Gene Editing Consortium of Biotech Companies: CRISPR Therapeutics $CRSP, Intellia Therapeutics $NTLA, Caribou Biosciences, ERS Genomics, UC, Berkeley (Doudna’s IP) and University of Vienna (Charpentier’s IP), is appealing the decision ruled that there was no interference between the two sides, to the U.S. Court of Appeals for the Federal Circuit, targeting patents from The Broad Institute.

Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2017/04/13/gene-editing-consortium-of-biotech-companies-crispr-therapeutics-crsp-intellia-therapeutics-ntla-caribou-biosciences-and-ers-genomics-uc-berkeley-doudnas-ip-and-university-of-vienna-charpe/

Part 2: CRISPR in 

Genomics Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology

https://pharmaceuticalintelligence.com/biomed-e-books/genomics-orientations-for-personalized-medicine/volume-two-genomics-methodologies-ngs-bioinformatics-simulations-and-the-genome-ontology/

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scPopCorn: A New Computational Method for Subpopulation Detection and their Comparative Analysis Across Single-Cell Experiments

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

 

Present day technological advances have facilitated unprecedented opportunities for studying biological systems at single-cell level resolution. For example, single-cell RNA sequencing (scRNA-seq) enables the measurement of transcriptomic information of thousands of individual cells in one experiment. Analyses of such data provide information that was not accessible using bulk sequencing, which can only assess average properties of cell populations. Single-cell measurements, however, can capture the heterogeneity of a population of cells. In particular, single-cell studies allow for the identification of novel cell types, states, and dynamics.

 

One of the most prominent uses of the scRNA-seq technology is the identification of subpopulations of cells present in a sample and comparing such subpopulations across samples. Such information is crucial for understanding the heterogeneity of cells in a sample and for comparative analysis of samples from different conditions, tissues, and species. A frequently used approach is to cluster every dataset separately, inspect marker genes for each cluster, and compare these clusters in an attempt to determine which cell types were shared between samples. This approach, however, relies on the existence of predefined or clearly identifiable marker genes and their consistent measurement across subpopulations.

 

Although the aligned data can then be clustered to reveal subpopulations and their correspondence, solving the subpopulation-mapping problem by performing global alignment first and clustering second overlooks the original information about subpopulations existing in each experiment. In contrast, an approach addressing this problem directly might represent a more suitable solution. So, keeping this in mind the researchers developed a computational method, single-cell subpopulations comparison (scPopCorn), that allows for comparative analysis of two or more single-cell populations.

 

The performance of scPopCorn was tested in three distinct settings. First, its potential was demonstrated in identifying and aligning subpopulations from single-cell data from human and mouse pancreatic single-cell data. Next, scPopCorn was applied to the task of aligning biological replicates of mouse kidney single-cell data. scPopCorn achieved the best performance over the previously published tools. Finally, it was applied to compare populations of cells from cancer and healthy brain tissues, revealing the relation of neoplastic cells to neural cells and astrocytes. Consequently, as a result of this integrative approach, scPopCorn provides a powerful tool for comparative analysis of single-cell populations.

 

This scPopCorn is basically a computational method for the identification of subpopulations of cells present within individual single-cell experiments and mapping of these subpopulations across these experiments. Different from other approaches, scPopCorn performs the tasks of population identification and mapping simultaneously by optimizing a function that combines both objectives. When applied to complex biological data, scPopCorn outperforms previous methods. However, it should be kept in mind that scPopCorn assumes the input single-cell data to consist of separable subpopulations and it is not designed to perform a comparative analysis of single cell trajectories datasets that do not fulfill this constraint.

 

Several innovations developed in this work contributed to the performance of scPopCorn. First, unifying the above-mentioned tasks into a single problem statement allowed for integrating the signal from different experiments while identifying subpopulations within each experiment. Such an incorporation aids the reduction of biological and experimental noise. The researchers believe that the ideas introduced in scPopCorn not only enabled the design of a highly accurate identification of subpopulations and mapping approach, but can also provide a stepping stone for other tools to interrogate the relationships between single cell experiments.

 

References:

 

https://www.sciencedirect.com/science/article/pii/S2405471219301887

 

https://www.tandfonline.com/doi/abs/10.1080/23307706.2017.1397554

 

https://ieeexplore.ieee.org/abstract/document/4031383

 

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0927-y

 

https://www.sciencedirect.com/science/article/pii/S2405471216302666

 

 

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