Healthcare analytics, AI solutions for biological big data, providing an AI platform for the biotech, life sciences, medical and pharmaceutical industries, as well as for related technological approaches, i.e., curation and text analysis with machine learning and other activities related to AI applications to these industries.
AACR and Dr. Margaret Foti Announce Free Virtual Annual Meeting for April 27, 28 2020 and other Free Resources
Reporter: Stephen J. Williams, PhD
Please see the following email from Dr. Foti and the AACR on VIRTUAL MEETING to be conducted April 27 and 28, 2020.
This is truly a wonderful job by AACR. In a previous posting I had considered the need for moving international scientific meetings to an online format which would make the information available to a wider audience as well as to those who don’t have the opportunity to travel to a meeting site. At @pharma_BI we will curate and live tweet the talks in order to enhance meeting engagement, as part of the usual eConference Proceedings we do.
Again Great Job by the AACR!
Dear Colleagues,
We hope you are staying safe and well and are adjusting to the challenges of the COVID-19 global pandemic. During this crisis, we remain steadfast in supporting our members and our mission.
I am pleased to announce a number of actions that we are taking to disseminate innovative cancer science and medicine to the global cancer research community:
AACR Virtual Annual Meeting 2020: Selected Presentations. We were excited to receive more than 225 clinical trials for presentation at the Annual Meeting. Due to the time-sensitive nature of these trials—many of which are practice-changing—we are making them available to the community at the time of the original April meeting. Therefore, as per our recent announcement, the AACR will host a slate of selected sessions online featuring these cutting-edge data.
This Virtual Annual Meeting will be held on April 27 and 28, 2020, and will include more than 30 oral presentations in several clinical trial plenary sessions along with commentaries from expert discussants, as well as clinical trial poster sessions consisting of short videos providing the authors’ perspectives. The Virtual Meeting will feature a New Drugs on the Horizon session as well as nine minisymposia that will showcase a broad sample of basic and translational science. Topics will include genomics, tumor microenvironment, novel targets, drug discovery, therapeutics, immunotherapy, biomarkers, and cancer prevention. A special minisymposium titled “Advancing Cancer Research Through an International Cancer Registry” will feature use cases of data available through AACR Project GENIE.
This Virtual Meeting will be available free to everyone, although attendees will be asked to register to participate. The session and presentation titles for the Virtual Meeting, as well as a link to the registration site, will be posted to the AACR website by Monday, April 13.
Release of Abstracts. All of the abstracts scheduled for presentation in the Virtual Meeting—and any other clinical trial abstracts that are scheduled for presentation at the rescheduled meeting—will be posted online on Monday, April 27. All other abstracts that have been accepted for presentation at the rescheduled meeting will be posted online on Friday, May 15.
AACR Annual Meeting 2019: Free Webcast Presentations. The complete webcasts of the AACR Annual Meeting are typically made freely available 15 months after the conclusion of the meeting. However, we have made these webcast presentations available free effective immediately, so that you can review the most compelling science from the Annual Meeting 2019 which was held in Atlanta.
Free Access to AACR Journals. To ensure that all members of the cancer research community have access to the information they need during this challenging time, we have opened access to our nine highly esteemed journals effective today through the end of the virtual meeting. Please be sure to visit the AACR journals webpage for journal highlights, and to sign-up for eTOC alerts.
Rescheduled AACR Annual Meeting. We are planning to reschedule the Annual Meeting for late August while at the same time closely monitoring the developments surrounding COVID-19. An official announcement of the rescheduled meeting will be made in the near future.
We hope that these plans will enable you to continue your important work during this global health crisis. Thank you for all you do to accelerate progress against cancer, and thank you for your loyalty to the AACR.
Sincerely,
Margaret Foti, PhD, MD (hc)
Chief Executive Officer
American Association for Cancer Research
For more information on Virtual Meetings please see
Leading Thoracic Oncologists from the United States and Milan, Italy shared their opinions and views on treating lung cancer patients during this COVID-19 pandemic. Included in the panel is a thoracic oncologist from Milan Italy who gave special insights into the difficulties and the procedures they are using to help control the spread of infection within this high at-risk patient population and changes to current treatment strategy in light of this current virus outbreak. Please see live notes and can follow on Twitter at #LungCancerandCOVID19. Included below is the recording of the Zoom session.
UPDATED 3/29/2020
Leading Lung Cancer Oncologists from around the world are meeting and discussing concerns for lung cancer patients and oncologist during the novel coronavirus (SARS-COV2; COVID19) pandemic. The town hall “COVID-19 and the Impact on Thoracic Oncology” will be held on Zoom on Saturday March 28, 2020 at 10:00 – 11:30 AM EST. sponsored by Axiom Healthcare Strategies . You can register at
Anne Chiang, MD, PhD, Associate Professor; Chief Network Officer and Deputy Chief Medical Officer, Smilow Cancer Network
Roy S. Herbst, MD, PhD, Ensign Professor of Medicine (Medical Oncology) and Professor of Pharmacology; Chief of Medical Oncology, Yale Cancer Center and Smilow Cancer Hospital; Associate Cancer Center Director for Translational Research, Yale Cancer Center
Kurt Schalper, MD, PhD Assistant Professor of Pathology; Director, Translational Immuno-oncology Laboratory
Martin J. Edelman, MD, Chair, Department of Hematology/Oncology, Fox Chase Cancer Center
Corey J. Langer, MD , Professor of Medicine, University of Pennsylvania
Hossain Borghaei, DO, MS , Chief of Thoracic Medical Oncology and Director of Lung Cancer Risk Assessment, Fox Chase Cancer Center
Marina Garassino, MD, Fondazione IRCCS Instituto Nazionale del Tumori
Kristen Ashley Marrone, MD, Thoracic Medical Oncologist. Johns Hopkins Bayview Medical Center
Taofeek Owonikoko, MD, PhD, MSCR, Medical Oncologist, Emory University School of Medicine
Jeffrey D. Bradley, MD, FACR, FASTRO , Emory University School of Medicine
— Hossein Borghaei, DO (@HosseinBorghaei) March 27, 2020
UPDATED 3/29/2020
Below is a collection of live Tweets from this meeting as well as some notes and comments from each of the speakers and panelists. The recording of this Town Hall will be posted on this site when available. The Town Hall was well attended with over 250 participants
Town Hall Notes
The following represent some notes taken at this Town Hall.
Dr. Owonkiko: 1-2% lethality in China; for patients newly diagnosed with lung cancer 1) limit contact between patient, physician and healthcare facility = telemedicine and oral chemo suggested 2) for immunotherapy if i.v. must monitor health carefully
Dr. Kurt Schalper: on COVID19 testing: Three types of tests each having pros and cons.
viral culture: not always practical as you need lots of specimen
ELISA: looking for circulating antibodies but not always specific for type of coronavirus
RT-PCR: most sensitive but right now not much clarity on best primers to use; he noted that there is a 15% variance in test results using different primers to different targeted COVID19 genes
Dr. Marina Garassino: The Lombardi outbreak was 1st in Italy and took them by surprise. She admits they were about one month behind in preparation where they did not have enough masks as late as January 31. It was impractical to socially distance given Italian customs in greeting each other. In addition, they had to determine which facilities would be COVID negative and COVID positive an this required access to testing. Right now they are only testing symptomatic patients and healthcare workers have to test negative multiple times. As concerning therapy with lung cancer patients, they have been delaying as much as possible the initiation of therapy. Patients that are on immunotherapy and immunosuppresive drugs are being monitored by CT scan more often during this pandemic so as instances of pneumotitis began increasing they were unsure if these patients are at increased risk of infection to COVID19 or just a bias in that they are screening more often so their risk to COVID 19 is unclear. Dr. Garissino also felt we need to move from hospital based to community based measures of prevention against COVID infection (social distancing, citizens more vigilant). She noted that usually the cancer patients are more careful with respect to preventative measures than the general populace. Healthcare workers have to test negative twice in three days if they had been in close contact with a COVID postitive patient. However her hospital is still running at 80% capacity so patients are getting treated. However there are ethical issues as to who gets treated, who gets respirators, and other ethical issues related to unfortunate rationing of care.
Dr. Anne Chiang: Scheduled visits have notably decreased. They have seen patients visits decrease from 4500 down to 2300 in two weeks but telemedicine visits or virtual visits have increased to 1000 so are replacing the on site visits. She also said they are trying to reduce or eliminate the extremely immuno-suppressive drugs from chemotherapy regimens. For example they are removing pemetrexemed from standard regimens and also considering neoadjuvant chemotherapy. As far as biopsies, liquid biopsies can be obtained in the home so more preferred as patients do not have to come in for biopsy.
Dr. Edelman: Fox Chase is somewhat unique in being an NCI center which only does oncology so they rely on neighboring Jeanes Hospital of the Temple University Health System for a lot of their outpatient and surgical and general medicine needs. Patients who will be transferred back to Fox Chase are screened for COVID19.
Brenden Stiles: Lung cancer surgeries have ground to a halt. He did only one last week. The hospital wants to conserve resources and considers lung cancer surgery to great a COVID risk. They have shut down elective surgeries and there are no clinical trials being conducted. He said that lung cancer research will be negatively impacted by the pandemic as resources are shuttled to COVID research efforts.
#lungcancerandcovid19@Annechiangmd talks on cutting pemetrexemed for tx regimen and considering more neoadjuvant tx. Also liquid biopsy can be performed in home setting
We currently have a post op lung cancer patient from another cancer center intubated in our #ICU with #COVID19 and a horrible air leak. Also had a patient w/ part solid tumor who I recommended to wait, tell me he is having surgery elsewhere.
Very thoughtful discussion about need for having prognosis and end of life discussions with lung cancer patients prior to going into hospital. Coordination with the long term treatment team, acute care team, and family are critical. #lcsm#COVID19https://t.co/7ni9YIbrsB
4) Surgery not w/o risk. Last week I only did 1 lung cancer case – on a woman w/ clear local progression on interval CT. She was healthy enough to go home pod#1 after lobectomy. However, we subsequently found out she was exposed to #COVID19. Please proceed carefully.
Executive Director Christine Mitchell discusses the importance of institutions talking through the implications of their decisions with the New Yorker.
By Isaac Chotiner
Center Executive Director Christine Mitchell spoke with the New Yorker’s Isaac Chotiner about the decisions that may need to be made on limiting movement and, potentially, rationing supplies and hospital space.
“So, in the debate about allocating resources in a pandemic, we have to work with our colleagues around what kind of space is going to be made available—which means that other people and other services have to be dislocated—what kind of supplies we’re going to have, whether we’re going to reuse them, how we will reallocate staff, whether we can have staff who are not specialists take care of patients because we have way more patients than the number of specialized staff,” says Mitchell.
Note: The following is taken from the Interview in the New Yorker.
As the novel coronavirus, covid-19, spreads across the globe, governments have been taking increasingly severe measures to limit the virus’s infection rate. China, where it originated, has instituted quarantines in areas with a large number of cases, and Italy—which is now facing perhaps the most serious threat outside of China—is entirely under quarantine. In the United States, the National Guard has been deployed to manage a “containment area” in New Rochelle, New York, where one of the country’s largest clusters has emerged. As the number of cases rises, we will soon face decisions on limiting movement and, potentially, rationing supplies and hospital space. These issues will be decided at the highest level by politicians, but they are often influenced by medical ethicists, who advise governments and other institutions about the way to handle medical emergencies.
One of those ethicists, with whom I recently spoke by phone, is Christine Mitchell, the executive director at the Center for Bioethics at Harvard Medical School. Mitchell, who has master’s degrees in nursing and philosophical and religious ethics, has been a clinical ethicist for thirty years. She founded the ethics program at Boston Children’s Hospital, and has served on national and international medical-ethics commissions. During our conversation, which has been edited for length and clarity, we discussed what ethicists tend to focus on during a health crisis, how existing health-care access affects crisis response, and the importance of institutions talking through the ethical implications of their decisions.
What coronavirus-related issue has most occupied your mental space over the past weeks?
The New Yorker’s coronavirus news coverage and analysis are free for all readers.
One of the things I think about but that we don’t often have an opportunity to talk about, when we are mostly focussing on what clinicians are doing and trying to prepare for, is the more general ways this affects our society. People get sick out there in the real world, and then they come to our hospitals, but, when they are sick, a whole bunch of them don’t have health insurance, or are afraid to come to a hospital, or they don’t have coverage for sick time or taking a day off when their child is sick, so they send their child to school. So these all have very significant influences on our ability to manage population health and community transmission that aren’t things that nurses and physicians and people who work in acute-care hospitals and clinics can really affect. They are elements of the way our society is structured and has failed to meet the needs of our general population, and they influence our ability to manage a crisis like this.
Is there anything specifically about a pandemic or something like coronavirus that makes these issues especially acute?
If a person doesn’t have health insurance and doesn’t come to be tested or treated, and if they don’t have sick-time coverage and can’t leave work, so they teach at a school, or they work at a restaurant, or do events that have large numbers of people, these are all ways in which the spread of a virus like this has to be managed—and yet can’t be managed effectively because of our social-welfare policies, not just our health-care resources.
Just to take a step back, and I want to get back to coronavirus stuff, but what got you interested in medical ethics?
What got me interested were the actual kinds of problems that came up when I was taking care of patients, starting as early as when I was in nursing school and was taking care of a patient who, as a teen-ager, had a terminal kind of cancer that his parents didn’t want him to know about, and which the health-care team had decided to defer to the parents. And yet I was spending every day taking care of him, and he was really puzzled about why he was so sick and whether he was going to get better, and so forth. And so of course I was faced with this question of, What do I do if he asks me? Which, of course, he did.
And this question about what you should tell an adolescent and whether the deference should be to his parents’ judgment about what’s best for him, which we would ordinarily respect, and the moral demands of the relationship that you have with a patient, was one of the cases that reminded me that there’s a lot more to being a nurse or a health-care provider than just knowing how to give cancer chemotherapy and change a bed, or change a dressing, or whatever. That a lot of it is in the relationship you have with a patient and the kinds of ethical choices they and their families are facing. They need your information, but also your help as they think things through. That’s the kind of thing that got me interested in it. There are a whole host of those kinds of cases, but they’re more individual cases.
As I began to work in a hospital as an ethicist, I began to worry about the broader organizational issues, like emergency preparedness. Some years ago, here in Boston, I had a joint appointment running the ethics program at Children’s Hospital and doing clinical ethics at Harvard Medical School. We pulled together a group, with the Department of Public Health and the emergency-preparedness clinicians in the Harvard-affiliated hospitals, to look at what the response within the state of Massachusetts should be to big, major disasters or rolling pandemics, and worked on some guidelines together.
When you looked at the response of our government, in a place like Washington State or in New York City, what things, from a medical-ethics perspective, are you noticing that are either good or maybe not so good?
To be candid and, probably, to use language that’s too sharp for publication, I’m appalled. We didn’t get ourselves ready. We’ve had outbreaks—sars in 2003, H1N1 in 2009, Ebola in 2013, Zika in 2016. We’ve known, and the general population in some ways has known. They even have movies like “Contagion” that did a great job of sharing publicly what this is like, although it is fictional, and that we were going to have these kinds of infectious diseases in a global community that we have to be prepared to handle. And we didn’t get ourselves as ready, in most cases, as we should have. There have been all these cuts to the C.D.C. budget, and the person who was the Ebola czar no longer exists in the new Administration.
And it’s not just this Administration. But the thing about this Administration that perhaps worries me the most is a fundamental lack of respect for science and the facts. Managing the crisis from a public-relations perspective and an economic, Dow Jones perspective are important, but they shouldn’t be fudging the facts. And that’s the piece that makes me feel most concerned—and not just as an ethicist. And then, of course, I want to see public education and information that’s forthright and helps people get the treatment that they need. But the disrespect for the public, and not providing honest information, is . . . yeah, that’s pretty disconcerting.
As part of the Harvard Medical School Series on Bioethics: author, clinician and professor Jerome Groopman, MD and Pamel Harzband, MD gave an online discussion of their book “Your Medical Mind”, a part of Harvard Medical School Center for Bioethics Program’s Critical Reading of Contemporary Books in Bioethics Series. The Contemporary Authors in Bioethics series brings together authors and the community to discuss books that explore new and developing topics in the field. This was held as an online Zoom meeting on March 26, 2020 at 5 pm EST and could be followed on Twitter using #HarvardBioethics. A recording of the discussion will be made available at the Harvard Med School Center for Bioethics.
Available at Amazon: From the Amazon book description:
An entirely new way to make the best medical decisions.
Making the right medical decisions is harder than ever. We are overwhelmed by information from all sides—whether our doctors’ recommendations, dissenting experts, confusing statistics, or testimonials on the Internet. Now Doctors Groopman and Hartzband reveal that each of us has a “medical mind,” a highly individual approach to weighing the risks and benefits of treatments. Are you a minimalist or a maximalist, a believer or a doubter, do you look for natural healing or the latest technology? The authors weave vivid narratives of real patients with insights from recent research to demonstrate the power of the medical mind. After reading this groundbreaking book, you will know how to arrive at choices that serve you best.
Doctors Groopman and Hartzband began the discussion with a recapping medical research studies and medical panels, which had reported conflicting results or reversal of recommendations, respectively. These included studies on the benefits of statin therapy in cholesterol management, studies on whether or not Vitamin D therapy is beneficial for postmenopausal women, the ongoing controversy on the frequency with which women should get mammograms, as well as the predictive value of Prostate Specific Antigen and prostate cancer screening. The authors singled out the research reports and medical panels reviewing the data on PSA in which the same medical panel first came out in support of using PSA levels to screen for prostate cancer and then later, after reconvening, recommended that PSA was not useful for mass screenings for prostate cancer.
In fact, both authors were
completed surprised of the diametrically opposed views within or between panels given similar data presented to those medical professionals.
The authors then asked a question: Why would the same medical panel come to a reversal of their decision and more, importantly, why are there such disparate conclusions from the same medical data sets, leading to varied clinical decision-making.
In general, Drs. Groopman and Hartzband asked how do physicians and patients make their decisions?
To answer this they looked at studies that Daniel Bernouli had conducted to model the economic behaviors of risk aversion in the marketplace. Bernouli’s theorem correlated market expectation with probability and outcomes
expectation = probability x utility of outcome
However, in medicine, one can measure probability (or risk) but it is very hard to measure utility (which is the value or worth of the outcome).
For example, they gave an example if a person was born blind but offered a risky to regain sight, the individual values their quality of life from their own perspective and might feel that, as their life is worthwhile as it is, they would not undergo a risky procedure. However a person who had suddenly lost their sight might value sight more, and be willing to undergo a risky procedure.
Three methods are used to put a value on utility or outcome worth with regards to medical decisions
linear scale (life or death; from 0 to 1)
time trade off: e.g. how much longer do I have to live
standard gamble: let’s try it
All of these methods however are flawed because one doesn’t know their future medical condition (e.g. new information on the disease) and people values and perceptions change over time.
An example of choice of methods the medical community uses to make decisions include:
In the United Kingdom, their system uses a time trade off method to determine value in order to determine appropriate course of action which may inadvertently, result in rationed care
in the United States, the medical community uses the time trade off to determine cost effectiveness
Therefore Drs. Groopman and Harztband, after conducing multiple interviews with patients and physicians were able to categorize medical decision making based on groups of mindsets
Maximalist: Proactive behavior, wants to stay ahead of the curve
Minimalist: less intervention is more; more hesitant to try any suggested therapy
Naturalist: more prone to choose natural based therapies or home remedies
Tech Oriented: wants to try the latest therapies and more apt to trust in branded and FDA approved therapeutics
Believer: trust in suggestions by physician; physician trusts medical panels suggestions
Doubter: naturally inquisitive and more prone to investigate risk benefits of any suggested therapy
The authors also identified many Cognitive Traps that both physicians and patients may fall into including:
Relative versus Absolute Numbers: for instance putting emphasis on one number or the other without regard to context; like looking at disease numbers without taking into consideration individual risk
Availability: availability or lack of available information; they noticed if you fall in this trap depends on whether you are a Minimalist or Maximalist
Framing: for example when people talk to others about their conditions and hear stories about others treatments, conditions .. mainly anecdotal evidence
Stories can be helpful but they sometimes increase our overestimation of risk or benefit so framing the information is very important for both the patient as well as the physician (even doctors as patients)
Both authors have noticed a big shift in US to minimalism probably because of the rising costs of healthcare.
How do these mindsets affect the patient-physician relationship?
A University of Michigan study revealed that patients who would be characterized as maximalists pushed their physicians to do more therapy and were more prone to seek outside advice.
Physicians need to understand and listen to their patients during the patients’s first visit and determine what medical mindset that this patient has.
About the authors:
Jerome Groopman, M.D. is the Dina and Raphael Recanati Professor of Medicine at Harvard Medical School, Chief of Experimental Medicine at Beth Israel Deaconess Medical Center, and one of the world’s leading researchers in cancer and AIDS. He is a staff writer for The New Yorker and has written for The New York Times, The Wall Street Journal,The Washington Post and The New Republic. He is author of The Measure of Our Days (1997), Second Opinions (2000), Anatomy of Hope (2004), How Doctors Think (2007), and the recently released, Your Medical Mind.
Dr. Pamela Hartzband is an Assistant Professor at the Harvard Medical School and Attending Physician in the Division of Endocrinology at the Beth Israel Deaconess Medical Center in Boston. She specializes in disorders of the thyroid and pituitary glands. A magna cum laude graduate of Radcliffe College, Harvard University, she received her M.D. from Harvard Medical School. She served her internship and residency in internal medicine at the Massachusetts General Hospital, and her specialty fellowships in endocrinology and metabolism at UCLA.
More articles on BioEthics and Patient experiences in this Online Open Access Journal Include:
NIH – agenda on data: diverse sets of data: Images of MRI, cells, of organs, of communities,
Share images and link it to tables
METADATA 34PB enable search – moving Data to clouds for Large-Scalable Analysis
Sequence Read Archive (SRA) – DNA seq.
COVID-19 from around the World SRA in Cloud Partnerships enabled
Open Science – enhance SW tools for making research cloud-ready
NIH has 12 Centers: Genomics, Neuro-imaging
SCH – Smart & Connected Health
IT, Sensor system hardware, effective usability, medical interpretation, Transformative data Science
Cancer, Alzheimer’s, Genomics, Medical Imaging, Brain circuits,
Coding it Forward: Students come to NIH Virtually from home to join CIVIL DIGITAL FELLOWSHIP
COVID-19: repositories of data for researches:
Treatment for Interventions
Long term Sequelae
Clinical platforms: BigData Catalyst, Allow US, ADSO, National COVID Cohort
Across platforms: workflow after RAS August Deploy: Passport for researchers to access data faster, Privacy-Preserving Tokens, Interoperability across clinical COVID data bases
Metadata super rich to link to other new data sources is a challenging issue to solve across studies
Scott Parker
Sinequa Corp
Director of Product Marketing
Disconnect between R&D & IT
Intelligence search Applications for sensitive information: Sinequa is a leader
shares one index cost for document go down & productivity increases
Rebecca Baker
NIH OD
Dir HEAL Initiative
END ADDICTION Project – NIH HEAL Initiative: 20 NIH collaborating on Studies
National Overdose Deaths overdose opioid drugs – synthetic Fentanyl
Heroin, Cocaine, Methamphetamine
During COVID Overdose increased during the pandemic
Increase in drug use overall and 67% of Fentanyl
Chronic Pain: Daily severe pain: can’t go to work – 25 Million
$500 Million/year Sustained Research Investment 25+ HEAL Research Programs
HEAL Initiative: Pain management, Translating research, New presention, enhance outcomes for affected newborns, novel medications options Pre-clinical translational research in Pain management
Improving treatments for opioid misuse & addiction
Opioid disorder people do not receive treatment: justice community, collaborative, ER, pregnant mothers
Medication-based treatment – do not stay long enough to achieve long-term recovery
People experience Pain differently: Muscular, neurological, : Biomarkers, endpoints, signatures, test non-addictive treatments for specific pains
Pain control balance of risks of long-term opioid therapy
HEAL Research – infant born after exposure to opioids in utero affect brain growth, born with withdrawal syndromes
Diversity of Data under HEAL Initiative –>> Harmonize the data
Common Data Elements in HEAL Clinical Research in Pain Management
CORE CDE & Supplemental CDE
Making HEAL Data FAIR: Findable, Accessible, Interpretable, Reusable
LINK HEAL data with communities studies, predict behaviours
Data sharing made available to the public
HEAL Data Lifecycle
effect of change due to change in dosage used – if dat is not collected – then we are not able to explore the relationships
Use the data to advance research beyond the current understanding of the problem
#NIHhealthInitiative
Ari Berman
BioTeam Inc
Chief Executive Officer
Distributed Questions from the Audience to the speakers
10:00 AM – 11:25 AM EDT on Tuesday, October 6
How to Hold on to Your Knowledge in an Agile World
Etzard Stolte
Roche Pharma
Global Head
October 7, 2020
The Chicagoland COVID-19 Commons: A Regional Data Commons Powering Research to Support Public Health Efforts
Matthew Trunnell
VP & Chief Data Officer
9:00 AM – 9:20 AM EDT on Wednesday, October 7
Seattle & COVID – samples from Seattle Flu Study
Public Health Practice vs Research – Data from Human Subjects: Avoid delute the control
Chicagoland COVID-19 Data Commons – in Chicago
Neighborhood level in Chicago
common data model
power efforts Predictive modeling : Case rate Total confirmed cases, Death cases
Panel Sizes – 500-1000x – the bigger the panel – more computational time more data need be investigated
Hotspot Panels,
Gene Panels,
Exomes
Cell free DNA Testing – Liquid biopsy
Apoptosis
Necrosis
FoundationONE
Patient Results: ALL mutations found, Mutation Burden,
Gene EGFR – no mutation
For every Mutation what Therapy is recommended for approved drugs
Clinical Trials for the mutations
VARIANTS of unknown significance
WORKFLOW: many MDs send sample get 38pps report
Genomic Classification and Prognosis in AML: Mutations subset and therapies available
Paradigm Shift in Classification
2013 – Lung Adenocarcinoma <<<- –
2011 – another cancer
mTOR System: A Database for Systems-Level Biomarker Discovery in Cancer
Iman Tavassoly – CANCELLED
C2i Genomics
Physician Scientist
10:20 AM – 10:40 AM EDT on Wednesday, October 7 Add to Calendar
mTOR system is a database I have designed for exploring biomarkers and systems-level data related to mTOR pathway in cancer. This database consists of different layers of molecular markers and quantitative parameters assigned to them through a current mathematical model. This database is an example of merging systems-level data with mathematical models for precision oncology.
FAIR and the (Tr)end of Data Lakes
Kees Van Bochove
The Hyve
Founder & Owner
10:20 AM – 10:40 AM EDT on Wednesday, October 7
Normalizing Regulatory Data Using Natural Language Processing (NLP)
Qais Hatim, Dr.
FDA CDER
Visiting Assoc
David Milward
Linguamatics
Senior Director, NLP Technology
10:40 AM – 11:00 AM EDT on Wednesday, October 7
ML focus on Disease
NLP – different words have same meanings, different expression same meaning, grammer & Meaning
Normalizes output
Disease
Genes
Dates
Mutations
Transform Unstructured into structured
Identifying Gaps in adverse events Labelling: Pain and Opioids
Improve drug safety
ChemAxon
Supplemental Approval Letters
Coding for Adverse events: “derived values of possible interest”
Use of Prominent Terminologies used at the FDA: UNII – Translation into ANSI tesaurus standard
Matching to the Variation found within Real Text: synonyms
Using ML for Normalization in Disease Context
Deep Learning PRE-TRAINING APPROACH for annotated date = supervised learning
A set of rules to handle overlapping entities
normalized the amp extracted from concepts
BERN and Terminologies: BioBERN, PubMed Central, PubMed Articles
NER – Named Entity Recognition
Evaluation of the Approach
Conclusions
NLP, ML, Hybrid methods, Terminology +ML methods
Building an Artificial Intelligence-Based Vaccine Discovery System: Applications in Infectious Diseases & Personalized Neoantigen-Related Immunotherapy for Treatment of Cancers
Kamal Rawal
Amity Univ
Assoc Prof
10:40 AM – 11:00 AM EDT on Wednesday, October 7
Classification of proteins
Data Collection
Feature Selection – Most important from 1447 features
Deep learning Model: Vaxi-DL: Layers, compilation
Overfitting Model strategy
Balancing Imbalanced
Hyper parameter tuning: Internal parameter of the model
Stratified K-Fold Training and Validation
Ensembling Approach: many weak classifier to create a STRONG Classifier
ROC Curve: Ensemble by Consensus
Before and after calibration
Benchmarking the system: Vaxi-DL Ensemble by Average vs by Consensus
Cohen Veterans Bioscience – not for profit – advancing Brain health
Biotyping and stratification
Biomarkers
Omics data
All meet in the Common – Brain Commons: Clinician, Geneticist, Scientist, Bioinformatician, R Studio, Python, Jupyterhub
Multidimensional Biomarkers in Multiple Sclerosis
Pietro Michelucci
Human Computation Institute
Director
Why machine can’t tackle AI on their own and AI can’t do Precision Medicine on their own
young people more than others N of 1 – Precision Mediicne
Scandinavians and Russians are immune
AI & Precision Medicine: can’t solve the complexity of messy data vs big data
Messy data: heterogeneous multidimensional, to many combinations to explore, select which combination to explore vs let the machine generate all the combination and do analysis on all and discover PATTERN
Causal vs spurious
Logical reasoning, right brain abstract and short cuts – Human brain does routinely
Human do better on context: Not all info is in pixels such as context
#ADS – SBIR suspected the hypothesis to be tested
improving crowd wisdom methods: 20 input by different people PLUS machine
combine crowd answers with machine faster and improved accuracy
Machine has no intuition – machine bias of Human and of machine is similar
Wisdom of Crowd: Bootstrapping hybrid Intelligence: CIVIUM
Advanced Imaging and AI Technologies Providing New Image and Data Analysis Challenges and Opportunities
Richard Goodwin
AstraZeneca
Dir & Head of Imaging & AI
2:30 PM – 2:50 PM EDT on Wednesday, October 7
AstraZeneca is empowering its scientists to see the complexity of a disease in unprecedented detail to enable effective development and selection of new medicines. This is enabled though the use of an extensive range of cutting-edge imaging technologies that support studies into the efficacy and safety of drugs through the R&D pipeline. This presentation will introduce the range of novel in vivo and ex vivo imaging technologies employed, describe the data challenges associated with scaling up the use of molecular imaging technologies, and address the new data integration and mining challenges. Novel computational methods are required for large cohort imaging studies that involve tissue based multi-omics analysis, which integrate spatial relationships in unprecedented detail.
Small molecule – not suitable for complex diseases
focus on quality vs quantity
compound for commercial value
right safety
Imaging supports R&D: Molecular, medical, big data and AI
convergence of ML for decision making
Spatial imaging: morphology
Multiplex imaging like MRI
Multimodal analysis: tissue data and invivo holistic understanding of drug delivery
spacial transcriptomics proteomics: imaging platforms in R&D
AZ invest in imaging technologies already impacting projects: AI-empowered imaging delivering subcellular resolution
Mass Spec Imaging (MSI) – ex-vivo imaging techniques- spatial distribution of molecular
cartography of cancer: Drug metabolite distribution – NEW understanding of disease and drug distribution in tissue
Digital pathology and beyond – AI Image Analysis – AI outperform pathololigst and radiologists
Data volume and dimensionality challenge and opportunity
Data volume and dimensionality: complete image
AZ Oncology – disease is understood for drug discovery using Imaging technology
PANEL: Framework and Approach to Unlock the Potential of Quantum Computing in Drug Discovery
Brian Martin
AbbVie Inc
Research Fellow & Head
Philipp Harbach
Merck KGaA
Head of In Silico Research in Germany
chemistry and manufacturing with QC – end user in Pharmaceutical
VC at Merck ask expert in Merck to guide investment of Merck in QC
50 people across Merck [three areas at Merck [Pharmaceutics, Animal Health, Diagnostics]
Celia Merzbacher
SRI Intl
Assoc Dir Quantum Economic Dev Consortium (QEDC)
Methodology from Pistoia to be used in QC
QC R&D developed in parallel
Simulation of all the components is possible
John Wise
Pistoia Alliance Inc (2007)
We are a global, not-for-profit members’ organization working to lower barriers to innovation in life science and healthcare R&D through pre-competitive collaboration.
Consultant
How Pharmaceutical Industry can benefit from quantum computing
9 of 10 big Pharma are members of the Pistoia Alliance
IP created on specifications
Zahid Tharia
Pistoia Alliance Inc
Consultant
Barriers to adoption of quantum computing (QC) in Pharma is training of staff and skills in the IT aspects of QC
3:10 PM – 4:00 PM EDT on Wednesday, October 7
In 2019, major life sciences companies mobilized to form a pre-competitive, collaborative quantum computing working group (QuPharm) and delineate a framework and approach to accelerate realizing the potential of quantum acceleration in drug discovery. Learn from industry thought leaders on how to valuate and map problems into quantum algorithms, set up organizations to enable and scale quantum computing pilots and establish effective cross-industry, tech, and start-up collaborations.
in UK 6 Labs for the entire countries: all send the data to Wellcome Sanger Institute for analysis
Metadata is the problem – coordination of each of the 6 labs to send the metadata created problems
Cindy Crowninshield
Cambridge Healthtech Institute
Executive Event Director
Vivien Bonazzi
Deloitte Consulting LLP
Managing Dir & Chief Biomedical Data Scientist
How organizations use bioscience data
Data Ecosystem: Hardware and software: Cloud and other options
Operationalize the two trends:
Platforms: End to end solutions resulting in SILOS, systems are native: data ingestions
Data Commons: Open arch, open source – integration and interdependence issues
Biomedical Agencies in NIH various Organizations in the Private sector: Sharing data must be more effective
IT, Data Science, Management – COVID – reduced barriers
Leadership: Different voices from different people
Data strategies & Governance not the whole but small pieces , incentives to share data
Chris Dagdigian
BioTeam Inc
Sr Dir
10th Anniversary to Trends from the Trenches
IT infrastructure changes
Research IT:
Genomics & BioInformatics
Image-based data acquisition and analysis: CryoEM, 3D microscopy, fMRI image analysis
ML and AI – GPU FPGAs, neural processors: Drive in organizations: bottom up
Chemistry & Molecular Dynamics
Storage and exploitation of data for insights
2020 Hype vs Reality
Scientific Data: managing and understanding, data movement, federated/access
Big Data: data storage, management & governance standards vs human curated data
IT needs guidance and decisions from Science Team
Culture change for joint management by Science & IT: data fidelity, attribution, allocation top down
NERSC File System quotas & Purging overviewSilos & So
Petabytes of open access data, collaborative research resources: Data rich environments
Data Lakes: Gen3 Data Commons
Data hygiene:metadata is Science side vs IT
Biased Data: Model & Data Bias
Failed Predictions:
Compilers matter again – not True
CPU benchmarking is back – WRONG
AMD vs Inter arm64 vs both
Policy driven auto-tiering storage – wrong, USER self-service for tiering, movement and archive decision. Let researchers tier/move/archive based on Project, Experiment or Group
Single storage namespace – Wrong: Data intensive science: scientists must do some IT jobs themselves
Kjiersten Fagnan
Lawrence Berkeley Natl Lab
CIO
Genome Project of DOE
Data management with other agencies
COVID: Collaborations, breaking down barriers, small labs and big labs ALL generate data and sharing
that collaboration is needed regardless of COVID – not happen
If twoo big one lab can’t handle it all
Funding and training does not support the Collaborations because next round of funding depend on individual publications – which requires silos
Data cleaning and data management:Standards are annoying and painful – not needed for publishing the results as soon as possible – just that someone else will be able to use it
Facebook have hundred of curators – the curation of scientific data requires same hunsrands od curators that are SCIENTISTS and Data scientists
Matthew Trunnell
Pandemic Response Commons, Seattle
VP & Chief Data Officer
Data commons for intra- and inter-mural data sharing
ML is needed for Data commons
Progress in FAIRness, NIH efforts driven by Susan Gregory across NIH all centers
Large amount of B-to-B Data sharing UBER sharing with a jurisdiction they operate
SNOWFLAKES – new cloud technology
COVID – plays an accelerator
Cancer vs COVID – transfer knowledge from COVID to Cancer
9:00 AM – 10:40 AM EDT on Thursday, October 8
The “Trends from the Trenches” will celebrate its 10th Anniversary at Bio-IT! Since 2010, the “Trends from the Trenches” presentation, given by Chris Dagdigian, has been one of the most popular annual traditions on the Bio-IT Program. The intent of the talk is to deliver a candid (and occasionally blunt) assessment of the best, the worthwhile, and the most overhyped information technologies (IT) for life sciences. The presentation has helped scientists, leadership, and IT professionals understand the basic topics related to computing, storage, data transfer, networks, and cloud that are involved in supporting data-intensive science. In 2020, Chris will give the “Trends from the Trenches” presentation in its original “state-of-the-state address” followed by guest speakers giving podium talks on relevant topics. An interactive Q&A moderated discussion with the audience follows. Come prepared with your questions and commentary for this informative and lively session.
Project vs enterprise – Sequencing for internal research vs for clients’ data
Tension in governmental agencies – no robust solutions: IT, Science, Management
different Use cases need different infrastructure: HW & SW: Storage and data exploration
Data Lakes: rule base, enterprising – training is an issue in organizations
Management, Scientists, IT in enterprises – terra byte of storage, budgets issues, conversation on the limits that IT can ofer putting more burden on the Scientists for triage and quotas – business and scientific value
New capabilities in organizations: hands on in data management tactical of data management not IT bur data engineering
Citizen Science: privacy vs plants and microbes – no privacy issues
Incentives need be changed for Data Citations in addition to Papers
Curation Citations as Authorship citation
Data sharing in Cancer: GEN3 – NCI Data Commons, Data Governance and Data Permission (Access) – NCI does work in data commons – much data outside this space
EBI – in UK Sanger Institute has the infrastructure in one place
Migrating Project based Data structure: that involves scientist decisions that should not be a quota (storage is full) in the IT space
Human to Human communications vs tools for data migration
Which Organizations get the data curation and annotation well: Subject matter from day 1 – hard to teach vs data engineering skills; TEAM as a solving is critical in Biomedical space no incentives
BBC – Meta tagging system is outstanding
NCAST TRANSLATOR – across organizations
Changing incentives – MORE organizations will do that task better
Common metadata across domains with predict uses of data in the Future – collaboration of CS to create in the science organization tagging like in BBC
NCI – Cancer Data Commons – concierge services to organization on data services
Ravi Madduri – CVD large cohort
Univ of Chicago
Scientist
Lara Mangravite
Sage Bionetworks
President
Kees Van Bochove
The Hyve
Founder & Owner
11:10 AM – 11:30 AM EDT on Thursday, October 8
BREAKOUT: Driving Scientific Discovery with Data / Digitization
Timothy Gardner
Riffyn Inc
CEO
11:35 AM – 12:00 PM EDT on Thursday, October 8
PLENARY KEYNOTE – 12:00 PM – 1:25 PM EDT on Thursday, October 8
Robert Green
Brigham & Womens Hospital
Co-founder of Genome Medicine
Prof & Dir G2P Research
Combining data to rapidly analyze COVID-19 Patients –
identify BIOMARKERS for vulnerability
Preventive Genomics – Angelina Jolly’s musectomy as a preventive clinical condition
Patients access to own genomics data
Population screening – to predict risks
Genetic Testing to Consumer: Preventive Genomics: conflated genotyping/sequencing and labs/care providers
Genetic Testing to Consumer: COST & Benefits – UNCLEAR
diagnosis of unsuspected genetic disease
stratification for surveillance
which pieces of the puzzle need to be brought to bear in patient care
Categories and Reporting criteria: Gene-Disease validity vs Variant Pathogenicity –>> Clinic
MedSeq Project: 10MM randomized study – all genome info shared with Patient, other arm only selective genome data shared with patient: 100 patients 20% carrymonogenic condition: Polygenic risk scores:
CAD – high Cholesterol biomarker, A-FIb, DM2, 52% Women 48% Men
No high risk error by PCP discussing and disclosing the results of the sequence
Filtering the results: Indication -based testing vs Screening
BabySeq Project: INFANTS sequencing to prevent disease: 11% carry a mutation in a monogenic gene for a monogenic condition -like abnormal narrowed aorta
MDR – Monogenic Disease Risk
MilSeq Project: US Air Force – Military active duty
5,8,10 – are all Polygenic studies
Polygenic Risk Scores – High risk
Classification need to be repeated every few years (2 years – re-sequence) due to changes in health and to efficiencies in new discovery in curated data which is improving as on-going
Vaccine preventable diseases – produce 1Billion vaccines a year
reduction of incidence: Pertusis – 92% eradication
manage risk profile
Science mechanism translatable to machines
high automated ingestible data for AI
Digital is about people: Good data Good algorithms Good GUI
Vivien Bonazzi
Deloitte Consulting LLP
Managing Dir & Chief Biomedical Data Scientist
12:00 PM – 1:25 PM EDT on Thursday, October 8 Add to Calendar
12:00 Organizer’s Remarks
Cindy Crowninshield, RDN, LDN, Executive Event Director, Cambridge Healthtech Institute
12:05 Keynote Introduction
Juergen A. Klenk, PhD, Principal, Deloitte Consulting LLP
12:15 Toward Preventive Genomics: Lessons from MedSeq and BabySeq
Robert Green, MD, MPH, Professor of Medicine (Genetics) and Director, G2P Research Program/Preventive Genomics Clinic, Brigham & Women’s Hospital, Broad Institute, and Harvard Medical School
12:40 AI in Pharma: Where We Are Today and How We Will Succeed in the Future
Natalija Jovanovic, PhD, Chief Digital Officer, Sanofi Pasteur
1:05 LIVE Q&A: Session Wrap-Up Panel Discussion
PANEL MODERATORS:
Juergen A. Klenk, PhD, Principal, Deloitte Consulting LLP
Vivien R. Bonazzi, PhD, Managing Director & Chief Biomedical Data Scientist, Deloitte Consulting LLP
Rachana Ananthakrishnan, Executive Director, Globus, University of Chicago
Michael A. Cianfrocco, PhD, Assistant Professor, Department of Biological Chemistry and Research Assistant Professor, Life Sciences Institute, University of Michigan
Brigitte E. Raumann, Product Manager, Globus, University of Chicago
3. Connect with peers from across the industry during these dedicated networking times.
Looking to meet fellow attendees and have meaningful conversations – just as you would at an in- person event? This is the perfect way to achieve just that. Get to know your fellow attendees by joining this interactive speed networking event. To participate, each attendee will be paired at random with another fellow attendee and given a chance to interact for 7 minutes in a private zoom room. Once the 7 minutes are up, you will move on to meet with another selected attendee. Maximize your networking at the meeting and join in.
Take a minute to revitalize and join our friends from VOS Fitness for a stretch break. The professional trainer from VOS will bring you through some easy moves that will help with screen fatigue and ease your muscles after a long day of sitting at the computer. All moves can be done right at your desk and is appropriate for all fitness levels.
Earn points by completing the activities listed on our Game tab. Some activities will only award points once, but others will award you every time you do it – so the more involved you are in the virtual event, the more points you will earn! You can start earning points one week before the event – so get ready to start sending meeting invitations, exploring our virtual expo and planning your schedule.
Attendees in the top 5% of points earned when the game closes at the end of the conference will be eligible to win a gift card worth $200 USD!
5. Take part in 1-on-1 networking with an easy-to-navigate profile search and scheduling platform.
Check out your recommended connections flagged as “Want to Meet” in the People Tab. These connections were chosen based on your similar roles, companies and conference program interests.
Take a moment to add relevant interest tags to your profile. Then search and connect with participants who have the same interests.
Engage with technology leaders in their booths and view relevant videos and demos.
Take part in live Q&A with speakers and participants following each educational session.
Create and join in ad hoc group discussions throughout the event.
In the spirit of open collaboration, the world’s premier bio-IT conference will bring together the community to focus on how we are using technologies and analytic approaches to solve problems, accelerate science, and drive the future of precision medicine. With a focus on AI, data science and other “data-driven” technologies that are advancing biomedical research, drug discovery and healthcare, the Bio-IT World Conference & Expo ’20 will bring together more than 3,000 participants to the Seaport World Trade Center in Boston from October 6-8, 2020.
The participants will have the chance to meet and share research/ideas with leading life sciences, pharmaceutical, clinical, healthcare, informatics and technology experts.
TRACK 3 Data Science and Analytics Technologies VIEW
TRACK 4 Software Applications and Services VIEW
TRACK 5 Data Security and Compliance VIEW
TRACK 6 Cloud Computing VIEW
TRACK 7 AI for Drug Discovery VIEW
TRACK 8 Emerging AI Technologies VIEW
TRACK 9 AI: Business Value Outcomes VIEW
TRACK 10 Data Visualization Tools VIEW
TRACK 11 Bioinformatics VIEW
TRACK 12 Pharmaceutical R&D Informatics VIEW
TRACK 13 Genome Informatics VIEW
TRACK 14 Clinical Research and Translational Informatics VIEW
TRACK 15 Cancer Informatics VIEW
TRACK 16 Open Access and Collaborations
2020 Plenary Keynote Speakers
Rebecca Baker, PhD
Director, HEAL (Helping to End Addiction Long-term) Initiative, Office of the Director, National Institutes of Health
Vivien Bonazzi, PhD
Chief Biomedical Data Scientist, Managing Director, Deloitte
Tim Cutts, PhD
Head, Scientific Computing, Wellcome Trust Sanger Institute
Chris Dagdigian
Co-Founder and Senior Director, Infrastructure, BioTeam, Inc
Kevin Davies, PhD
Executive Editor, The CRISPR Journal, Mary Ann Liebert, Inc.
Kjiersten Fagnan, PhD
Chief Informatics Officer, Data Science and Informatics Leader, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Robert Green, MD, MPH
Professor of Medicine (Genetics) and Director, G2P Research Program/Preventive Genomics Clinic, Brigham & Women’s Hospital, Broad Institute, and Harvard Medical School
Susan K. Gregurick, PhD
Associate Director, Data Science (ADDS) and Director, Office of Data Science Strategy (ODSS), National Institutes of Health
Natalija Jovanovic, PhD
Chief Digital Officer, Sanofi Pasteur
Pietro Michelucci, PhD
Director, Human Computation Institute
Matthew Trunnell
Vice President and Chief Data Officer, Fred Hutchinson Cancer Research Center
Glycobiology vs Proteomics: Glycobiologists Prespective in the effort to explain the origin, etiology and potential therapeutics for the Coronavirus Pandemic (COVID-19)
Curator: Ofer Markman, PhD
The sugars involved in a viral disease are unique in many ways when compared with the DNA/RNA or the proteins involved: they are almost totally dependent on the infected cells and thus are not affected by the viral mutation rate or by the virus at all. Nevertheless they are affected by the cells, their type and their sugar production mechanisms and in some respect to the production rate by which the virus is replicated in the infected cells. Mutations may have nevertheless major effect not on the structures of the glycans but rather on the existence of the glycosylation site, and thus the glycan at all, but not on its structures.
This may make the gycomolecule a good target for diagnostics as stability in the molecule may mean longer life shelve of diagnostics kits.
Unique sugars are already predicted/found in the virus from certain Chinese origin, in this case an o-linked glycan/s not previously detected.
Nevertheless, if the virus can infect multiple cells once current cells are not going to be available for any reason those viruses may present other glycans.
Once one starts to treat the infected person via modulation of protein production or by other means the change in the dynamic of protein production vs. protein glycosylation may cause changes in protein glycosyation, including their structures, this is well known to biotechnologists producing glycoproteins in labs and production.
This may either be a problem in understanding the state of disease or an advantage as it may help following response to the treatment and help as a co-treatment diagnostics.
Early Studies include the following:
Carbohydrate-based Diagnostics: A New Approach to COVID-19 Testing?
Glycans may play a role in treatment as well. TAMIFLU a case in point. Tamiflu is directed to the flu enzyme Neuraminidaze that is part of the viral structures. This approach was also explored to develop treatments.
Pneumagen Ltd Leverages its Novel Glycan Approach to Target Coronavirus (COVID-19) Infections
Glycans do not only effect their own involvement in treatment/diagnostics they also are effecting protein based diagnostics for this see statement by Dr. Michael Mercier of UAH
We’re dealing with COVID-19, but what’s a virus in the first place?
The coronavirus pandemic has affected almost every country in every continent however, after months of the novel advent of novel COVID-19 cases, it has become apparent that the varied clinical responses in this epidemic (and outcomes) have laid bare some of the strong and weak aspects in, both our worldwide capabilities to respond to infectious outbreaks in a global coordinated response and in individual countries’ response to their localized epidemics.
Some nations, like Israel, have initiated a coordinated government-private-health system wide action plan and have shown success in limiting both new cases and COVID-19 related deaths. After the initial Wuhan China outbreak, China closed borders and the government initiated health related procedures including the building of new hospitals. As of writing today, Wuhan has experienced no new cases of COVID-19 for two straight days.
However, the response in the US has been perplexing and has highlighted some glaring problems that have been augmented in this crisis, in the view of this writer. In my view, which has been formulated after social discussion with members in the field ,these issues can be centered on three major areas of deficiencies in the United States that have hindered a rapid and successful response to this current crisis and potential future crises of this nature.
The mistrust or misunderstanding of science in the United States
Lack of communication and connection between patients and those involved in the healthcare industry
Socio-geographical inequalities within the US healthcare system
1. The mistrust or misunderstanding of science in the United States
For the past decade, anyone involved in science, whether directly as active bench scientists, regulatory scientists, scientists involved in science and health policy, or environmental scientists can attest to the constant pressure to not only defend their profession but also to defend the entire scientific process and community from an onslaught of misinformation, mistrust and anxiety toward the field of science. This can be seen in many of the editorials in scientific publications including the journal Science and Scientific American (as shown below)
Boston rally coincides with annual American Association for the Advancement of Science (AAAS) conference and is a precursor to the March for Science in Washington, D.C.
Responding to the troubling suppression of science under the Trump administration, thousands of scientists, allies, and frontline communities are holding a rally in Boston’s Copley Square on Sunday.
“Science serves the common good,” reads the call to action. “It protects the health of our communities, the safety of our families, the education of our children, the foundation of our economy and jobs, and the future we all want to live in and preserve for coming generations.”
It continues:
But it’s under attack—both science itself, and the unalienable rights that scientists help uphold and protect.
From the muzzling of scientists and government agencies, to the immigration ban, the deletion of scientific data, and the de-funding of public science, the erosion of our institutions of science is a dangerous direction for our country. Real people and communities bear the brunt of these actions.
The rally was planned to coincide with the annual American Association for the Advancement of Science (AAAS) conference, which draws thousands of science professionals, and is a precursor to the March for Science in Washington, D.C. and in cities around the world on April 22.
However, some feel that scientists are being too sensitive and that science policy and science-based decision making may not be under that much of a threat in this country. Yet even as some people think that there is no actual war on science and on scientists they realize that the public is not engaged in science and may not be sympathetic to the scientific process or trust scientists’ opinions.
Certainly, opponents of genetically modified crops, vaccinations that are required for children and climate science have become louder and more organized in recent times. But opponents typically live in separate camps and protest single issues, not science as a whole, said science historian and philosopher Roberta Millstein of the University of California, Davis. She spoke at a standing-room only panel session at the American Association for the Advancement of Science’s annual meeting, held in Washington, D.C. All the speakers advocated for a scientifically informed citizenry and public policy, and most discouraged broadly applied battle-themed rhetoric.
In general, it appears to be a major misunderstanding by the public of the scientific process, and principles of scientific discovery, which may be the fault of miscommunication by scientists or agendas which have the goals of subverting or misdirecting public policy decisions from scientific discourse and investigation.
This can lead to an information vacuum, which, in this age of rapid social media communication,
can quickly perpetuate misinformation.
This perpetuation of misinformation was very evident in a Twitter feed discussion with Dr. Eric Topol, M.D. (cardiologist and Founder and Director of the Scripps Research Translational Institute) on the US President’s tweet on the use of the antimalarial drug hydroxychloroquine based on President Trump referencing a single study in the International Journal of Antimicrobial Agents. The Twitter thread became a sort of “scientific journal club” with input from international scientists discussing and critiquing the results in the paper.
Please note that when we scientists CRITIQUE a paper it does not mean CRITICIZE it. A critique is merely an in depth analysis of the results and conclusions with an open discussion on the paper. This is part of the normal peer review process.
Below is the original Tweet by Dr. Eric Topol as well as the ensuing tweet thread
I reviewed the cited paperhttps://t.co/E4Iw7GpVh6 an open-label, non=randomized study The endpoint was viral PCR (mostly + or -, many ND) by nasopharyngeal swab. 6 of the 36 people were asymptomatic. 6 with pneumonia (LRTI) 6 people received "H + A" pic.twitter.com/KBjR1QcZRV
Eric – a huge issue here is they only report data on 20 of the 26 patients, and of the 6 – all deteriorated! Six hydroxychloroquine-treated patients were lost in follow-up: they worsened and weee sent to the ICU! They need to do last observation carried forward for those.
— Christopher Cannon, M.D. 🇺🇦 (@cpcannon) March 21, 2020
OMG, do you realize none of the patients in the treatment arm were definitive positives to start with? They were all in the "gray zone". JFC, this study was worse than I thought when I skimmed it the first time!
Within the tweet thread it was discussed some of the limitations or study design flaws of the referenced paper leading the scientists in this impromptu discussion that the study could not reasonably conclude that hydroxychloroquine was not a reliable therapeutic for this coronavirus strain.
The lesson:The public has to realizeCRITIQUE does not mean CRITICISM.
Scientific discourse has to occur to allow for the proper critique of results. When this is allowed science becomes better, more robust, and we protect ourselves from maybe heading down an incorrect path, which may have major impacts on a clinical outcome, in this case.
2. Lack of communication and connection between patients and those involved in the healthcare industry
In normal times, it is imperative for the patient-physician relationship to be intact in order for the physician to be able to communicate proper information to their patient during and after therapy/care. In these critical times, this relationship and good communication skills becomes even more important.
Recently, I have had multiple communications, either through Twitter, Facebook, and other social media outlets with cancer patients, cancer advocacy groups, and cancer survivorship forums concerning their risks of getting infected with the coronavirus and how they should handle various aspects of their therapy, whether they were currently undergoing therapy or just about to start chemotherapy. This made me realize that there were a huge subset of patients who were not receiving all the information and support they needed; namely patients who are immunocompromised.
These are patients represent
cancer patient undergoing/or about to start chemotherapy
Patients taking immunosuppressive drugs: organ transplant recipients, patients with autoimmune diseases, multiple sclerosis patients
Patients with immunodeficiency disorders
These concerns prompted me to write a posting curating the guidance from National Cancer Institute (NCI) designated cancer centers to cancer patients concerning their risk to COVID19 (which can be found here).
Surprisingly, there were only 14 of the 51 US NCI Cancer Centers which had posted guidance (either there own or from organizations like NCI or the National Cancer Coalition Network (NCCN). Most of the guidance to patients had stemmed from a paper written by Dr. Markham of the Fred Hutchinson Cancer Center in Seattle Washington, the first major US city which was impacted by COVID19.
Also I was surprised at the reactions to this posting, with patients and oncologists enthusiastic to discuss concerns around the coronavirus problem. This led to having additional contact with patients and oncologists who, as I was surprised, are not having these conversations with each other or are totally confused on courses of action during this pandemic. There was a true need for each party, both patients/caregivers and physicians/oncologists to be able to communicate with each other and disseminate good information.
Last night there was a Tweet conversation on Twitter #OTChat sponsored by @OncologyTimes. A few tweets are included below
The Lesson: Rapid Communication of Vital Information in times of stress is crucial in maintaining a good patient/physician relationship and preventing Misinformation.
3. Socio-geographical Inequalities in the US Healthcare System
It has become very clear that the US healthcare system is fractioned and multiple inequalities (based on race, sex, geography, socio-economic status, age) exist across the whole healthcare system. These inequalities are exacerbated in times of stress, especially when access to care is limited.
Some of the passengers had to be extricated from the wrecked cars. Many of the passengers and local residents helped first responders during the rescue operation. Five local hospitals treated the injured. The derailment disrupted train service for several days.
What was not reported was the difficulties that first responders, namely paramedics had in finding an emergency room capable of taking on the massive load of patients. In the years prior to this accident, several hospitals, due to monetary reasons, had to close their emergency rooms or reduce them in size. In addition only two in Philadelphia were capable of accepting gun shot victims (Temple University Hospital was the closest to the derailment but one of the emergency rooms which would accept gun shot victims. This was important as Temple University ER, being in North Philadelphia, is usually very busy on any given night. The stress to the local health system revealed how one disaster could easily overburden many hospitals.
Over the past decade many hospitals, especially rural hospitals, have been shuttered or consolidated into bigger health systems. The graphic below shows this
Note the huge swath of hospital closures in the midwest, especially in rural areas. This has become an ongoing problem as the health care system deals with rising costs.
Lesson:Epidemic Stresses an already stressed out US healthcare system
How is the 3D Printing Community Responding to COVID-19?
Reporter: Irina Robu, PhD
As the new pandemic COVID-19 takes over the globe, several countries are implementing travel restrictions, social distancing and work from home policies. Healthcare systems are overloaded and fatigued by this new coronavirus (COVID-19). Since COVID-19 is a respiratory illness, patients require specialist respirators to take over the role of the lungs. These respirators are in short supply, however, along with medical personnel, hospital space and other personal safety equipment required to treat patients.
Professional AM providers, makers and designers in the 3D printing community have started to answer to the global crisis by volunteering their respective skills to ease the pressure on supply chains and governments. The additive manufacturing and 3D printing community has numerous members keen to support during the COVID-19 pandemic.
A hospital in Brescia, Italy with 250 Coronavirus patients lacking breathing machines has recently run out of the respiratory valves needed to connect the patients to the machines. In response to the situation, the CEO of Isinnova, Cristian Fracassi used 3D bioprinting to produce 100 respirator valves in 24 hours, which are currently being put to use in the Brescian hospital.
At the same time, Materialise, has released files for a 3D printed hands-free door handle attachment to lessen Coronavirus transmission via one of the most common mediums. Door handles are exposed to a lot of physical contact over the course of a day, especially in public spaces such as offices and hospitals. The 3D printable add-on allows users to carry out the lever action required to pop open most modern doors using their elbows.
Protolabs, a leading on-demand manufacturer with 3D Printing is using rapid production methods to good use during the current Coronavirus outbreak by producing components for #COVID19 test kits and ventilators. California-based Airwolf3D volunteered their own fleet of 3D printers for the manufacturing of respirator valves and custom medical components. The company is also offering remote technical support for medical staff that would like to know more about 3D printing.
Volkswagen has started a task force that will adapt its car-making capacity and manufacturing facilities to the production of hospital ventilators and medical devices. Using their own 125 industrial 3D printers to tackle the COVID-19 pandemic. At the same time, Volkswagen is donating face masks to healthcare providers and local authorities as part of an agreement made with German Health Minister.
Stratasys has organized its global 3D printing resources to respond to the COVID-19 pandemic by printing full-face shields to provide protection to healthcare workers. The company showed that the strength of 3D bioprinting can be adapted on the fly to address shortages of parts related to shields, masks, and ventilators, among other things.
Doctors, hospital technicians and 3D-printing specialists are also using Google Docs, WhatsApp groups and online databases to trade tips for building, fixing and modifying machines like ventilators to help treat the rising number of patients with COVID-19, the disease caused by the coronavirus.
The efforts come as supply shortages loom in one of the biggest challenges for health care systems around the world.
Researchers and epidemiologists’ race to develop vaccines to block the new Covid-19 pathogen that currently emerged. It’s a rush against the clock, and sometimes the good guys lose: It simply takes too long to identify an effective antigen and produce enough of it to make a dent.
Even as companies rush to advance and test vaccines against the new coronavirus, the Bill and Melinda Gates Foundation and the National Institutes of Health are gambling that scientists can do even better than what’s now in the pipeline. The traditional vaccine-development development is decades old. It involves shipping a sample of the purified virus to a vaccine-development laboratory, developing a nonpathogenic variant of the virus, propagating that new variant in eggs or cultured cells and harvesting them to produce the vaccine.
To develop a coronavirus vaccine, synthetic biologists are currently racing against the clock. It is quite possible that the new Covid-19 virus will become a permanent part of the world’s microbial menagerie rather than being eradicated like the earlier SARS coronavirus, next-gen approaches will be needed to address inadequacies of even the most cutting-edge vaccines: They take years to develop and manufacture, they become obsolete if the virus evolves, and the immune response they produce is often weak.
Neil King, a researcher from University of Washington has been hunting for a coronavirus vaccine since 2017, because he knew that would be another coronavirus epidemic similar to SARS and MERS. His group designed and built nanoparticles out of proteins and attach viral molecules in a repetitive array with the intention of, when the whole thing is packed into a vaccine, it can make people resistant to the new coronavirus. Using computers, they are designing new, self-assembling protein nanoparticles scattered with antigens. If tests in lab animals of the first such nanoparticle vaccine are any indication, it should be more potent than either old-fashioned viral vaccines like those for influenza or the viral antigens on their own (without the nanoparticle).
King and his colleagues (Cell, 2019) developed an experimental vaccine against respiratory syncytial virus (RSV) made of a computer-designed nanoparticle that self-assembles from protein building blocks and is scattered with an engineered version of RSV’s key antigen. When tested in mice and monkeys, it produced 10 times more antibodies than an experimental RSV vaccine based on traditional technology. They believe that with a few tweaks, the nanoparticle can be scattered with molecules from additional coronaviruses such as the original SARS virus, MERS, and a mutated form of the Covid-19-causing virus. As Covid-19 spreads, King and his colleagues are carefully optimistic that it might work.
But even though, Moderna Terapeutics, CureVac and Inovio pharmaceuticals are speeding toward human testing via experimental vaccines that contain synthetic strands of RNA or DNA, the synthetic biology approach has its own advantages. These experimental vaccines contain synthetic strands of RNA or DNA that code for protein molecules on the virus’s surface. Once the vaccine delivers the genetic material into cells, the cells follow the genetic instructions to churn out the viral protein. The knowledge is that the body would perceive that as foreign, generate antibodies to it, and if all goes well thus acquire immunity to the virus.
Researchers already know how to do vaccine development the old-fashioned way, and their manufacturing facilities are set up accordingly. The regulatory approvals required to produce their vaccines are geared to this older technology, as well, and updating those processes and approvals could take considerable time. So even though, researchers are racing against time to find a solution to Covid-19 virus, synthetic biology has such a vast potential.
The Relevance of Glycans in the Viral Pathology of COVID-19
Reporter: Ofer Markman, PhD
While we are constantly cautioning people from putting too high validity to the results seen in the bellow mentioned Study,
The ABO blood groups are a result of various and different glycans on the surfaces of red blood cells and their definition is related to Blood Immunology and Blood Typing classification used for Blood Donations. It was the hallmark of the 1930 Nobel prize of medicine.
Glycans are involved in the interaction of the flu virus to the host cell and the antiviral drug Tamiflu (Oseltamivir ) is based on the inhibition of that sort of interaction/modulation.
The Relevance of Glycans in the Viral Pathology of COVID-19
Even if true, the numbers in this paper show statistical significant difference but mildly significant difference in the risk profile suggesting we are to pay too much attention to the phenomena or worry, regardless of the fact these result have no significance on behavioral instructions nor would call for testing one’s blood type in regards to a viral infection. I would neither totally ignore the finding as it may shed light on viral pathology and infection mechanisms and understanding of the later may lead us to treatment or effective vaccines. But we are still early on this path.
yet a more relevant understanding of glycans in the biology of the virus:-
this week NEJM interview shed some more light on the issue in their 2nd part of the talk when they discussed again blood group risk factors in the covid-19 context.
2012pharmaceutical
sjwilliamspa