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Archive for the ‘Scientist: Career considerations’ Category

Developing Machine Learning Models for Prediction of Onset of Type-2 Diabetes

Reporter: Amandeep Kaur, B.Sc., M.Sc.

A recent study reports the development of an advanced AI algorithm which predicts up to five years in advance the starting of type 2 diabetes by utilizing regularly collected medical data. Researchers described their AI model as notable and distinctive based on the specific design which perform assessments at the population level.

The first author Mathieu Ravaut, M.Sc. of the University of Toronto and other team members stated that “The main purpose of our model was to inform population health planning and management for the prevention of diabetes that incorporates health equity. It was not our goal for this model to be applied in the context of individual patient care.”

Research group collected data from 2006 to 2016 of approximately 2.1 million patients treated at the same healthcare system in Ontario, Canada. Even though the patients were belonged to the same area, the authors highlighted that Ontario encompasses a diverse and large population.

The newly developed algorithm was instructed with data of approximately 1.6 million patients, validated with data of about 243,000 patients and evaluated with more than 236,000 patient’s data. The data used to improve the algorithm included the medical history of each patient from previous two years- prescriptions, medications, lab tests and demographic information.

When predicting the onset of type 2 diabetes within five years, the algorithm model reached a test area under the ROC curve of 80.26.

The authors reported that “Our model showed consistent calibration across sex, immigration status, racial/ethnic and material deprivation, and a low to moderate number of events in the health care history of the patient. The cohort was representative of the whole population of Ontario, which is itself among the most diverse in the world. The model was well calibrated, and its discrimination, although with a slightly different end goal, was competitive with results reported in the literature for other machine learning–based studies that used more granular clinical data from electronic medical records without any modifications to the original test set distribution.”

This model could potentially improve the healthcare system of countries equipped with thorough administrative databases and aim towards specific cohorts that may encounter the faulty outcomes.

Research group stated that “Because our machine learning model included social determinants of health that are known to contribute to diabetes risk, our population-wide approach to risk assessment may represent a tool for addressing health disparities.”

Sources:

https://www.cardiovascularbusiness.com/topics/prevention-risk-reduction/new-ai-model-healthcare-data-predict-type-2-diabetes?utm_source=newsletter

Reference:

Ravaut M, Harish V, Sadeghi H, et al. Development and Validation of a Machine Learning Model Using Administrative Health Data to Predict Onset of Type 2 Diabetes. JAMA Netw Open. 2021;4(5):e2111315. doi:10.1001/jamanetworkopen.2021.11315 https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2780137

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

AI in Drug Discovery: Data Science and Core Biology @Merck &Co, Inc., @GNS Healthcare, @QuartzBio, @Benevolent AI and Nuritas

Reporters: Aviva Lev-Ari, PhD, RN and Irina Robu, PhD

https://pharmaceuticalintelligence.com/2020/08/27/ai-in-drug-discovery-data-science-and-core-biology-merck-co-inc-gns-healthcare-quartzbio-benevolent-ai-and-nuritas/

Can Blockchain Technology and Artificial Intelligence Cure What Ails Biomedical Research and Healthcare

Curator: Stephen J. Williams, Ph.D.

https://pharmaceuticalintelligence.com/2018/12/10/can-blockchain-technology-and-artificial-intelligence-cure-what-ails-biomedical-research-and-healthcare/

HealthCare focused AI Startups from the 100 Companies Leading the Way in A.I. Globally

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2018/01/18/healthcare-focused-ai-startups-from-the-100-companies-leading-the-way-in-a-i-globally/

AI in Psychiatric Treatment – Using Machine Learning to Increase Treatment Efficacy in Mental Health

Reporter: Aviva Lev- Ari, PhD, RN

https://pharmaceuticalintelligence.com/2019/06/04/ai-in-psychiatric-treatment-using-machine-learning-to-increase-treatment-efficacy-in-mental-health/

Vyasa Analytics Demos Deep Learning Software for Life Sciences at Bio-IT World 2018 – Vyasa’s booth (#632)

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2018/05/10/vyasa-analytics-demos-deep-learning-software-for-life-sciences-at-bio-it-world-2018-vyasas-booth-632/

New Diabetes Treatment Using Smart Artificial Beta Cells

Reporter: Irina Robu, PhD

https://pharmaceuticalintelligence.com/2017/11/08/new-diabetes-treatment-using-smart-artificial-beta-cells/

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Reporter: Stephen J. Williams, PhD

In an announcement televised on C-Span, President Elect Joseph Biden announced his new Science Team to advise on science policy matters, as part of the White House Advisory Committee on Science and Technology. Below is a video clip and the transcript, also available at

https://www.c-span.org/video/?508044-1/president-elect-biden-introduces-white-house-science-team

 

 

COMING UP TONIGHT ON C-SPAN, NEXT, PRESIDENT-ELECT JOE BIDEN AND VICE PRESIDENT-ELECT KAMALA HARRIS ANNOUNCE SEVERAL MEMBERS OF THEIR WHITE HOUSE SCIENCE TEAM. AND THEN SENATE MINORITY LEADER CHUCK SCHUMER TALKS ABOUT THE IMPEACHMENT OF PRESIDENT TRUMP IN THE WEEKLY DEMOCRATIC ADDRESS. AND AFTER THAT, TODAY’S SPEECH BY VICE PRESIDENT MIKE PENCE TO SAILORS AT NAVAL AIR STATION LAMORE IN CALIFORNIA. NEXT, PRESIDENT-ELECT JOE BIDEN AND VICE PRESIDENT-ELECT KAMALA HARRIS ANNOUNCE SEVERAL MEMBERS OF THEIR WHITE HOUSE SCIENCE TEAM. FROM WILMINGTON, DELAWARE, THIS IS ABOUT 40 MINUTES. PRESIDENT-ELECT BIDEN: GOOD AFTERNOON, FOLKS. I WAS TELLING THESE FOUR BRILLIANT SCIENTISTS AS I STOOD IN THE BACK, IN A WAY, THEY — THIS IS THE MOST EXCITING ANNOUNCEMENT THAT I’VE GOTTEN TO MAKE IN THE ENTIRE CABINET RAISED TO A CABINET LEVEL POSITION IN ONE CASE. THESE ARE AMONG THE BRIGHTEST MOST DEDICATED PEOPLE NOT ONLY IN THE COUNTRY BUT THE WORLD. THEY’RE COMPOSED OF SOME OF THE MOST SCIENTIFIC BRILLIANT MINDS IN THE WORLD. WHEN I WAS VICE PRESIDENT AS — I I HAD INTENSE INTEREST IN EVERYTHING THEY WERE DOING AND I PAID ENORMOUS ATTENTION. AND I WOULD — LIKE A KID GOING BACK TO SCHOOL. SIT DOWN AND CAN YOU EXPLAIN TO ME AND THEY WERE — VERY PATIENT WITH ME. AND — BUT AS PRESIDENT, I WANTED YOU TO KNOW I’M GOING TO PAY A GREAT DEAL OF ATTENTION. WHEN I TRAVEL THE WORLD AS VICE PRESIDENT, I WAS OFTEN ASKED TO EXPLAIN TO WORLD LEADERS, THEY ASKED ME THINGS LIKE DEFINE AMERICA. TELL ME HOW CAN YOU DEFINE AMERICA? WHAT’S AMERICA? AND I WAS ON A TIBETAN PLATEAU WITH AT THE TIME WITH XI ZIN PING AND WE HAD AN INTERPRETER CAN I DEFINE AMERICA FOR HIM? I SAID YES, I CAN. IN ONE WORD. POSSIBILITIES. POSSIBILITIES. I THINK IT’S ONE OF THE REASONS WHY WE’VE OCCASIONALLY BEEN REFERRED TO AS UGLY AMERICANS. WE THINK ANYTHING’S POSSIBLE GIVEN THE CHANCE, WE CAN DO ANYTHING. AND THAT’S PART OF I THINK THE AMERICAN SPIRIT. AND WHAT THE PEOPLE ON THIS STAGE AND THE DEPARTMENTS THEY WILL LEAD REPRESENT ENORMOUS POSSIBILITIES. THEY’RE THE ONES ASKING THE MOST AMERICAN OF QUESTIONS, WHAT NEXT? WHAT NEXT? NEVER SATISFIED, WHAT’S NEXT? AND WHAT’S NEXT IS BIG AND BREATHTAKING. HOW CAN — HOW CAN WE MAKE THE IMPOSSIBLE POSSIBLE? AND THEY WERE JUST ASKING QUESTIONS FOR THE SAKE OF QUESTIONS, THEY’RE ASKING THESE QUESTIONS AS CALL TO ACTION. , TO INSPIRE, TO HELP US IMAGINE THE FUTURE AND FIGURE OUT HOW TO MAKE IT REAL AND IMPROVE THE LIVES OF THE AMERICAN PEOPLE AND PEOPLE AROUND THE WORLD. THIS IS A TEAM THAT ASKED US TO IMAGINE EVERY HOME IN AMERICA BEING POWERED BY RENEWABLE ENERGY WITHIN THE NEXT 10 YEARS. OR 3-D IMAGE PRINTERS RESTORING TISSUE AFTER TRAUMATIC INJURIES AND HOSPITALS PRINTING ORGANS FOR ORGAN TRANSPLANTS. IMAGINE, IMAGINE. AND THEY REALLY — AND, YOU KNOW, THEN RALLY, THE SCIENTIFIC COMMUNITY TO GO ABOUT DOING WHAT WE’RE IMAGINING. YOU NEED SCIENCE, DATA AND DISCOVERY WAS A GOVERNING PHILOSOPHY IN THE OBAMA-BIDEN ADMINISTRATION. AND EVERYTHING FROM THE ECONOMY TO THE ENVIRONMENT TO CRIMINAL JUSTICE REFORM AND TO NATIONAL SECURITY. AND ON HEALTH CARE. FOR EXAMPLE, A BELIEF IN SCIENCE LED OUR EFFORTS TO MAP THE HUMAN BRAIN AND TO DEVELOP MORE PRECISE INDIVIDUALIZED MEDICINES. IT LED TO OUR ONGOING MISSION TO END CANCER AS WE KNOW IT, SOMETHING THAT IS DEEPLY PERSONAL TO BOTH MY FAMILY AND KAMALA’S FAMILY AND COUNTLESS FAMILIES IN AMERICA. WHEN PRESIDENT OBAMA ASKED ME TO LEAD THE CANCER MOON SHOT, I KNEW WE HAD TO INJECT A SENSE OF URGENCY INTO THE FIGHT. WE BELIEVED WE COULD DOUBLE THE RATE OF PROGRESS AND DO IN FIVE YEARS WHAT OTHERWISE WOULD TAKE 10. MY WIFE, JILL, AND I TRAVELED AROUND THE COUNTRY AND THE WORLD MEETING WITH THOUSANDS OF CANCER PATIENTS AND THEIR FAMILIES, PHYSICIANS, RESEARCHERS, PHILANTHROPISTS, TECHNOLOGY LEADERS AND HEADS OF STATE. WE SOUGHT TO BETTER UNDERSTAND AND BREAK DOWN THE SILOS AND STOVE PIPES THAT PREVENT THE SHARING OF INFORMATION AND IMPEDE ADVANCES IN CANCER RESEARCH AND TREATMENT WHILE BUILDING A FOCUSED AND COORDINATED EFFORT HERE AT HOME AND ABROAD. WE MADE PROGRESS. BUT THERE’S SO MUCH MORE THAT WE CAN DO. WHEN I ANNOUNCED THAT I WOULD NOT RUN IN 2015 AT THE TIME, I SAID I ONLY HAD ONE REGRET IN THE ROSE GARDEN AND IF I HAD ANY REGRETS THAT I HAD WON, THAT I WOULDN’T GET TO BE THE PRESIDENT TO PRESIDE OVER CANCER AS WE KNOW IT. WELL, AS GOD WILLING, AND ON THE 20TH OF THIS MONTH IN A COUPLE OF DAYS AS PRESIDENT I’M GOING TO DO EVERYTHING I CAN TO GET THAT DONE. I’M GOING TO — GOING TO BE A PRIORITY FOR ME AND FOR KAMALA AND IT’S A SIGNATURE ISSUE FOR JILL AS FIRST LADY. WE KNOW THE SCIENCE IS DISCOVERY AND NOT FICTION. AND IT’S ALSO ABOUT HOPE. AND THAT’S AMERICA. IT’S IN THE D.N.A. OF THIS COUNTRY, HOPE. WE’RE ON THE CUSP OF SOME OF THE MOST REMARKABLE BREAKTHROUGHS THAT WILL FUNDAMENTALLY CHANGE THE WAY OF LIFE FOR ALL LIFE ON THIS PLANET. WE CAN MAKE MORE PROGRESS IN THE NEXT 10 YEARS, I PREDICT, THAN WE’VE MADE IN THE LAST 50 YEARS. AND EXPONENTIAL MOVEMENT. WE CAN ALSO FACE SOME OF THE MOST DIRE CRISES IN A GENERATION WHERE SCIENCE IS CRITICAL TO WHETHER OR NOT WE MEET THE MOMENT OF PERIL AND PROMISE THAT WE KNOW IS WITHIN OUR REACH. IN 1944, FRANKLIN ROOSEVELT ASKED HIS SCIENCE ADVISOR HOW COULD THE UNITED STATES FURTHER ADVANCE SCIENTIFIC RESEARCH IN THE CRITICAL YEARS FOLLOWING THE SECOND WORLD WAR? THE RESPONSE LED TO SOME OF THE MOST GROUND BREAKING DISCOVERIES IN THE LAST 75 YEARS. AND WE CAN DO THAT AGAIN. AND WE CAN DO MORE. SO TODAY, I’M PROUD TO ANNOUNCE A TEAM OF SOME OF THE COUNTRY’S MOST BRILLIANT AND ACCOMPLISHED SCIENTISTS TO LEAD THE WAY. AND I’M ASKING THEM TO FOCUS ON FIVE KEY AREAS. FIRST THE PANDEMIC AND WHAT WE CAN LEARN ABOUT WHAT IS POSSIBLE OR WHAT SHOULD BE POSSIBLE TO ADDRESS THE WIDEST RANGE OF PUBLIC HEALTH NEEDS. SECONDLY, THE ECONOMY, HOW CAN WE BUILD BACK BETTER TO ENSURE PROSPERITY IS FULLY SHARED ALL ACROSS AMERICA? AMONG ALL AMERICANS? AND THIRDLY, HOW SCIENCE HELPS US CONFRONT THIS CLIMATE CRISIS WE FACE IN AMERICA AND THE WORLD BUT IN AMERICA HOW IT HELPS US CONFRONT THE CLIMATE CRISIS WITH AMERICAN JOBS AND INGENUITY. AND FOURTH, HOW CAN WE ENSURE THE UNITED STATES LEADS THE WORLD IN TECHNOLOGIES AND THE INDUSTRIES THAT THE FUTURE THAT WILL BE CRITICAL FOR OUR ECONOMIC PROSPERITY AND NATIONAL SECURITY? ESPECIALLY WITH THE INTENSE INCREASED COMPETITION AROUND THE WORLD FROM CHINA ON? AND FIFTH, HOW CAN WE ASSURE THE LONG-TERM HEALTH AND TRUST IN SCIENCE AND TECHNOLOGY IN OUR NATION? YOU KNOW, THESE ARE EACH QUESTIONS THAT CALL FOR ACTION. AND I’M HONORED TO ANNOUNCE A TEAM THAT IS ANSWERING THE CALL TO SERVE. AS THE PRESIDENTIAL SCIENCE ADVISOR AND DIRECTOR OF THE OFFICE OF SCIENCE AND TECHNOLOGY POLICY, I NOMINATE ONE OF THE MOST BRILLIANT GUYS I KNOW, PERSONS I KNOW, DR. ERIC LANDER. AND THANK YOU, DOC, FOR COMING BACK. THE PIONEER — HE’S A PIONEER IN THE STIFFING COMMUNITY. PRINCIPAL LEADER IN THE HUMAN GENOME PROJECT. AND NOT HYPERBOLE TO SUGGEST THAT DR. LANDER’S WORK HAS CHANGED THE COURSE OF HUMAN HISTORY. HIS ROLE IN HELPING US MAP THE GENOME PULLED BACK THE CURTAIN ON HUMAN DISEASE, ALLOWING SCIENTISTS, EVER SINCE, AND FOR GENERATIONS TO COME TO EXPLORE THE MOLECULAR BASIS FOR SOME OF THE MOST DEVASTATING ILLNESSES AFFECTING OUR WORLD. AND THE APPLICATION OF HIS PIONEERING WORK AS — ARE POISED TO LEAD TO INCREDIBLE CURES AND BREAKTHROUGHS IN THE YEARS TO COME. DR. LANDER NOW SERVES AS THE PRESIDENT AND FOUNDING DIRECTOR OF THE BRODE INSTITUTE AT M.I.T. AND HARVARD, THE WORLD’S FOREMOST NONPROFIT GENETIC RESEARCH ORGANIZATION. AND I CAME TO APPRECIATE DR. LANDER’S EXTRAORDINARY MIND WHEN HE SERVED AS THE CO-CHAIR OF THE PRESIDENT’S COUNCIL ON ADVISORS AND SCIENCE AND TECHNOLOGY DURING THE OBAMA-BIDEN ADMINISTRATION. AND I’M GRATEFUL, I’M GRATEFUL THAT WE CAN WORK TOGETHER AGAIN. I’VE ALWAYS SAID THAT BIDEN-HARRIS ADMINISTRATION WILL ALSO LEAD AND WE’RE GOING TO LEAD WITH SCIENCE AND TRUTH. WE BELIEVE IN BOTH. [LAUGHTER] GOD WILLING OVERCOME THE PANDEMIC AND BUILD OUR COUNTRY BETTER THAN IT WAS BEFORE. AND THAT’S WHY FOR THE FIRST TIME IN HISTORY, I’M GOING TO BE ELEVATING THE PRESIDENTIAL SCIENCE ADVISOR TO A CABINET RANK BECAUSE WE THINK IT’S THAT IMPORTANT. AS DEPUTY DIRECTOR OF THE OFFICE OF SCIENCE AND TECHNOLOGY POLICY AND SCIENCE AND — SCIENCE AND SOCIETY, I APPOINT DR. NELSON. SHE’S A PROFESSOR AT THE INSTITUTE OF ADVANCED STUDIES AT PRINCETON UNIVERSITY. THE PRESIDENT OF THE SOCIAL SCIENCE RESEARCH COUNCIL. AND ONE OF AMERICA’S LEADING SCHOLARS IN THE — AN AWARD-WINNING AUTHOR AND RESEARCHER AND EXPLORING THE CONNECTIONS BETWEEN SCIENCE AND OUR SOCIETY. THE DAUGHTER OF A MILITARY FAMILY, HER DAD SERVED IN THE UNITED STATES NAVY AND HER MOM WAS AN ARMY CRIPPING TO RAFFER. DR. NELSON DEVELOPED A LOVE OF TECHNOLOGY AT A VERY YOUNG AGE PARTICULARLY WITH THE EARLY COMPUTER PRODUCTS. COMPUTING PRODUCTS AND CODE-BREAKING EQUIPMENT THAT EVERY KID HAS AROUND THEIR HOUSE. AND SHE GREW UP WITHIN HER HOME. WHEN I WROTE THAT DOWN, I THOUGHT TO MYSELF, I MEAN, HOW MANY KIDS — ANY WAY, THAT PASSION WAS A PASSION FORGED A LIFELONG CURIOSITY ABOUT THE INEQUITIES AND THE POWER DIAMONDICS THAT SIT BENEATH THE SURFACE OF SCIENTIFIC RESEARCH AND THE TECHNOLOGY WE BUILD. DR. NELSON IS FOCUSED ON THOSE INSIGHTS. AND THE SCIENCE, TECHNOLOGY AND SOCIETY, LIKE FEW BEFORE HER EVER HAVE IN AMERICAN HISTORY. BREAKING NEW GROUND ON OUR UNDERSTANDING OF THE ROLE SCIENCE PLAYS IN AMERICAN LIFE AND OPENING THE DOOR TO — TO A FUTURE WHICH SCIENCE BETTER SERVES ALL PEOPLE. AS CO-CHAIR OF THE PRESIDENT’S COUNCIL ON ADVISORS OF SCIENCE AND TECHNOLOGY,APPOINT DR. FRANCIS ARNOLD, DIRECTOR OF THE ROSE BIOENGINEERING CENTER AT CALTECH AND ONE OF THE WORLD’S LEADING EXPERTS IN PROTEIN ENGINEERING, A LIFE-LONG CHAMPION OF RENEWABLE ENERGY SOLUTIONS WHO HAS BEEN INDUCTED INTO THE NATIONAL INVENTORS’ HALL OF FAME. THAT AIN’T A BAD PLACE TO BE. NOT ONLY IS SHE THE FIRST WOMAN TO BE ELECTED TO ALL THREE NATIONAL ACADEMIES OF SCIENCE, MEDICINE AND ENGINEERING AND ALSO THE FIRST WOMAN, AMERICAN WOMAN, TO WIN A NOBEL PRIZE IN CHEMISTRY. A VERY SLOW LEARNER, SLOW STARTER, THE DAUGHTER OF PITTSBURGH, SHE WORKED AS A CAB DRIVER, A JAZZ CLUB SERVER, BEFORE MAKING HER WAY TO BERKELEY AND A CAREER ON THE LEADING EDGE OF HUMAN DISCOVERY. AND I WANT TO MAKE THAT POINT AGAIN. I WANT — IF ANY OF YOUR CHILDREN ARE WATCHING, LET THEM KNOW YOU CAN DO ANYTHING. THIS COUNTRY CAN DO ANYTHING. ANYTHING AT ALL. AND SO SHE SURVIVED BREAST CANCER, OVERCAME A TRAGIC LOSS IN HER FAMILY WHILE RISING TO THE TOP OF HER FIELD, STILL OVERWHELMINGLY DOMINATED BY MEN. HER PASSION HAS BEEN A STEADFAST COMMITMENT TO RENEWABLE ENERGY FOR THE BETTERMENT OF OUR PLANET AND HUMANKIND. SHE IS AN INSPIRING FIGURE TO SCIENTISTS ACROSS THE FIELD AND ACROSS NATIONS. AND I WANT TO THANK DR. ARNOLD FOR AGREEING TO CO-CHAIR A FIRST ALL WOMAN TEAM TO LEAD THE PRESIDENT’S COUNCIL OF ADVISORS ON SCIENCE AND TECHNOLOGY WHICH LEADS ME TO THE NEXT MEMBER OF THE TEAM. AS CO-CHAIR, THE PRESIDENT’S COUNCIL OF ADVISORS ON SCIENCE AND TECHNOLOGY, I APPOINT DR. MARIE ZUBER. A TRAIL BLAZER BRAISING GEO PHYSICIST AND PLANETARY SCIENTIST A. FORMER CHAIR OF THE NATIONAL SCIENCE BOARD. FIRST WOMAN TO LEAD THE SCIENCE DEPARTMENT AT M.I.T. AND THE FIRST WOMAN TO LEAD NASA’S ROBOTIC PLANETARY MISSION. GROWING UP IN COLE COUNTRY NOT FAR FROM HEAVEN, SCRANTON, PENNSYLVANIA, IN CARBON COUNTY, PENNSYLVANIA, ABOUT 50 MILES SOUTH OF WHERE I WAS A KID, SHE DREAMED OF EXPLORING OUTER SPACE. COULD HAVE TOLD HER SHE WOULD JUST GO TO GREEN REACH IN SCRANTON AND FIND WHERE IT WAS. AND I SHOULDN’T BE SO FLIPPANT. BUT I’M SO EXCITED ABOUT THESE FOLKS. YOU KNOW, READING EVERY BOOK SHE COULD FIND AND LISTENING TO HER MOM’S STORIES ABOUT WATCHING THE EARLIEST ROCKET LAUNCH ON TELEVISION, MARIE BECAME THE FIRST PERSON IN HER FAMILY TO GO TO COLLEGE AND NEVER LET GO OF HER DREAM. TODAY SHE OVERSEES THE LINCOLN LABORATORY AT M.I.T. AND LEADS THE INSTITUTION’S CLIMATE ACTION PLAN. GROWING UP IN COLD COUNTRY, NOT AND FINALLY, COULD NOT BE HERE TODAY, BUT I’M PLEASED TO ANNOUNCE THAT I’VE HAD A LONG CONVERSATION WITH DR. FRANCIS COLLINS AND COULD NOT BE HERE TODAY. AND I’VE ASKED THEM TO STAY ON AS DIRECTOR OF THE INSTITUTE OF HEALTH AND — AT THIS CRITICAL MOMENT. I’VE KNOWN DR. COLLINS FOR MANY YEARS. I WORKED WITH HIM CLOSELY. HE’S BRILLIANT. A PIONEER. A TRUE LEADER. AND ABOVE ALL, HE’S A MODEL OF PUBLIC SERVICE AND I’M HONORED TO BE WORKING WITH HIM AGAIN. AND IT IS — IN HIS ABSENCE I WANT TO THANK HIM AGAIN FOR BEING WILLING TO STAY ON. I KNOW THAT WASN’T HIS ORIGINAL PLAN. BUT WE WORKED AN AWFUL LOT ON THE MOON SHOT AND DEALING WITH CANCER AND I JUST WANT TO THANK HIM AGAIN. AND TO EACH OF YOU AND YOUR FAMILIES, AND I SAY YOUR FAMILIES, THANK YOU FOR THE WILLINGNESS TO SERVE. AND NOT THAT YOU HAVEN’T BEEN SERVING ALREADY BUT TO SERVE IN THE ADMINISTRATION. AND THE AMERICAN PEOPLE, TO ALL THE AMERICAN PEOPLE, THIS IS A TEAM THAT’S GOING TO HELP RESTORE YOUR FAITH IN AMERICA’S PLACE IN THE FRONTIER OF SCIENCE AND DISCOVER AND HOPE. I’M NOW GOING TO TURN THIS OVER STARTING WITH DR. LANDER, TO EACH OF OUR NOMINEES AND THEN WITH — HEAR FROM THE VICE PRESIDENT. BUT AGAIN, JUST CAN’T THANK YOU ENOUGH AND I REALLY MEAN IT. THANK YOU, THANK YOU, THANK YOU FOR WILLING TO DO THIS. DOCTOR, IT’S ALL YOURS. I BETTER PUT MY MASK ON OR I’M GOING TO GET IN TROUBLE.

 

Director’s Page

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Danny Bar-Zohar, MD –  New R&D Leader for new pipelines at Merck KGaA as Luciano Rossetti steps out

Reporter: Aviva Lev-Ari, PhD, RN

 

Danny Bar-Zohar, MD – A Pharmaceutical Executive Profile in R&D: Ex-Novastis, Ex-Teva

Experience

Education

SOURCE

https://www.linkedin.com/in/danny-bar-zohar-513904a/

 

Novartis vet Danny Bar-Zohar leaps back into R&D, taking over the development team at Merck KGaA as Luciano Rossetti steps out

John Carroll
Editor & Founder

After a brief stint as a biotech investor at Syncona, Novartis vet Danny Bar-Zohar is back in R&D, and he’s taking the lead position at Merck KGaA’s drug division.

Bar-Zohar had led late-stage clinical development across a variety of areas — neuroscience, immunology, oncology and ophthalmology, among others — before joining the migration of talent out of the Basel-based multinational. He had been at Novartis for 7 years, which followed an earlier chapter in research at Teva.

Luciano Rossetti
The scientist is taking the lead on development at Merck KGaA, in place of Luciano Rossetti, who had a mixed record in R&D that nevertheless marked a big improvement over the dismal run the company had endured earlier. Joern-Peter Halle will continue on as global head of research. Rossetti is retiring after 6 years of running the research group, which has extensive operations in Germany as well as Massachusetts.

Their PD-L1 Bavencio — allied with Pfizer — has had a few successes, and a whole slate of failures. Sprifermin was touted as a big potential advance in osteoarthritis, but Merck KGaA is now auctioning off that part of the portfolio. One of the few late-stage bright spots has been their MET inhibitor tepotinib, which won breakthrough status and now is under priority review. That drug faces a rival at Novartis — capmatinib — that won an accelerated OK at the FDA in May.

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There’s also a BTK inhibitor, evobrutinib, that’s being developed for MS. But that’s a very crowded field, and Sanofi has been bullish about its prospects in the same research niche after buying out Principia.

Moving back into mid-stage development, there’s a major program underway for bintrafusp alfa, a bifunctional fusion protein targeting TGF-β and PD-L1, which Merck KGaA has high hopes for.

That all marks some bright, though limited, prospects for Merck KGaA, highlighting the need to find something new to beef up the pipeline. Bar-Zohar will get a say in that.

AUTHOR
John Carroll

SOURCE

https://endpts.com/novartis-vet-danny-bar-zohar-leaps-back-into-rd-taking-over-the-team-at-merck-kgaa-as-luciano-rossetti-steps-out/

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Live Notes, Real Time Conference Coverage AACR 2020 #AACR20: Tuesday June 23, 2020 Noon-2:45 Educational Sessions

Live Notes, Real Time Conference Coverage AACR 2020: Tuesday June 23, 2020 Noon-2:45 Educational Sessions

Reporter: Stephen J. Williams, PhD

Follow Live in Real Time using

#AACR20

@pharma_BI

@AACR

Register for FREE at https://www.aacr.org/

 

Presidential Address

Elaine R Mardis, William N Hait

DETAILS

Welcome and introduction

William N Hait

 

Improving diagnostic yield in pediatric cancer precision medicine

Elaine R Mardis
  • Advent of genomics have revolutionized how we diagnose and treat lung cancer
  • We are currently needing to understand the driver mutations and variants where we can personalize therapy
  • PD-L1 and other checkpoint therapy have not really been used in pediatric cancers even though CAR-T have been successful
  • The incidence rates and mortality rates of pediatric cancers are rising
  • Large scale study of over 700 pediatric cancers show cancers driven by epigenetic drivers or fusion proteins. Need for transcriptomics.  Also study demonstrated that we have underestimated germ line mutations and hereditary factors.
  • They put together a database to nominate patients on their IGM Cancer protocol. Involves genetic counseling and obtaining germ line samples to determine hereditary factors.  RNA and protein are evaluated as well as exome sequencing. RNASeq and Archer Dx test to identify driver fusions
  • PECAN curated database from St. Jude used to determine driver mutations. They use multiple databases and overlap within these databases and knowledge base to determine or weed out false positives
  • They have used these studies to understand the immune infiltrate into recurrent cancers (CytoCure)
  • They found 40 germline cancer predisposition genes, 47 driver somatic fusion proteins, 81 potential actionable targets, 106 CNV, 196 meaningful somatic driver mutations

 

 

Tuesday, June 23

12:00 PM – 12:30 PM EDT

Awards and Lectures

NCI Director’s Address

Norman E Sharpless, Elaine R Mardis

DETAILS

Introduction: Elaine Mardis

 

NCI Director Address: Norman E Sharpless
  • They are functioning well at NCI with respect to grant reviews, research, and general functions in spite of the COVID pandemic and the massive demonstrations on also focusing on the disparities which occur in cancer research field and cancer care
  • There are ongoing efforts at NCI to make a positive difference in racial injustice, diversity in the cancer workforce, and for patients as well
  • Need a diverse workforce across the cancer research and care spectrum
  • Data show that areas where the clinicians are successful in putting African Americans on clinical trials are areas (geographic and site specific) where health disparities are narrowing
  • Grants through NCI new SeroNet for COVID-19 serologic testing funded by two RFAs through NIAD (RFA-CA-30-038 and RFA-CA-20-039) and will close on July 22, 2020

 

Tuesday, June 23

12:45 PM – 1:46 PM EDT

Virtual Educational Session

Immunology, Tumor Biology, Experimental and Molecular Therapeutics, Molecular and Cellular Biology/Genetics

Tumor Immunology and Immunotherapy for Nonimmunologists: Innovation and Discovery in Immune-Oncology

This educational session will update cancer researchers and clinicians about the latest developments in the detailed understanding of the types and roles of immune cells in tumors. It will summarize current knowledge about the types of T cells, natural killer cells, B cells, and myeloid cells in tumors and discuss current knowledge about the roles these cells play in the antitumor immune response. The session will feature some of the most promising up-and-coming cancer immunologists who will inform about their latest strategies to harness the immune system to promote more effective therapies.

Judith A Varner, Yuliya Pylayeva-Gupta

 

Introduction

Judith A Varner
New techniques reveal critical roles of myeloid cells in tumor development and progression
  • Different type of cells are becoming targets for immune checkpoint like myeloid cells
  • In T cell excluded or desert tumors T cells are held at periphery so myeloid cells can infiltrate though so macrophages might be effective in these immune t cell naïve tumors, macrophages are most abundant types of immune cells in tumors
  • CXCLs are potential targets
  • PI3K delta inhibitors,
  • Reduce the infiltrate of myeloid tumor suppressor cells like macrophages
  • When should we give myeloid or T cell therapy is the issue
Judith A Varner
Novel strategies to harness T-cell biology for cancer therapy
Positive and negative roles of B cells in cancer
Yuliya Pylayeva-Gupta
New approaches in cancer immunotherapy: Programming bacteria to induce systemic antitumor immunity

 

 

Tuesday, June 23

12:45 PM – 1:46 PM EDT

Virtual Educational Session

Cancer Chemistry

Chemistry to the Clinic: Part 2: Irreversible Inhibitors as Potential Anticancer Agents

There are numerous examples of highly successful covalent drugs such as aspirin and penicillin that have been in use for a long period of time. Despite historical success, there was a period of reluctance among many to purse covalent drugs based on concerns about toxicity. With advances in understanding features of a well-designed covalent drug, new techniques to discover and characterize covalent inhibitors, and clinical success of new covalent cancer drugs in recent years, there is renewed interest in covalent compounds. This session will provide a broad look at covalent probe compounds and drug development, including a historical perspective, examination of warheads and electrophilic amino acids, the role of chemoproteomics, and case studies.

Benjamin F Cravatt, Richard A. Ward, Sara J Buhrlage

 

Discovering and optimizing covalent small-molecule ligands by chemical proteomics

Benjamin F Cravatt
  • Multiple approaches are being investigated to find new covalent inhibitors such as: 1) cysteine reactivity mapping, 2) mapping cysteine ligandability, 3) and functional screening in phenotypic assays for electrophilic compounds
  • Using fluorescent activity probes in proteomic screens; have broad useability in the proteome but can be specific
  • They screened quiescent versus stimulated T cells to determine reactive cysteines in a phenotypic screen and analyzed by MS proteomics (cysteine reactivity profiling); can quantitate 15000 to 20,000 reactive cysteines
  • Isocitrate dehydrogenase 1 and adapter protein LCP-1 are two examples of changes in reactive cysteines they have seen using this method
  • They use scout molecules to target ligands or proteins with reactive cysteines
  • For phenotypic screens they first use a cytotoxic assay to screen out toxic compounds which just kill cells without causing T cell activation (like IL10 secretion)
  • INTERESTINGLY coupling these MS reactive cysteine screens with phenotypic screens you can find NONCANONICAL mechanisms of many of these target proteins (many of the compounds found targets which were not predicted or known)

Electrophilic warheads and nucleophilic amino acids: A chemical and computational perspective on covalent modifier

The covalent targeting of cysteine residues in drug discovery and its application to the discovery of Osimertinib

Richard A. Ward
  • Cysteine activation: thiolate form of cysteine is a strong nucleophile
  • Thiolate form preferred in polar environment
  • Activation can be assisted by neighboring residues; pKA will have an effect on deprotonation
  • pKas of cysteine vary in EGFR
  • cysteine that are too reactive give toxicity while not reactive enough are ineffective

 

Accelerating drug discovery with lysine-targeted covalent probes

 

Tuesday, June 23

12:45 PM – 2:15 PM EDT

Virtual Educational Session

Molecular and Cellular Biology/Genetics

Virtual Educational Session

Tumor Biology, Immunology

Metabolism and Tumor Microenvironment

This Educational Session aims to guide discussion on the heterogeneous cells and metabolism in the tumor microenvironment. It is now clear that the diversity of cells in tumors each require distinct metabolic programs to survive and proliferate. Tumors, however, are genetically programmed for high rates of metabolism and can present a metabolically hostile environment in which nutrient competition and hypoxia can limit antitumor immunity.

Jeffrey C Rathmell, Lydia Lynch, Mara H Sherman, Greg M Delgoffe

 

T-cell metabolism and metabolic reprogramming antitumor immunity

Jeffrey C Rathmell

Introduction

Jeffrey C Rathmell

Metabolic functions of cancer-associated fibroblasts

Mara H Sherman

Tumor microenvironment metabolism and its effects on antitumor immunity and immunotherapeutic response

Greg M Delgoffe
  • Multiple metabolites, reactive oxygen species within the tumor microenvironment; is there heterogeneity within the TME metabolome which can predict their ability to be immunosensitive
  • Took melanoma cells and looked at metabolism using Seahorse (glycolysis): and there was vast heterogeneity in melanoma tumor cells; some just do oxphos and no glycolytic metabolism (inverse Warburg)
  • As they profiled whole tumors they could separate out the metabolism of each cell type within the tumor and could look at T cells versus stromal CAFs or tumor cells and characterized cells as indolent or metabolic
  • T cells from hyerglycolytic tumors were fine but from high glycolysis the T cells were more indolent
  • When knock down glucose transporter the cells become more glycolytic
  • If patient had high oxidative metabolism had low PDL1 sensitivity
  • Showed this result in head and neck cancer as well
  • Metformin a complex 1 inhibitor which is not as toxic as most mito oxphos inhibitors the T cells have less hypoxia and can remodel the TME and stimulate the immune response
  • Metformin now in clinical trials
  • T cells though seem metabolically restricted; T cells that infiltrate tumors are low mitochondrial phosph cells
  • T cells from tumors have defective mitochondria or little respiratory capacity
  • They have some preliminary findings that metabolic inhibitors may help with CAR-T therapy

Obesity, lipids and suppression of anti-tumor immunity

Lydia Lynch
  • Hypothesis: obesity causes issues with anti tumor immunity
  • Less NK cells in obese people; also produce less IFN gamma
  • RNASeq on NOD mice; granzymes and perforins at top of list of obese downregulated
  • Upregulated genes that were upregulated involved in lipid metabolism
  • All were PPAR target genes
  • NK cells from obese patients takes up palmitate and this reduces their glycolysis but OXPHOS also reduced; they think increased FFA basically overloads mitochondria
  • PPAR alpha gamma activation mimics obesity

 

 

Tuesday, June 23

12:45 PM – 2:45 PM EDT

Virtual Educational Session

Clinical Research Excluding Trials

The Evolving Role of the Pathologist in Cancer Research

Long recognized for their role in cancer diagnosis and prognostication, pathologists are beginning to leverage a variety of digital imaging technologies and computational tools to improve both clinical practice and cancer research. Remarkably, the emergence of artificial intelligence (AI) and machine learning algorithms for analyzing pathology specimens is poised to not only augment the resolution and accuracy of clinical diagnosis, but also fundamentally transform the role of the pathologist in cancer science and precision oncology. This session will discuss what pathologists are currently able to achieve with these new technologies, present their challenges and barriers, and overview their future possibilities in cancer diagnosis and research. The session will also include discussions of what is practical and doable in the clinic for diagnostic and clinical oncology in comparison to technologies and approaches primarily utilized to accelerate cancer research.

 

Jorge S Reis-Filho, Thomas J Fuchs, David L Rimm, Jayanta Debnath

DETAILS

Tuesday, June 23

12:45 PM – 2:45 PM EDT

 

High-dimensional imaging technologies in cancer research

David L Rimm

  • Using old methods and new methods; so cell counting you use to find the cells then phenotype; with quantification like with Aqua use densitometry of positive signal to determine a threshold to determine presence of a cell for counting
  • Hiplex versus multiplex imaging where you have ten channels to measure by cycling of flour on antibody (can get up to 20plex)
  • Hiplex can be coupled with Mass spectrometry (Imaging Mass spectrometry, based on heavy metal tags on mAbs)
  • However it will still take a trained pathologist to define regions of interest or field of desired view

 

Introduction

Jayanta Debnath

Challenges and barriers of implementing AI tools for cancer diagnostics

Jorge S Reis-Filho

Implementing robust digital pathology workflows into clinical practice and cancer research

Jayanta Debnath

Invited Speaker

Thomas J Fuchs
  • Founder of spinout of Memorial Sloan Kettering
  • Separates AI from computational algothimic
  • Dealing with not just machines but integrating human intelligence
  • Making decision for the patients must involve human decision making as well
  • How do we get experts to do these decisions faster
  • AI in pathology: what is difficult? =è sandbox scenarios where machines are great,; curated datasets; human decision support systems or maps; or try to predict nature
  • 1) learn rules made by humans; human to human scenario 2)constrained nature 3)unconstrained nature like images and or behavior 4) predict nature response to nature response to itself
  • In sandbox scenario the rules are set in stone and machines are great like chess playing
  • In second scenario can train computer to predict what a human would predict
  • So third scenario is like driving cars
  • System on constrained nature or constrained dataset will take a long time for commuter to get to decision
  • Fourth category is long term data collection project
  • He is finding it is still finding it is still is difficult to predict nature so going from clinical finding to prognosis still does not have good predictability with AI alone; need for human involvement
  • End to end partnering (EPL) is a new way where humans can get more involved with the algorithm and assist with the problem of constrained data
  • An example of a workflow for pathology would be as follows from Campanella et al 2019 Nature Medicine: obtain digital images (they digitized a million slides), train a massive data set with highthroughput computing (needed a lot of time and big software developing effort), and then train it using input be the best expert pathologists (nature to human and unconstrained because no data curation done)
  • Led to first clinically grade machine learning system (Camelyon16 was the challenge for detecting metastatic cells in lymph tissue; tested on 12,000 patients from 45 countries)
  • The first big hurdle was moving from manually annotated slides (which was a big bottleneck) to automatically extracted data from path reports).
  • Now problem is in prediction: How can we bridge the gap from predicting humans to predicting nature?
  • With an AI system pathologist drastically improved the ability to detect very small lesions

 

Virtual Educational Session

Epidemiology

Cancer Increases in Younger Populations: Where Are They Coming from?

Incidence rates of several cancers (e.g., colorectal, pancreatic, and breast cancers) are rising in younger populations, which contrasts with either declining or more slowly rising incidence in older populations. Early-onset cancers are also more aggressive and have different tumor characteristics than those in older populations. Evidence on risk factors and contributors to early-onset cancers is emerging. In this Educational Session, the trends and burden, potential causes, risk factors, and tumor characteristics of early-onset cancers will be covered. Presenters will focus on colorectal and breast cancer, which are among the most common causes of cancer deaths in younger people. Potential mechanisms of early-onset cancers and racial/ethnic differences will also be discussed.

Stacey A. Fedewa, Xavier Llor, Pepper Jo Schedin, Yin Cao

Cancers that are and are not increasing in younger populations

Stacey A. Fedewa

 

  • Early onset cancers, pediatric cancers and colon cancers are increasing in younger adults
  • Younger people are more likely to be uninsured and these are there most productive years so it is a horrible life event for a young adult to be diagnosed with cancer. They will have more financial hardship and most (70%) of the young adults with cancer have had financial difficulties.  It is very hard for women as they are on their childbearing years so additional stress
  • Types of early onset cancer varies by age as well as geographic locations. For example in 20s thyroid cancer is more common but in 30s it is breast cancer.  Colorectal and testicular most common in US.
  • SCC is decreasing by adenocarcinoma of the cervix is increasing in women’s 40s, potentially due to changing sexual behaviors
  • Breast cancer is increasing in younger women: maybe etiologic distinct like triple negative and larger racial disparities in younger African American women
  • Increased obesity among younger people is becoming a factor in this increasing incidence of early onset cancers

 

 

Other Articles on this Open Access  Online Journal on Cancer Conferences and Conference Coverage in Real Time Include

Press Coverage

Live Notes, Real Time Conference Coverage 2020 AACR Virtual Meeting April 28, 2020 Symposium: New Drugs on the Horizon Part 3 12:30-1:25 PM

Live Notes, Real Time Conference Coverage 2020 AACR Virtual Meeting April 28, 2020 Session on NCI Activities: COVID-19 and Cancer Research 5:20 PM

Live Notes, Real Time Conference Coverage 2020 AACR Virtual Meeting April 28, 2020 Session on Evaluating Cancer Genomics from Normal Tissues Through Metastatic Disease 3:50 PM

Live Notes, Real Time Conference Coverage 2020 AACR Virtual Meeting April 28, 2020 Session on Novel Targets and Therapies 2:35 PM

 

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Old Industrial Revolution Paradigm of Education Needs to End: How Scientific Curation Can Transform Education

Curator: Stephen J. Williams, PhD.

Dr. Cathy N. Davidson from Duke University gives a talk entitled: Now You See It.  Why the Future of Learning Demands a Paradigm Shift

In this talk, shown below, Dr. Davidson shows how our current education system has been designed for educating students for the industrial age type careers and skills needed for success in the Industrial Age and how this educational paradigm is failing to prepare students for the challenges they will face in their future careers.

Or as Dr. Davidson summarizes

Designing education not for your past but for their future

As the video is almost an hour I will summarize some of the main points below

PLEASE WATCH VIDEO

Summary of talk

Dr. Davidson starts the talk with a thesis: that Institutions tend to preserve the problems they were created to solve.

All the current work, teaching paradigms that we use today were created for the last information age (19th century)

Our job to to remake the institutions of education work for the future not the one we inherited

Four information ages or technologies that radically changed communication

  1. advent of writing: B.C. in ancient Mesopotamia allowed us to record and transfer knowledge and ideas
  2. movable type – first seen in 10th century China
  3. steam powered press – allowed books to be mass produced and available to the middle class.  First time middle class was able to have unlimited access to literature
  4. internet- ability to publish and share ideas worldwide

Interestingly, in the early phases of each of these information ages, the same four complaints about the new technology/methodology of disseminating information was heard

  • ruins memory
  • creates a distraction
  • ruins interpersonal dialogue and authority
  • reduces complexity of thought

She gives an example of Socrates who hated writing and frequently stated that writing ruins memory, creates a distraction, and worst commits ideas to what one writes down which could not be changed or altered and so destroys ‘free thinking’.

She discusses how our educational institutions are designed for the industrial age.

The need for collaborative (group) learning AND teaching

Designing education not for your past but for the future

In other words preparing students for THEIR future not your past and the future careers that do not exist today.

In the West we were all taught to answer silently and alone.  However in Japan, education is arranged in the han or group think utilizing the best talents of each member in the group.  In Japan you are arranged in such groups at an early age.  The concept is that each member of the group contributes their unique talent and skill for the betterment of the whole group.  The goal is to demonstrate that the group worked well together.

see https://educationinjapan.wordpress.com/education-system-in-japan-general/the-han-at-work-community-spirit-begins-in-elementary-school/ for a description of “in the han”

In the 19th century in institutions had to solve a problem: how to get people out of the farm and into the factory and/or out of the shop and into the firm

Takes a lot of regulation and institutionalization to convince people that independent thought is not the best way in the corporation

keywords for an industrial age

  • timeliness
  • attention to task
  • standards, standardization
  • hierarchy
  • specialization, expertise
  • metrics (measures, management)
  • two cultures: separating curriculum into STEM versus artistic tracts or dividing the world of science and world of art

This effort led to a concept used in scientific labor management derived from this old paradigm in education, an educational system controlled and success measured using

  • grades (A,B,C,D)
  • multiple choice tests

keywords for our age

  • workflow
  • multitasking attention
  • interactive process (Prototype, Feedback)
  • data mining
  • collaboration by difference

Can using a methodology such as scientific curation affect higher education to achieve this goal of teaching students to collaborate in an interactive process using data mining to create a new workflow for any given problem?  Can a methodology of scientific curation be able to affect such changes needed in academic departments to achieve the above goal?

This will be the subject of future curations tested using real-world in class examples.

However, it is important to first discern that scientific content curation takes material from Peer reviewed sources and other expert-vetted sources.  This is unique from other types of content curation in which take from varied sources, some of which are not expert-reviewed, vetted, or possibly ‘fake news’ or highly edited materials such as altered video and audio.  In this respect, the expert acts not only as curator but as referee.  In addition, collaboration is necessary and even compulsory for the methodology of scientific content curation, portending the curator not as the sole expert but revealing the CONTENT from experts as the main focus for learning and edification.

Other article of note on this subject in this Open Access Online Scientific Journal include:

The above articles will give a good background on this NEW Conceived Methodology of Scientific Curation and its Applicability in various areas such as Medical Publishing, and as discussed below Medical Education.

To understand the new paradigm in medical communication and the impact curative networks have or will play in this arena please read the following:

Scientific Curation Fostering Expert Networks and Open Innovation: Lessons from Clive Thompson and others

This article discusses a history of medical communication and how science and medical communication initially moved from discussions from select individuals to the current open accessible and cooperative structure using Web 2.0 as a platform.

 

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In Data Science, A Pioneer Practitioner’s Portfolio of Algorithm-based Decision Support Systems for Operations Management in Several Industrial Verticals: Analytics Designer, Aviva Lev-Ari, PhD, RN

An overview of Data Science as a discipline is presented in

Data Science & Analytics: What do Data Scientists Do in 2020 and a Pioneer Practitioner’s Portfolio of Algorithm-based Decision Support Systems for Operations Management in Several Industrial Verticals

 

On this landscape about IT, The Internet, Analytics, Statistics, Big Data, Data Science and Artificial Intelligence, I am to tell stories on my own pioneering work in data science, Algorithm-based decision support systems design for different organizations in several sectors of the US economy:

Images on 12/7/2019

  • Startups:
  1. TimeØ Group – The leader in Digital Marketplaces Design
  2. Concept Five Technologies, Inc. – Commercialization of DoD funded technologies
  3. MDSS, Inc. – SAAS in Analytical Services
  4. LPBI Group – Pharmaceutical & Media
  • Top Tier Management Consulting: SRI International, Monitor Group;
  • OEM: Amdahl Corporation;
  • Top 6th System Integrator: Perot System Corporation;
  • FFRDC: MITRE Corporation.
  • Publishing industry: was Director of Research at McGraw-Hill/CTB.
  • Northeastern University, Researcher on Cardiovascular Pharmacotherapy at Bouve College of Health Sciences (Independent research guided by Professor of Pharmacology)

Type of institutions:

  • For-Profit corporations: Amdahl Corp, PSC, McGraw-Hill
  • For-Profit Top Tier Consulting: Monitor Company, Now Deloitte
  • Not-for-Profit Top Tier Consulting: SRI International
  • FFRDC: MITRE
  • Pharmaceutical & Media Start up in eScientific Publishing: LPBI Group:
  1. Developers of Curation methodology for e-Articles [N = 5,700],
  2. Developers of electronic Table of Contents for e-Books in Medicine [N = 16, https://lnkd.in/ekWGNqA] and
  3. Developers of Methodologies for real time press coverage and production of e-Proceedings of Biotech Conferences [N = 70].

 

Autobiographical Annotations: Tribute to My Professors

 

Pioneering implementations of analytics to business decision making: contributions to domain knowledge conceptualization, research design, methodology development, data modeling and statistical data analysis: Aviva Lev-Ari, UCB, PhD’83; HUJI MA’76

https://pharmaceuticalintelligence.com/2018/05/28/pioneering-implementations-of-analytics-to-business-decision-making-contributions-to-domain-knowledge-conceptualization-research-design-methodology-development-data-modeling-and-statistical-data-a/

Recollections of Years at UC, Berkeley, Part 1 and Part 2

  • Recollections: Part 1 – My days at Berkeley, 9/1978 – 12/1983 – About my doctoral advisor, Allan Pred, other professors and other peers

https://pharmaceuticalintelligence.com/2018/03/15/recollections-my-days-at-berkeley-9-1978-12-1983-about-my-doctoral-advisor-allan-pred-other-professors-and-other-peer/

  • Recollections: Part 2 – “While Rolling” is preceded by “While Enrolling” Autobiographical Alumna Recollections of Berkeley – Aviva Lev-Ari, PhD’83

https://pharmaceuticalintelligence.com/2018/05/24/recollections-part-2-while-rolling-is-preceded-by-while-enrolling-autobiographical-alumna-recollections-of-berkeley-aviva-lev-ari-phd83/

Accomplishments

The Digital Age Gave Rise to New Definitions – New Benchmarks were born on the World Wide Web for the Intangible Asset of Firm’s Reputation: Pay a Premium for buying e-Reputation

For @AVIVA1950, Founder, LPBI Group @pharma_BI: Twitter Analytics [Engagement Rate, Link Clicks, Retweets, Likes, Replies] & Tweet Highlights [Tweets, Impressions, Profile Visits, Mentions, New Followers] https://analytics.twitter.com/user/AVIVA1950/tweets

Thriving at the Survival Calls during Careers in the Digital Age – An AGE like no Other, also known as, DIGITAL

Professional Self Re-Invention: From Academia to Industry – Opportunities for PhDs in the Business Sector of the Economy

Reflections on a Four-phase Career: Aviva Lev-Ari, PhD, RNMarch 2018

Was prepared for publication in American Friends of the Hebrew University (AFHU), May 2018 Newsletter, Hebrew University’s HUJI Alumni Spotlight Section.

Aviva Lev-Ari’s profile was up on 5/3/2018 on AFHU website under the Alumni Spotlight at https://www.afhu.org/

On 5/11/2018, Excerpts were Published in AFHU e-news.

https://us10.campaign-archive.com/?u=5c25136c60d4dfc4d3bb36eee&id=757c5c3aae&e=d09d2b8d72

https://www.afhu.org/2018/05/03/aviva-lev-ari/

 

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Funding Research by Lottery?: How Lucky Do You Feel After Submitting a Grant

Reporter: Stephen J. Williams, Ph.D.

A recent article in Nature: “Science Funders Gamble on Grant Lotteries” discusses an odd twist to the anxiety most researchers feel after submitting grants to an agency.  Now, along with the hours of fretting over details and verbiage in a grant application, it appears that not only great science, but the luck of the draw may be necessary to get your work funded.  The article, by David Adam, discusses the funding strategy of the Health Research Council of New Zealand, which since 2015, has implemented a strategy of awarding grants through random selection.  Although limited in scope and size (mainly these grants are on very highly speculative and potentially transformative research and awards are usually less that $150,000 NZD) was meant to promote the applicants in submitting more risky ideas that are usually submitted in traditional peer reviewed grants.

Random chance will create more openness to ideas that are not in the mainstream

–  Margit Osterloh, economist at University of Zurich

Margit also mentions that many mid-ranking applications which are never funded could benefit from such a lottery system.

The Swiss National Science Foundation (SSFS) is also experimenting with this idea of random selection.  The Health Research Council states the process in not entirely random.  A computer selects the projects at random based on a random number generator.  A panel then decides if they are a reasonably good and well written application.

Some researchers have felt this random process could help eliminate much bias that can be baked into the traditional peer review process.  However there are many who feel the current process of peer review panels are a necessary and rigorous step in the granting process, analyzing applications which would most likely have the best chances to succeed based on the rigor of the proposed science.

However Osterloh feels that the lottery idea produces a humbling effect. As Margit said

If you know you have got a grant or a publication which is selected partly randomly, then you will know very well you are not the king of the Universe

Humility in science: a refreshing idea.  However the lottery idea will not mean that scientists need not prepare a careful and well written application.  Applications that are ranked very low would not be in the lottery.  However, if one feels lucky, maybe the obscene hours of worrying about each sentence written, or that figures for preliminary data should be altered at the 11th hour before submission might be a thing of the past.

Of course if you are a lucky person.

 

 

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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.

4.2.5

4.2.5   scPopCorn: A New Computational Method for Subpopulation Detection and their Comparative Analysis Across Single-Cell Experiments, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 4: Single Cell Genomics

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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Real Time Coverage @BIOConvention #BIO2019: Precision Medicine Beyond Oncology June 5 Philadelphia PA

Reporter: Stephen J Williams PhD @StephenJWillia2

Precision Medicine has helped transform cancer care from one-size-fits-all chemotherapy to a new era, where patients’ tumors can be analyzed and therapy selected based on their genetic makeup. Until now, however, precision medicine’s impact has been far less in other therapeutic areas, many of which are ripe for transformation. Efforts are underway to bring the successes of precision medicine to neurology, immunology, ophthalmology, and other areas. This move raises key questions of how the lessons learned in oncology can be used to advance precision medicine in other fields, what types of data and tools will be important to personalizing treatment in these areas, and what sorts of partnerships and payer initiatives will be needed to support these approaches and their ultimate commercialization and use. The panel will also provide an in depth look at precision medicine approaches aimed at better understanding and improving patient care in highly complex disease areas like neurology.
Speaker panel:  The big issue now with precision medicine is there is so much data and hard to put experimental design and controls around randomly collected data.
  • The frontier is how to CURATE randomly collected data to make some sense of it
  • One speaker was at a cancer meeting and the oncologist had no idea what to make of genomic reports they were given.  Then there is a lack of action or worse a misdiagnosis.
  • So for e.g. with Artificial Intelligence algorithms to analyze image data you can see things you can’t see with naked eye but if data quality not good the algorithms are useless – if data not curated properly data is wasted
Data needs to be organized and curated. 
If relying of AI for big data analysis the big question still is: what are the rates of false negative and false positives?  Have to make sure so no misdiagnosis.

Please follow LIVE on TWITTER using the following @ handles and # hashtags:

@Handles

@pharma_BI

@AVIVA1950

@BIOConvention

# Hashtags

#BIO2019 (official meeting hashtag)

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Reporter: Stephen J. Williams, PhD @StephenJWillia2

Science and technology bring tremendous value to society in years of life and quality of life, yet the public often perceives science as difficult, irrelevant or even threatening. Moreover, the inspirational and moving stories of scientists and innovators working around the world are often hidden or misrepresented in popular culture. Whose responsibility is it to communicate science and engage the public in supporting the scientific enterprise? Can everyone be a Champion of Science and what are the solutions to enlist and engage more champions of science across generations and geographies? How do we work together to enhance transparency, accessibility and relevance of science for everyone, everywhere? Can science become more inclusive and engage hearts and not only minds?

Join this exciting session as Johnson & Johnson announces the winners of the Champions of Science – BioGENEius Storytelling Challenge, and brings together other key stakeholders in a discussion about the importance of engaging the public to fall in love in science all over again.

Sponsored by: Johnson & Johnson Innovation

Seema: We need to solve the problem of the lack of trust in scientists.  Some of JNJ winners of their acheivement program went on to become Nobel Laureates.   Arthur Horwich and Hans Ullrich won the Jannsen Award for discovering compounds that could refold proteins, including protein chaperones.  Many diseases occur because of protein misfolding like neuro-degenerative diseases.
Seema:  Great science going on in Africa.  JNJ wanted to showcase the great science in Africa. they awarded four individuals with storytelling award (Emily).
Dr. Horwich: got interested in science early on.  Worked on N terminal mitochondrial signal peptides.  also then got interested in how proteins fold and unfold and refold since the 1950s.  He had changed the thinking of how proteins are processed within cells and over many years he had worked on this.
Emily Wang:  Parents and schoolteachers prodded her curiosity in biology. The impact of day to day work of scientists is arduous but the little things can lead to advances that may help people.  If passionate and have a great mentor then can get a foot in the door.  Worked at Stanford in the lab.
Dr. Mukherjee: He likes to cure diseases, physican first, scientist second, writer third but he doesn’t separate this.  In older times scientists wrote to think and true today. How we visualize the word, or use our hands, is similar.  He takes the word translational research very seriously.  Can you say in one sentence how this will help patients in three years?
There are multitude ways of love for science.
Dr. Pinela: loved asking big question and loved storytelling but asking bigger questions. Moved from Columbia and moved to US; loved the freedom and government funding situation at that time.  Need the training and mentorship so mentors are a very big aspect in innovation as it led her to entrepreneurship.  We need to use technology to disrupt and innovate.
Nsikin:  A lot of mentors nurture curiosity.  People like to see them in that story of curiosity.  That is how is bases the PBS science videos: did  a study on engagement and people wants a morality, and a science identity (an inner nerd in all of us i.e. spark the interest).  The feedback if they focus on this has been positive.

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#BIO2019 (official meeting hashtag)

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