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Archive for the ‘Scientist: Career considerations’ Category


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.

 

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.

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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Newly Elect President of Technion, Professor Uri Sivan: Key Contributions to Scientific Innovations

 

Reporter: Aviva Lev-Ari, PhD, RN

 

February 7, 2019
By: Office of the Technion Spokesperson

The Technion Council, headed by Mr. Gideon Frank, has elected Professor Uri Sivan of the Faculty of Physics as the next president of Technion. The Council’s decision was based on the recommendation of the Search Committee for the Technion President and received sweeping support from the Academic Assembly. The appointment is subject to the final approval of the International Board of Governors, which is set to convene in June.

Professor Uri Sivan

Prof. Sivan will commence his term as President of Technion on October 1 2019, and will replace the outgoing President Prof. Peretz Lavie, who will complete his term after a decade in office.

Prof. Sivan, 64, a resident of Haifa, is married and the father of three. He served as a pilot in the Israeli Air Force. He has a BSc in Physics and Mathematics, an MSc and PhD in Physics, all with honors from Tel Aviv University.

In 1991, after three years at IBM’s T. J. Watson Research Center in New York, Prof. Sivan joined the Faculty of Physics at Technion.

SOURCE

https://ats.org/news/professor-uri-sivan-elected-new-president-of-the-technion/

 

Key Contributions to Scientific Innovations

  • His research has covered a wide range of fields including quantum mesoscopic physics and the harnessing of molecular and cellular biology for the self-assembly of miniature electronic devices. Prof. Sivan, along with colleagues Profs. Erez Braun and Yoav Eichen, demonstrated for the first time how to harness molecular recognition by DNA molecules for wiring an electric circuit. This study gained considerable resonance and helped pave the way for a new field in nanotechnology using the self-assembly properties of biological molecules to construct miniature engineering systems.
  • His research has focused on the way water orders next to molecules and the effect of this ordering on inter-molecular interactions in biologically relevant solutions. Within this framework, Prof. Sivan’s group designs and builds unique, ultra-high-resolution atomic force microscopes.
  • His research has led to patents and industrial applications. Recently, an Israeli start-up company was established in the field of single cell analysis for cancer diagnostics, based on the technology developed in Prof. Sivan’s lab.
  •  Prof. Sivan is the founding director of the Russell Berrie Nanotechnology Institute (RBNI), which he headed between 2005 and 2010.  RBNI has led the scientific revolution in nanotechnology at Technion and has placed the university at the forefront of global research in the field. RBNI made headlines when Prof. Sivan and Dr. Ohad Zohar engraved the entire Hebrew Bible onto a tiny silicon chip. The Nano Bible was written as part of an educational program developed by the Institute to increase young people’s interest in science and especially in nanotechnology. In 2009, President Shimon Peres presented the Nano Bible to Pope Benedict XVI during his official visit to Israel. Today, there are three copies of the chip worldwide: at the Vatican Library, the Smithsonian Museum in Washington D.C., and the Israel Museum in Jerusalem. The establishment of RBNI spearheaded the development of Israel’s national nanotechnology program, and together with centers established in other Israeli universities, has positioned the country as a world leader in nanotechnology.

APPOINTMENTS

Recently, Prof. Sivan was appointed to head the National Advisory Committee in Quantum Science and Technology of the Council for Higher Education’s Planning and Budgeting Committee (PBC). The committee outlined the national quantum academic program, which was adopted and launched last year.

Prof. Sivan has served as a member of the Israeli National Committee for Research and Development (MOLMOP) and the Scientific Advisory Committee of the Batsheva de Rothschild Foundation. He currently serves on the Advisory Committee of the Maof Fellowships Committee for advancing Arab faculty and is a member of the Israeli Wolfson Foundation Advisory Board.

AWARDS

Prof. Sivan is a renowned lecturer in Israel and abroad. He was awarded with numerous prizes including

  • the Mifal Hapais Landau Prize for the Sciences and Research,
  • the Rothschild Foundation Bruno Prize,
  • the Israel Academy of Sciences Bergmann Prize,
  • the Technion’s Hershel Rich Innovation Award, and
  • the Taub Award for Excellence in Research.

 

SOURCE

https://ats.org/news/professor-uri-sivan-elected-new-president-of-the-technion/

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