Linking Phenotype Changes to Internal/External Longitudinal Time Series in a ...Larry Smarr
Invited Presentation at EMBC ‘16
38th International Conference of the IEEE Engineering in Medicine and Biology Society Symposium: The Quantified Self: Visions for the Next Decade of Persistent Physiological Monitoring
Orlando, FL
August 18, 2016
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsLarry Smarr
This presentation on February 27, 2014 to NGS and the Future of Medicine at Illumina Headquarters in La Jolla, CA, was made by Calit2 Director Larry Smarr.
Linking Phenotype Changes to Internal/External Longitudinal Time Series in a ...Larry Smarr
Invited Presentation at EMBC ‘16
38th International Conference of the IEEE Engineering in Medicine and Biology Society Symposium: The Quantified Self: Visions for the Next Decade of Persistent Physiological Monitoring
Orlando, FL
August 18, 2016
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsLarry Smarr
This presentation on February 27, 2014 to NGS and the Future of Medicine at Illumina Headquarters in La Jolla, CA, was made by Calit2 Director Larry Smarr.
Observing the Dynamics of the Human Immune System Coupled to the Microbiome i...Larry Smarr
Calit2 Director Larry Smarr delivered this presentation to the CASIS Workshop on Biomedical Research Aboard the ISS at Columbia University in NY, NY, on May 28, 2014.
The Human Microbiome and the Revolution in Digital HealthLarry Smarr
2014.01.22
Calit2 Director Larry Smarr speaks as part of the Pensacola Evening Lecture Series, organized by the Florida Institute for Human and Machine Cognition, in Pensacola, FL.
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...Larry Smarr
Invited Presentation Microbiology and the Microbiome and the Implications for Human Health Analytic, Life Science & Diagnostic Association (ALDA) 2016 Senior Management Conference
Half Moon Bay, CA
October 3, 2016
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step FurtherLarry Smarr
Calit2 Director Larry Smarr gives the closing keynote address to the 2nd annual Learning Conference on Integrated Delivery Systems in San Diego on May 7, 2014.
Hacking for Healing at SXSW InteractiveDrBonnie360
Content and Visual Design by Tiffany Simms
Do you know why you should take steps to get healthy when you already think you are healthy?
DrBonnie360 brings together Linda Avey (We Are Curious Inc.), Poonacha Machaiah (JIYO), and Nicole Guthrie (HopeLab), to present you with your #HacktoHeal.
With Chronic Disease, especially autoimmune disease, slowly creeping up on us at an epidemic level, we can no longer ignore the importance of being healthy. The stage is set for personalized prevention. The science, research, data, digital health, and patients, are all ready for personalized prevention to become a reality.
We Are Curious, JIYO, and Hopelab bring SXSW the steps to finding and maintaining their optimal health.
The key to all this is finding the right feedback loops for each of you and maintaining balance.
Observing the Dynamics of the Human Immune System Coupled to the Microbiome i...Larry Smarr
Calit2 Director Larry Smarr delivered this presentation to the CASIS Workshop on Biomedical Research Aboard the ISS at Columbia University in NY, NY, on May 28, 2014.
The Human Microbiome and the Revolution in Digital HealthLarry Smarr
2014.01.22
Calit2 Director Larry Smarr speaks as part of the Pensacola Evening Lecture Series, organized by the Florida Institute for Human and Machine Cognition, in Pensacola, FL.
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...Larry Smarr
Invited Presentation Microbiology and the Microbiome and the Implications for Human Health Analytic, Life Science & Diagnostic Association (ALDA) 2016 Senior Management Conference
Half Moon Bay, CA
October 3, 2016
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step FurtherLarry Smarr
Calit2 Director Larry Smarr gives the closing keynote address to the 2nd annual Learning Conference on Integrated Delivery Systems in San Diego on May 7, 2014.
Hacking for Healing at SXSW InteractiveDrBonnie360
Content and Visual Design by Tiffany Simms
Do you know why you should take steps to get healthy when you already think you are healthy?
DrBonnie360 brings together Linda Avey (We Are Curious Inc.), Poonacha Machaiah (JIYO), and Nicole Guthrie (HopeLab), to present you with your #HacktoHeal.
With Chronic Disease, especially autoimmune disease, slowly creeping up on us at an epidemic level, we can no longer ignore the importance of being healthy. The stage is set for personalized prevention. The science, research, data, digital health, and patients, are all ready for personalized prevention to become a reality.
We Are Curious, JIYO, and Hopelab bring SXSW the steps to finding and maintaining their optimal health.
The key to all this is finding the right feedback loops for each of you and maintaining balance.
2014.02.06
Calit2 Director Larry Smarr lecture to the Osher Lifelong Learning Institute as part of the Winter 2014 Qualcomm Institute lecture series for Osher.
In a speech for the Global Health Program at the Council on Foreign Relations in New York City, Calit2 director Larry Smarr addresses the issue of biological diversity and the importance of monitoring the microbiome.
Exploring the Dynamics of The Microbiome in Health and DiseaseLarry Smarr
Remote Invited Provocateur Lecture
2017 Innovation Lab on Quantitative Approaches to Biomedical Data Science:
Challenges in our Understanding of the Microbiome
San Diego, CA
June 19, 2017
Know Thyself: Quantifying Your Human Body and Its One Hundred Trillion MicrobesLarry Smarr
Understanding Cultures and Addressing Disparities in Society: Degrees of Health and Well-Being Public Lecture Series
University of California, San Diego
January 20, 2016
The Emerging Personalized Medicine Paradigm of Time-Series Tracking of Mind, ...Larry Smarr
Invited Zoom Remote Lecture
For Sara Gottfried, MD Personalized Medicine for Mental Health Course
Integrative Psychiatry Institute
Recorded June 28, 2022
Title: Sense of Taste
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
These simplified slides by Dr. Sidra Arshad present an overview of the non-respiratory functions of the respiratory tract.
Learning objectives:
1. Enlist the non-respiratory functions of the respiratory tract
2. Briefly explain how these functions are carried out
3. Discuss the significance of dead space
4. Differentiate between minute ventilation and alveolar ventilation
5. Describe the cough and sneeze reflexes
Study Resources:
1. Chapter 39, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 34, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 17, Human Physiology by Lauralee Sherwood, 9th edition
4. Non-respiratory functions of the lungs https://academic.oup.com/bjaed/article/13/3/98/278874
Prix Galien International 2024 Forum ProgramLevi Shapiro
June 20, 2024, Prix Galien International and Jerusalem Ethics Forum in ROME. Detailed agenda including panels:
- ADVANCES IN CARDIOLOGY: A NEW PARADIGM IS COMING
- WOMEN’S HEALTH: FERTILITY PRESERVATION
- WHAT’S NEW IN THE TREATMENT OF INFECTIOUS,
ONCOLOGICAL AND INFLAMMATORY SKIN DISEASES?
- ARTIFICIAL INTELLIGENCE AND ETHICS
- GENE THERAPY
- BEYOND BORDERS: GLOBAL INITIATIVES FOR DEMOCRATIZING LIFE SCIENCE TECHNOLOGIES AND PROMOTING ACCESS TO HEALTHCARE
- ETHICAL CHALLENGES IN LIFE SCIENCES
- Prix Galien International Awards Ceremony
These lecture slides, by Dr Sidra Arshad, offer a quick overview of physiological basis of a normal electrocardiogram.
Learning objectives:
1. Define an electrocardiogram (ECG) and electrocardiography
2. Describe how dipoles generated by the heart produce the waveforms of the ECG
3. Describe the components of a normal electrocardiogram of a typical bipolar leads (limb II)
4. Differentiate between intervals and segments
5. Enlist some common indications for obtaining an ECG
Study Resources:
1. Chapter 11, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 9, Human Physiology - From Cells to Systems, Lauralee Sherwood, 9th edition
3. Chapter 29, Ganong’s Review of Medical Physiology, 26th edition
4. Electrocardiogram, StatPearls - https://www.ncbi.nlm.nih.gov/books/NBK549803/
5. ECG in Medical Practice by ABM Abdullah, 4th edition
6. ECG Basics, http://www.nataliescasebook.com/tag/e-c-g-basics
Pulmonary Thromboembolism - etilogy, types, medical- Surgical and nursing man...VarunMahajani
Disruption of blood supply to lung alveoli due to blockage of one or more pulmonary blood vessels is called as Pulmonary thromboembolism. In this presentation we will discuss its causes, types and its management in depth.
- Video recording of this lecture in English language: https://youtu.be/lK81BzxMqdo
- Video recording of this lecture in Arabic language: https://youtu.be/Ve4P0COk9OI
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
Lung Cancer: Artificial Intelligence, Synergetics, Complex System Analysis, S...Oleg Kshivets
RESULTS: Overall life span (LS) was 2252.1±1742.5 days and cumulative 5-year survival (5YS) reached 73.2%, 10 years – 64.8%, 20 years – 42.5%. 513 LCP lived more than 5 years (LS=3124.6±1525.6 days), 148 LCP – more than 10 years (LS=5054.4±1504.1 days).199 LCP died because of LC (LS=562.7±374.5 days). 5YS of LCP after bi/lobectomies was significantly superior in comparison with LCP after pneumonectomies (78.1% vs.63.7%, P=0.00001 by log-rank test). AT significantly improved 5YS (66.3% vs. 34.8%) (P=0.00000 by log-rank test) only for LCP with N1-2. Cox modeling displayed that 5YS of LCP significantly depended on: phase transition (PT) early-invasive LC in terms of synergetics, PT N0—N12, cell ratio factors (ratio between cancer cells- CC and blood cells subpopulations), G1-3, histology, glucose, AT, blood cell circuit, prothrombin index, heparin tolerance, recalcification time (P=0.000-0.038). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and PT early-invasive LC (rank=1), PT N0—N12 (rank=2), thrombocytes/CC (3), erythrocytes/CC (4), eosinophils/CC (5), healthy cells/CC (6), lymphocytes/CC (7), segmented neutrophils/CC (8), stick neutrophils/CC (9), monocytes/CC (10); leucocytes/CC (11). Correct prediction of 5YS was 100% by neural networks computing (area under ROC curve=1.0; error=0.0).
CONCLUSIONS: 5YS of LCP after radical procedures significantly depended on: 1) PT early-invasive cancer; 2) PT N0--N12; 3) cell ratio factors; 4) blood cell circuit; 5) biochemical factors; 6) hemostasis system; 7) AT; 8) LC characteristics; 9) LC cell dynamics; 10) surgery type: lobectomy/pneumonectomy; 11) anthropometric data. Optimal diagnosis and treatment strategies for LC are: 1) screening and early detection of LC; 2) availability of experienced thoracic surgeons because of complexity of radical procedures; 3) aggressive en block surgery and adequate lymph node dissection for completeness; 4) precise prediction; 5) adjuvant chemoimmunoradiotherapy for LCP with unfavorable prognosis.
ARTIFICIAL INTELLIGENCE IN HEALTHCARE.pdfAnujkumaranit
Artificial intelligence (AI) refers to the simulation of human intelligence processes by machines, especially computer systems. It encompasses tasks such as learning, reasoning, problem-solving, perception, and language understanding. AI technologies are revolutionizing various fields, from healthcare to finance, by enabling machines to perform tasks that typically require human intelligence.
Ozempic: Preoperative Management of Patients on GLP-1 Receptor Agonists Saeid Safari
Preoperative Management of Patients on GLP-1 Receptor Agonists like Ozempic and Semiglutide
ASA GUIDELINE
NYSORA Guideline
2 Case Reports of Gastric Ultrasound
1. “The Digital Transformation
of Healthcare”
Guest Lecture
Pharmacy Informatics 2014
University of California San Diego
June 2, 2014
Dr. Larry Smarr
Director, California Institute for Telecommunications and Information Technology
Harry E. Gruber Professor,
Dept. of Computer Science and Engineering
Jacobs School of Engineering, UCSD
http://lsmarr.calit2.net 1
2. The Vision of Digitally Enabled Genomic Medicine
is an Emerging Reality
2
July/August 2011 February 2012
3. The Emergence of P4 Medicine --
Predictive, Preventive, Personalized, Participatory
Converging Megatrends
Driving the Transformation of Healthcare for Patients
Systems Biology &
Systems Medicine
Consumer-Driven
Social Networks
P4
MEDICINE
Digital Revolution
Big Data
Source: Lee Hood, ISB
4. 100 Pioneer Wellness Project:
Started March 2014 –I Am One of The 100
Source:
Lee Hood, ISB
5. By Measuring the State of My Body and “Tuning” It
Using Nutrition and Exercise, I Became Healthier
2000
Age
41
2010
Age
61
1999
1989
Age
51
1999
How Did I Get Started? I Arrived in La Jolla in 2000
and Decided to Move Against the Obesity Epidemic
I Reversed My Body’s Decline By
Quantifying and Altering Nutrition and Exercise
http://lsmarr.calit2.net/repository/LS_reading_recommendations_FiRe_2011.pdf
7. Quantifying My Sleep Pattern Using a Zeo -
Increased My Average to 8 Hours/Night
REM is Normally 20% of Sleep
Mine is Between 45-65% of Sleep
An Infant Typically
Has 50% REM
Stroke risk increased by sleeping less than six hours a night
-M. Ruiter, Sleep 2012
9. Visualizing Time Series of
150 LS Blood and Stool Variables, Each Over 5-10 Years
Calit2 64 megapixel VROOM
10. Only One of My Blood Measurements
Was Far Out of Range--Indicating Chronic Inflammation
Normal Range
<1 mg/L
Normal
27x Upper Limit
Episodic Peaks in Inflammation
Followed by Spontaneous Drops
Complex Reactive Protein (CRP) is a Blood Biomarker
for Detecting Presence of Inflammation
11. But by Using Stool Analysis Time Series, I Discovered
I Had Oscillating Immune Variables Far Above Normal
Normal Range
<7.3 µg/mL
124x Upper Limit
Lactoferrin is a Protein Shed from Neutrophils -
An Immune System Antibacterial that Sequesters Iron
Typical
Lactoferrin
Value for
Active
IBD
13. Descending Colon
Sigmoid Colon
Threading Iliac Arteries
Major Kink
Confirming the IBD (Crohn’s) Hypothesis:
Finding the “Smoking Gun” with MRI Imaging
I Obtained the MRI Slices
From UCSD Medical Services
and Converted to Interactive 3D
Working With
Calit2 Staff & DeskVOX Software
Transverse Colon
Liver
Small Intestine
Diseased Sigmoid Colon
Cross Section
MRI Jan 2012
14. Why Did I Have an Autoimmune Disease like IBD?
Despite decades of research,
the etiology of Crohn's disease
remains unknown.
Its pathogenesis may involve
a complex interplay between
host genetics,
immune dysfunction,
and microbial or environmental factors.
--The Role of Microbes in Crohn's Disease
Paul B. Eckburg & David A. Relman
Clin Infect Dis. 44:256-262 (2007)
So I Set Out to Quantify All Three!
15. The Cost of Sequencing a Megabase of DNA
Has Fallen Over 10,000x in the Last Ten Years!
This Has Enabled Sequencing of
Both Human and Microbial Genomes
16. I Wondered if Crohn’s is an Autoimmune Disease,
Did I Have a Personal Genomic Polymorphism?
From www.23andme.com
SNPs Associated with CD
Polymorphism in
Interleukin-23 Receptor Gene
— 80% Higher Risk
of Pro-inflammatory
Immune Response
NOD2
ATG16L1
IRGM
I am Now an Advisor
on the
23andme IBD Project
19. Treating the Human Superorganism:
Your Body Has Ten Microbes for Every Human Cell!
Nature Reviews
Microbiology
v.9, p. 279 (2011)
20. To Map Out the Dynamics of My Microbiome Ecology
I Partnered with the J. Craig Venter Institute
• JCVI Did Metagenomic
Sequencing on Seven of
My Stool Samples
Over 1.5 Years
• Sequencing on
Illumina HiSeq 2000
– Generated 200 Million
100bp Reads
• JCVI Lab Manager,
Genomic Medicine
– Manolito Torralba
• IRB PI Karen Nelson
– President JCVI
Illumina HiSeq 2000 at JCVI
Manolito Torralba, JCVI Karen Nelson, JCVI
21. We Downloaded Additional Gut Microbiomes
from NIH HMP For Comparative Analysis
5 Ileal Crohn’s Patients,
3 Points in Time
2 Ulcerative Colitis Patients,
6 Points in Time
“Healthy” Individuals
From Sequences to Bacterial Species Relative Abundance
Required 25 CPU-Years at San Diego Supercomputer Center
Source: Jerry Sheehan, Calit2
Weizhong Li, Sitao Wu, CRBS, UCSD
Total of 27 Billion Reads
Or 2.7 Trillion Bases
IBD Patients
250 Subjects
1 Point in Time
Larry Smarr
6 Points in Time
22. We Found Major Shifts in Microbial Ecology
Between Healthy and Two Forms of IBD
Collapse of
Bacteroidetes
Explosion of
Proteobacteria On the IBD Spectrum
23. Tracking How 1 Month Antibiotic, 2 Months Prednisone Therapy
Alters the Gut Microbial Ecology
Reduced 45x
Reduced 90x
Therapy Greatly Reduced Two Phyla,
But Massive Reduction in Bacteroidetes
And Large % Proteobacteria Remain
Small Changes
With No Therapy
How Does One Get Back
to a “Healthy” Gut Microbiome?
24. Comparing Changes in Gut Microbiome Ecology with
Oscillations of the Innate and Adaptive Immune System
Normal
Innate Immune System
Normal
Adaptive Immune System
Time Points of
Metagenomic
Sequencing
of LS Stool Samples
Therapy: 1 Month Antibiotics
+2 Month Prednisone
LS Data from Yourfuturehealth.com Stool Tests
25. Time Series Reveals Autoimmune Dynamics
of Gut Microbiome by Phyla
Therapy
Six Metagenomic Time Samples Over 16 Months
27. Inexpensive 16S Time Series of Microbiome
Now Possible Through Ubiome
Data source: LS (Yellow Lines Stool Samples);
Sequencing and Analysis Ubiome
28. From War to Gardening:
New Therapeutical Tools for Managing the Microbiome
“I would like to lose the language of warfare,”
said Julie Segre, a senior investigator at
the National Human Genome Research Institute.
”It does a disservice to all the bacteria
that have co-evolved with us
and are maintaining the health of our bodies.”
29. Evidence for the Efficacy of Probiotics is IBD is Mixed -
More Clinical Research Needed
“...there is virtually no evidence of probiotic efficacy in Crohn’s disease.”
30. From the Single “Bad” Microbe Medical Target
to the Microbiome Ecology Paradigm
Sci Transl Med 4, 137rv5 (2012);
Science 336, 1255 (2012)
Problem of Alternative Stable States
In Ecological System Dynamics
31. Microbiome Transfer
May Be a Radical New Treatment for IBD
www.gihealthfoundation.org/reuters/articles.cfm?article=20111102drgd011
Dr. Alexander Khoruts, NY Times
www.nytimes.com/2010/07/13/science/13micro.html
Not FDA Approved Yet;
Increasing Number of Doctors Performing Procedure;
Clinical Trials Under Way;
Encouraging Results…
Procedures
Starting With
Natural Microbiome
Next Steps:
Create
Synthetic Microbiomes
Tuned to the Patient
See
Microbiome 1:3 (2013)
32. Next Decade Will See New Microbiome
“Gardening Tools”
Journal of Nanotechnology (2012)
August 7, 2012
33. The Disruption of Consumer Health Data Gathering
Is Growing Rapidly
Blood Variable Time Series Stool Variable Time Series
MicrobiomeTime SeriesHuman Genetic Variations
34. Thanks to Our Great Team!
UCSD Metagenomics Team
Weizhong Li
Sitao Wu
Calit2@UCSD
Future Patient Team
Jerry Sheehan
Tom DeFanti
Kevin Patrick
Jurgen Schulze
Andrew Prudhomme
Philip Weber
Fred Raab
Joe Keefe
Ernesto Ramirez
JCVI Team
Karen Nelson
Shibu Yooseph
Manolito Torralba
SDSC Team
Michael Norman
Mahidhar Tatineni
Robert Sinkovits
UCSD Health Sciences Team
William J. Sandborn
Elisabeth Evans
John Chang
Brigid Boland
David Brenner