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.
Stability in Health vs. Abrupt Changes in Disease in the Human Gut Microbiome...Larry Smarr
The document summarizes research on analyzing changes in human gut microbiome composition over time using 16S rRNA gene sequencing and the UniFrac metric. It presents findings that:
1) A healthy person's gut microbiome composition generally remains stable over periods of 60 days based on samples from multiple body sites.
2) In contrast, for people with C. difficile infections, their gut microbiome composition can abruptly shift to a healthy state within days after a fecal microbiota transplant from a healthy donor.
3) Analysis of one individual's gut microbiome samples over 3.5 years found the composition abruptly shifted between two distinct stable states that correlated with changes in symptoms and weight, before and after a
Linking Phenotype Changes to Internal/External Longitudinal Time Series in a ...Larry Smarr
This document summarizes Dr. Larry Smarr's presentation on quantifying physiological data from his own body over the past decade. Some key points:
- Smarr has gathered longitudinal time series data on over 200 biomarkers and microbiome samples to study phenotype changes from his autoimmune disease.
- Sensors have tracked daily metrics like weight, activity levels, and symptoms, revealing oscillations and episodes of inflammation.
- Imaging and biomarker analysis identified the specific location and nature of his Crohn's disease.
- Analysis of his microbiome samples over time uncovered a shift in microbial ecology that correlated with changes in drugs and symptoms.
- Expanding this type of personalized, quantitative approach could transform medicine by deeply characterizing individuals
Dynamics of Your Gut Microbiome in Health and DiseaseLarry Smarr
This document summarizes a presentation by Dr. Larry Smarr on the dynamics of the gut microbiome in health and disease. It discusses how the gut microbiome contains hundreds of microbial species that vary significantly between healthy and diseased states. Dr. Smarr has tracked his own gut microbiome and biomarkers over time, discovering an autoimmune disease. He is now collaborating on a project combining deep metagenomic sequencing and supercomputing to map differences in the gut microbiome between healthy and inflammatory bowel disease patients.
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...Larry Smarr
This document provides a 3-sentence summary of a presentation by Dr. Larry Smarr on tracking changes in his immune biomarkers and gut microbiome in relation to inflammation, Crohn's disease, and colon cancer:
Over the past decade, Dr. Smarr has quantified over a billion data points on his body through measures like blood tests, MRI/CT scans, and analysis of his gut microbiome, discovering through this data that he has episodic chronic inflammation and Crohn's disease affecting his colon. By comparing his biomarkers and symptoms over time and visualizing his microbiome ecology, Dr. Smarr has gained insights into the dynamics and invasiveness of species in his gut microbiome as it relates to his autoimmune
Stability in Health vs. Abrupt Changes in Disease in the Human Gut Microbiome...Larry Smarr
The document summarizes research on analyzing changes in human gut microbiome composition over time using 16S rRNA gene sequencing and the UniFrac metric. It presents findings that:
1) A healthy person's gut microbiome composition generally remains stable over periods of 60 days based on samples from multiple body sites.
2) In contrast, for people with C. difficile infections, their gut microbiome composition can abruptly shift to a healthy state within days after a fecal microbiota transplant from a healthy donor.
3) Analysis of one individual's gut microbiome samples over 3.5 years found the composition abruptly shifted between two distinct stable states that correlated with changes in symptoms and weight, before and after a
Linking Phenotype Changes to Internal/External Longitudinal Time Series in a ...Larry Smarr
This document summarizes Dr. Larry Smarr's presentation on quantifying physiological data from his own body over the past decade. Some key points:
- Smarr has gathered longitudinal time series data on over 200 biomarkers and microbiome samples to study phenotype changes from his autoimmune disease.
- Sensors have tracked daily metrics like weight, activity levels, and symptoms, revealing oscillations and episodes of inflammation.
- Imaging and biomarker analysis identified the specific location and nature of his Crohn's disease.
- Analysis of his microbiome samples over time uncovered a shift in microbial ecology that correlated with changes in drugs and symptoms.
- Expanding this type of personalized, quantitative approach could transform medicine by deeply characterizing individuals
Dynamics of Your Gut Microbiome in Health and DiseaseLarry Smarr
This document summarizes a presentation by Dr. Larry Smarr on the dynamics of the gut microbiome in health and disease. It discusses how the gut microbiome contains hundreds of microbial species that vary significantly between healthy and diseased states. Dr. Smarr has tracked his own gut microbiome and biomarkers over time, discovering an autoimmune disease. He is now collaborating on a project combining deep metagenomic sequencing and supercomputing to map differences in the gut microbiome between healthy and inflammatory bowel disease patients.
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...Larry Smarr
This document provides a 3-sentence summary of a presentation by Dr. Larry Smarr on tracking changes in his immune biomarkers and gut microbiome in relation to inflammation, Crohn's disease, and colon cancer:
Over the past decade, Dr. Smarr has quantified over a billion data points on his body through measures like blood tests, MRI/CT scans, and analysis of his gut microbiome, discovering through this data that he has episodic chronic inflammation and Crohn's disease affecting his colon. By comparing his biomarkers and symptoms over time and visualizing his microbiome ecology, Dr. Smarr has gained insights into the dynamics and invasiveness of species in his gut microbiome as it relates to his autoimmune
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Analysis of the speaker's own gut microbiome over time revealed changes in bacterial phyla between healthy and inflammatory bowel disease states. Collecting biomarkers from the speaker's body over years showed oscillations linked to gut microbes and immune response. Ongoing research aims to better understand dynamics of the human immune system and gut microbiome.
Machine Learning Opportunities in the Explosion of Personalized Precision Med...Larry Smarr
This document summarizes a presentation given by Dr. Larry Smarr on machine learning opportunities in personalized precision medicine using massive datasets from individuals. Some key points:
- Smarr has tracked over 100 of his own blood biomarkers and microbiome over time, revealing health issues like chronic inflammation.
- Analysis of Smarr's microbiome alongside others revealed major shifts between healthy and disease states that can be classified using machine learning.
- Further analysis of microbial proteins identified which were over or under abundant in disease, helping characterize Smarr's own condition.
- Smarr's microbiome appeared to undergo an abrupt shift between two stable states correlated with a change in symptoms and drug therapy.
Large Memory High Performance ComputingEnables Comparison Across Human Gut M...Larry Smarr
This document summarizes a talk about research analyzing gut microbiome data from patients with autoimmune diseases and healthy subjects. The research used large memory high performance computing on the Gordon supercomputer to analyze over 1.2 trillion DNA bases of metagenomic sequencing data from the gut microbiomes. Analysis found major shifts in microbial ecology between healthy subjects and those with Crohn's disease or ulcerative colitis. Therapies for one subject's Crohn's disease reduced certain phyla but others remained at high levels. The research aims to develop noninvasive microbial diagnostics and new therapeutic tools for managing the microbiome.
Tracking Immune Biomarkers and the Human Gut Microbiome: Inflammation, Croh...Larry Smarr
Larry Smarr presented on tracking immune biomarkers and the human gut microbiome in relation to inflammation, Crohn's disease, and colon cancer. He turned his own body into a "genomic observatory" by tracking over 100 of his own blood and stool biomarkers and sequencing his gut microbiome multiple times. His research found high levels of inflammation and an abundance of Fusobacteria in his microbiome when inflammation was highest. Following antibiotic and steroid therapy, inflammation and Fusobacteria were greatly reduced. This integrated personal omics approach provides insights into the links between inflammation, gut microbes, and colon cancer risk.
Discovering the 100 Trillion Bacteria Living Within Each of UsLarry Smarr
This document provides a summary of a lecture on the human microbiome given by Dr. Larry Smarr. Some key points:
- The human microbiome refers to the trillions of bacteria that live within the human body. Each person contains 100 trillion bacteria, outnumbering human cells.
- Research into the microbiome is a rapidly growing field that provides insights into health and disease. The microbiome plays a role in processes like drug metabolism and immunity.
- The microbiome is established early in life and influenced by factors like birth method and antibiotic use in the first years. This early development can impact future health.
- Microbiome imbalances are linked to diseases like inflammatory bowel disease. New treatments are
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.
The Human Gut Microbiome: A New Diagnostic for Disease?Larry Smarr
The document summarizes research on analyzing human gut microbiomes to better understand health and disease. It describes how the researchers used 25 CPU-years of computing and analyzed over 2.7 trillion DNA bases to map and compare the microbial ecology between healthy individuals and those with inflammatory bowel disease. Their analyses revealed major differences in microbial phyla between healthy and diseased states. Machine learning techniques discovered specific protein families that differentiate disease subtypes and healthy cohorts. The researchers aim to develop a novel microbiome-based diagnostic for disease by continuing to study gut microbiome dynamics using larger datasets and populations over time.
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism BodyLarry Smarr
The document summarizes a talk given by Dr. Larry Smarr on his research tracking extensive health data on himself over many years. Some key points:
1) Smarr collected over a billion data points defining his body, including DNA sequencing, medical images, and daily biomarkers, revealing episodic inflammation related to his Crohn's disease.
2) Analysis of his gut microbiome via metagenomic sequencing showed many typically abundant bacterial species were severely depleted compared to healthy individuals.
3) Tracking changes over time demonstrated the coupled dynamics of his immune system and gut microbiome in response to therapies, similar to ecological models of invasive species dominating after natives are disturbed.
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...Larry Smarr
This document summarizes a lecture on inflammation, the gut microbiome, bacteriophages, and the initiation of colorectal cancer. The lecturer discusses his personal experience with Crohn's disease and extensive self-monitoring. Analysis of his microbiome data over time revealed shifts correlated with inflammation levels. Certain bacteria like Fusobacterium nucleatum and E. coli were found at highest levels during peak inflammation. The lecturer's genetic analysis revealed SNPs linked to autoimmune disease that may have predisposed him to Crohn's. The lecture explores the role of the microbiome in mediating inflammation and cancer initiation in the gut.
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.
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
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.
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
The Human Microbiome, Supercomputers,and the Advancement of MedicineLarry Smarr
The keynote presentation discusses the importance of the human microbiome and how understanding its dynamics can advance medicine. It notes that the human microbiome contains tens of trillions of microbial cells and hundreds of times as many genes as human cells. Understanding the microbiome as an ecology rather than focusing on single pathogens is crucial. The presentation describes research tracking one person's microbiome and biomarkers over time, finding shifts between healthy and diseased states. It advocates developing tools to manage the microbiome and new therapies like fecal transplants. National initiatives now recognize the microbiome's importance in health and disease.
Finding the Patterns in the Big Data From Human Microbiome EcologyLarry Smarr
This document summarizes a talk on analyzing human microbiome data to better understand health and disease. It discusses how sequencing and supercomputing is used to map microbial ecology in hundreds of people. Advanced analytics tools like Ayasdi are helping discover patterns separating healthy from disease states like inflammatory bowel disease. Future goals include applying these techniques to larger datasets and using molecular networks to better understand disease development at the genetic and protein level.
Machine Learning in Healthcare by Mehrdad YazdaniData Con LA
Abstract:- Using Machine Learning to Identify Major Shifts in Human Gut MicrobiomeProtein Family Abundance in Disease Inflammatory Bowel Disease (IBD) is an autoimmune condition that is observed to be associated with major alterations in the gut microbiome taxonomic composition. Here we classify major changes in microbiome protein family abundances between healthy subjects and IBD patients. We use machine learning to analyze results obtained previously from computing relative abundance of ~10,000 KEGG orthologous protein families in the gut microbiome of a set of healthy individuals and IBD patients. We develop a machine learning pipeline, involving the Kolomogorv-Smirnov test, to identify the 100 most statistically significant entries in the KEGG database. Then we use these 100 as a training set for a Random Forest classifier to determine ~5% the KEGGs which are best at separating disease and healthy states. Lastly, we developed a Natural Language Processing classifier of the KEGG description files to predict KEGG relative over- or under- abundance. As we expand our analysis from 10,000 KEGG protein families to one million proteins identified in the gut microbiome, scalable methods for quickly identifying such anomalies between health and disease states will be increasingly valuable for biological interpretation of sequence data.
How Studying Astrophysics and Coral Reefs Enabled Me to Become an Empowered,...Larry Smarr
This document summarizes Dr. Larry Smarr's talk on how his background in astrophysics and studying coral reefs enabled him to become an empowered patient by closely monitoring his gut microbiome. Some key findings from analyzing his stool samples over time included discovering oscillations in his immune system, invasions of opportunistic bacteria after disruptions, and evidence of chaos theory at play. Larger studies are now analyzing data from many individuals to better understand the dynamics of the human immune and microbiome systems.
2014.02.06
Calit2 Director Larry Smarr invited short talk to a workshop on "Enriching Human Life and Society," one of the planned themes for the UCSD Strategic Plan to be adopted in 2014.
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Analysis of the speaker's own gut microbiome over time revealed changes in bacterial phyla between healthy and inflammatory bowel disease states. Collecting biomarkers from the speaker's body over years showed oscillations linked to gut microbes and immune response. Ongoing research aims to better understand dynamics of the human immune system and gut microbiome.
Machine Learning Opportunities in the Explosion of Personalized Precision Med...Larry Smarr
This document summarizes a presentation given by Dr. Larry Smarr on machine learning opportunities in personalized precision medicine using massive datasets from individuals. Some key points:
- Smarr has tracked over 100 of his own blood biomarkers and microbiome over time, revealing health issues like chronic inflammation.
- Analysis of Smarr's microbiome alongside others revealed major shifts between healthy and disease states that can be classified using machine learning.
- Further analysis of microbial proteins identified which were over or under abundant in disease, helping characterize Smarr's own condition.
- Smarr's microbiome appeared to undergo an abrupt shift between two stable states correlated with a change in symptoms and drug therapy.
Large Memory High Performance ComputingEnables Comparison Across Human Gut M...Larry Smarr
This document summarizes a talk about research analyzing gut microbiome data from patients with autoimmune diseases and healthy subjects. The research used large memory high performance computing on the Gordon supercomputer to analyze over 1.2 trillion DNA bases of metagenomic sequencing data from the gut microbiomes. Analysis found major shifts in microbial ecology between healthy subjects and those with Crohn's disease or ulcerative colitis. Therapies for one subject's Crohn's disease reduced certain phyla but others remained at high levels. The research aims to develop noninvasive microbial diagnostics and new therapeutic tools for managing the microbiome.
Tracking Immune Biomarkers and the Human Gut Microbiome: Inflammation, Croh...Larry Smarr
Larry Smarr presented on tracking immune biomarkers and the human gut microbiome in relation to inflammation, Crohn's disease, and colon cancer. He turned his own body into a "genomic observatory" by tracking over 100 of his own blood and stool biomarkers and sequencing his gut microbiome multiple times. His research found high levels of inflammation and an abundance of Fusobacteria in his microbiome when inflammation was highest. Following antibiotic and steroid therapy, inflammation and Fusobacteria were greatly reduced. This integrated personal omics approach provides insights into the links between inflammation, gut microbes, and colon cancer risk.
Discovering the 100 Trillion Bacteria Living Within Each of UsLarry Smarr
This document provides a summary of a lecture on the human microbiome given by Dr. Larry Smarr. Some key points:
- The human microbiome refers to the trillions of bacteria that live within the human body. Each person contains 100 trillion bacteria, outnumbering human cells.
- Research into the microbiome is a rapidly growing field that provides insights into health and disease. The microbiome plays a role in processes like drug metabolism and immunity.
- The microbiome is established early in life and influenced by factors like birth method and antibiotic use in the first years. This early development can impact future health.
- Microbiome imbalances are linked to diseases like inflammatory bowel disease. New treatments are
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.
The Human Gut Microbiome: A New Diagnostic for Disease?Larry Smarr
The document summarizes research on analyzing human gut microbiomes to better understand health and disease. It describes how the researchers used 25 CPU-years of computing and analyzed over 2.7 trillion DNA bases to map and compare the microbial ecology between healthy individuals and those with inflammatory bowel disease. Their analyses revealed major differences in microbial phyla between healthy and diseased states. Machine learning techniques discovered specific protein families that differentiate disease subtypes and healthy cohorts. The researchers aim to develop a novel microbiome-based diagnostic for disease by continuing to study gut microbiome dynamics using larger datasets and populations over time.
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism BodyLarry Smarr
The document summarizes a talk given by Dr. Larry Smarr on his research tracking extensive health data on himself over many years. Some key points:
1) Smarr collected over a billion data points defining his body, including DNA sequencing, medical images, and daily biomarkers, revealing episodic inflammation related to his Crohn's disease.
2) Analysis of his gut microbiome via metagenomic sequencing showed many typically abundant bacterial species were severely depleted compared to healthy individuals.
3) Tracking changes over time demonstrated the coupled dynamics of his immune system and gut microbiome in response to therapies, similar to ecological models of invasive species dominating after natives are disturbed.
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...Larry Smarr
This document summarizes a lecture on inflammation, the gut microbiome, bacteriophages, and the initiation of colorectal cancer. The lecturer discusses his personal experience with Crohn's disease and extensive self-monitoring. Analysis of his microbiome data over time revealed shifts correlated with inflammation levels. Certain bacteria like Fusobacterium nucleatum and E. coli were found at highest levels during peak inflammation. The lecturer's genetic analysis revealed SNPs linked to autoimmune disease that may have predisposed him to Crohn's. The lecture explores the role of the microbiome in mediating inflammation and cancer initiation in the gut.
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.
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
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.
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
The Human Microbiome, Supercomputers,and the Advancement of MedicineLarry Smarr
The keynote presentation discusses the importance of the human microbiome and how understanding its dynamics can advance medicine. It notes that the human microbiome contains tens of trillions of microbial cells and hundreds of times as many genes as human cells. Understanding the microbiome as an ecology rather than focusing on single pathogens is crucial. The presentation describes research tracking one person's microbiome and biomarkers over time, finding shifts between healthy and diseased states. It advocates developing tools to manage the microbiome and new therapies like fecal transplants. National initiatives now recognize the microbiome's importance in health and disease.
Finding the Patterns in the Big Data From Human Microbiome EcologyLarry Smarr
This document summarizes a talk on analyzing human microbiome data to better understand health and disease. It discusses how sequencing and supercomputing is used to map microbial ecology in hundreds of people. Advanced analytics tools like Ayasdi are helping discover patterns separating healthy from disease states like inflammatory bowel disease. Future goals include applying these techniques to larger datasets and using molecular networks to better understand disease development at the genetic and protein level.
Machine Learning in Healthcare by Mehrdad YazdaniData Con LA
Abstract:- Using Machine Learning to Identify Major Shifts in Human Gut MicrobiomeProtein Family Abundance in Disease Inflammatory Bowel Disease (IBD) is an autoimmune condition that is observed to be associated with major alterations in the gut microbiome taxonomic composition. Here we classify major changes in microbiome protein family abundances between healthy subjects and IBD patients. We use machine learning to analyze results obtained previously from computing relative abundance of ~10,000 KEGG orthologous protein families in the gut microbiome of a set of healthy individuals and IBD patients. We develop a machine learning pipeline, involving the Kolomogorv-Smirnov test, to identify the 100 most statistically significant entries in the KEGG database. Then we use these 100 as a training set for a Random Forest classifier to determine ~5% the KEGGs which are best at separating disease and healthy states. Lastly, we developed a Natural Language Processing classifier of the KEGG description files to predict KEGG relative over- or under- abundance. As we expand our analysis from 10,000 KEGG protein families to one million proteins identified in the gut microbiome, scalable methods for quickly identifying such anomalies between health and disease states will be increasingly valuable for biological interpretation of sequence data.
How Studying Astrophysics and Coral Reefs Enabled Me to Become an Empowered,...Larry Smarr
This document summarizes Dr. Larry Smarr's talk on how his background in astrophysics and studying coral reefs enabled him to become an empowered patient by closely monitoring his gut microbiome. Some key findings from analyzing his stool samples over time included discovering oscillations in his immune system, invasions of opportunistic bacteria after disruptions, and evidence of chaos theory at play. Larger studies are now analyzing data from many individuals to better understand the dynamics of the human immune and microbiome systems.
2014.02.06
Calit2 Director Larry Smarr invited short talk to a workshop on "Enriching Human Life and Society," one of the planned themes for the UCSD Strategic Plan to be adopted in 2014.
The Quantified Self Movement: Technologies Revolutionizing Health and FitnessLarry Smarr
2014.01.15
Calit2 Director Larry Smarr talks to the MIT Enterprise Forum San Diego about the self-monitoring revolution and its impact on technologies for health and fitness.
Discovering Yourself with Computational BioinformaticsLarry Smarr
This document summarizes a presentation given by Dr. Larry Smarr on his self-experimentation with quantifying biomarkers and 'omics data to gain insights into his health. Smarr has tracked over 100 blood biomarkers, sequenced his microbiome, and analyzed over 1 million SNPs from his genome. Computational analysis of this data helped diagnose Smarr with Crohn's disease and revealed shifts in his microbiome from healthy to diseased states. Smarr advocates integrating multi-omics data to achieve predictive, preventative and participatory medicine.
Deciphering the Dynamic Coupling of the Human Immune System and the Gut Micro...Larry Smarr
This document discusses Dr. Larry Smarr's research into understanding the relationship between the human immune system and gut microbiome in Crohn's disease. Dr. Smarr sequenced his own genome to identify genetic polymorphisms associated with higher risk of Crohn's disease. He also conducted fine-time resolution sampling to study the distinct dynamics of the innate and adaptive immune system in health and disease. Additionally, he found major shifts in the gut microbiome between healthy individuals and those with two forms of inflammatory bowel disease.
A Systems Approachto Personalized MedicineLarry Smarr
A Systems Approach to Personalized Medicine
This talk discusses how one man used various omics technologies like genomics, metagenomics, metabolomics, and imaging to gain insights into his own health. Over a decade, he tracked over a billion data points about himself including his microbiome, genome, blood variables, and medical images. This led to the discovery that he had an inflammatory bowel disease. He then used multi-omics analyses and computing resources to study his condition and microbiome in detail over time. This is an example of a systems approach to personalized medicine.
Quantifying your Superorganism: Your Gut Microbiome and its Interactions with...Larry Smarr
This document summarizes a lecture given by Dr. Larry Smarr on quantifying one's gut microbiome and its interactions with the immune system. Dr. Smarr discussed how analyzing his own medical data over many years revealed he had an autoimmune disease like inflammatory bowel disease (IBD). By sequencing his microbiome, he found major shifts between healthy and IBD states, with collapses in some bacterial phyla and explosions in others. Dr. Smarr's therapy reduced two phyla greatly but massive reductions remained, leaving him "trapped" in an unfavorable microbial ecology. However, he is now able to track his microbiome over time using new technologies, giving him data and hope to improve his condition.
Four Disruptive Trends for the Next DecadeLarry Smarr
Four disruptive trends will shape the next decade: 1) Distributed software systems will drive disintermediation and disrupt industries like transportation and hospitality; 2) Networked virtual reality will allow for planetary-scale collaboration and remote viewing; 3) Climate change will require adaptation of infrastructure to become intelligent, secure, low-carbon and climate-resilient; 4) Brain-inspired computing utilizing massive data and exascale supercomputers will enable emulation of the human brain within a decade and usher in an era of cognitive technologies.
Using Dell’s HPC Cloud & Advanced Analytic Software to Discover Radical Chang...Larry Smarr
This document summarizes a talk given by Dr. Larry Smarr on how he used Dell's HPC Cloud and advanced analytics software to analyze over 300 human gut microbiome samples. He was able to discover distinct microbial signatures associated with health and different diseases like ulcerative colitis and Crohn's disease. Dell's analytics software effectively separated and classified the samples by health status and disease type using only a few key microbial species. This research could lead to new microbial diagnostics for inflammatory bowel diseases.
A California-Wide Cyberinfrastructure for Data-Intensive ResearchLarry Smarr
The document discusses creating a California-wide cyberinfrastructure for data-intensive research. It outlines efforts to connect all UC campuses and other research institutions across California with high-speed optical networks. This would create a "big data plane" to share large datasets. Several campuses have received NSF grants to upgrade their networks and implement Science DMZ architectures with 10-100Gbps connections to CENIC. Connecting these resources would provide researchers access to high-performance computing, large scientific instruments, and datasets. This would support collaborative big data science across disciplines like physics, climate modeling, genomics and microscopy.
The Pacific Research Platform (PRP) is a multi-institutional cyberinfrastructure project that connects researchers across California and beyond to share large datasets. It spans the 10 University of California campuses, major private research universities, supercomputer centers, and some out-of-state universities. Fifteen multi-campus research teams in fields like physics, astronomy, earth sciences, biomedicine, and multimedia will drive the technical needs of the PRP over five years. The goal is to create a "big data freeway" to allow high-speed sharing of data between research labs, supercomputers, and repositories across multiple networks without performance loss over long distances.
Introduction to the UCSD Division of Calit2Larry Smarr
Calit2 is a research institute at UC San Diego that focuses on digital transformation of fields like health, environment, and education through technologies like mobile phones, sensors, virtual/augmented reality, and high-performance computing networks. The director gave a tour of Calit2's facilities, which include laboratories for nanotechnology, digital media, and medical research using technologies like social mobile apps, environmental sensors on phones, human-robot interaction, and optical networks connecting instruments and storage. Calit2 works with affiliated academic units and industry partners to develop innovative applications and testbeds for areas like telemedicine, digital cinema, virtual reality displays, and telepresence.
An Integrated Science Cyberinfrastructure for Data-Intensive ResearchLarry Smarr
This document summarizes Dr. Larry Smarr's vision for an integrated science cyberinfrastructure to support data-intensive research. It discusses the exponential growth of digital data and need for dedicated high-bandwidth networks and data repositories. Specific examples are provided of initiatives at UCSD, regional optical networks connecting research institutions, and national projects like the Open Science Grid and Cancer Genomics Hub that are creating cyberinfrastructure to enable data-intensive scientific discovery.
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.
Capturing the Interactive Dynamics of the Human Host/Microbiome SystemLarry Smarr
1) Dr. Larry Smarr reported on results from a decade of self-quantification, including longitudinal measurements of his gut microbiome and over 100 biomarkers, to better understand the interactive dynamics of the human-microbiome system in health and disease.
2) Analysis found that Smarr's gut microbiome was unstable with high levels of E. coli, unlike healthy individuals, and computational analysis linked this dysbiosis to chronic inflammation identified in his biomarkers.
3) Smarr underwent robotic colon resection surgery in 2016, and analysis found his gut microbiome changed more dramatically after surgery than from colonoscopy or typical differences between individuals, eventually achieving a healthy post-surgical state.
Measuring the Human Brain-Gut Microbiome-Immune System Dynamics: a Big Data C...Larry Smarr
This document summarizes a talk given by Dr. Larry Smarr on measuring the human brain-gut microbiome-immune system dynamics and the challenges of analyzing big data related to these systems. It discusses how understanding the interactions between human genetics, behavior, and the human microbiome is important for understanding human health and disease. As an example, it details Dr. Smarr's own research into his Crohn's disease, analyzing his gut microbiome, immune markers, genetics, and symptoms over time. It shows how computational analysis of metagenomic sequencing data from many healthy and IBD patients can reveal differences in microbial ecology and gene families between health and disease states.
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Recent advances now allow sequencing these microbial genomes and analyzing massive datasets to map the dynamics of the immune-microbial system and its connection to disease states. A key focus is generating high-resolution time series data of the gut microbiome and immune variables from large cohorts to understand how they influence conditions like inflammatory bowel disease. There is potential to design gut microbes as sensors of disease states by programming them to detect specific conditions.
Using Supercomputers to Discover the 100 Trillion Bacteria Living Within Each...Larry Smarr
This document summarizes a talk given by Dr. Larry Smarr on using supercomputers to analyze the human microbiome. It discusses how next-generation sequencing and analysis of microbial DNA reveals major differences between healthy and diseased gut microbiomes. Computational analysis of Smarr's own microbiome time series, in addition to data from hundreds of individuals, provides insights into inflammatory bowel disease. Large supercomputers and visualization resources were crucial for processing and comparing petabytes of sequencing data to advance understanding of microbiome dynamics and their links to human health and disease.
Interactions of the Immune System with the Gut Microbiome in Inflammatory Bo...Larry Smarr
Larry Smarr presented on his research quantifying interactions between his immune system, gut microbiome, and genetics in relation to his diagnosis of Crohn's disease. Over many years, he collected over 150 biological variables from blood and stool samples, and obtained genomic and metagenomic sequencing. Analysis revealed periods of chronic inflammation correlated with shifts in bacterial abundance and invasive strains. Treatment with antibiotics and immunosuppressants reduced inflammation and allowed rare bacteria to decrease while more beneficial firms increased. The research aims to better understand coupled human-microbiome dynamics and how genetics may predispose individuals to conditions like inflammatory bowel disease.
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
The Systems Biology Dynamics of the Human Immune System and Gut MicrobiomeLarry Smarr
This document summarizes Dr. Larry Smarr's talk on modeling the human immune system and gut microbiome dynamics. It discusses how the growing diversity of gut bacteria after birth helps train the immune system. In health, constant feedback between the immune system and microbiome leads to homeostasis, but in diseases like Crohn's, this balance fails. The talk demonstrates this dysbiotic state using data from Dr. Smarr's own gut microbiome and biomarkers over five years. It reviews efforts to computationally model this important biological system.
The document summarizes a seminar given by Dr. Larry Smarr on supercomputing the human microbiome. Some key points:
- The human microbiome contains 100 trillion microorganisms and their DNA contains 300 times as many genes as human DNA.
- Dr. Smarr has been collecting extensive data from his own body over 7 years to study his personal microbiome and immune system interactions using high performance computing.
- Analyzing microbiome data requires massive computing resources, such as millions of core hours on supercomputers. This reveals details of microbial ecology and genetics in health and disease.
- Computational analysis of microbiome sequencing data from many subjects shows major shifts in microbial populations between healthy and
The document discusses supercomputing analysis of the human microbiome. It describes how the human body hosts 100 trillion microorganisms containing 300 times as many genes as human DNA. Dr. Smarr has been collecting extensive personal health data over 7 years, including microbiome samples, to study the coupled immune-microbial system. Analyzing this data requires elaborate software running on high performance computers. The analysis can compare individuals with diseases to healthy populations and track disease progression over time.
Using Supercomputers and Gene Sequencers to Discover Your Inner MicrobiomeLarry Smarr
This keynote talk discusses research using supercomputers and gene sequencing to study the human microbiome. The human microbiome contains 100 trillion microorganisms and their genes outnumber human genes 300 to 1. The speaker has been collecting data from his own body over 7 years to study his microbiome and immune system interactions. Collaborating researchers have sequenced his gut microbiome over time as well as samples from autoimmune disease patients. Supercomputers are needed to analyze the massive amount of sequencing data and reveal details of microbial ecology and genetics in health and disease. Studying the human microbiome will revolutionize medicine in the next decade.
From Me To We: Discovering the Trillions of Microorganisms That are a Part of UsLarry Smarr
The document summarizes a lecture about the human microbiome and its importance in health and disease. It discusses how sequencing DNA has revealed that the human body hosts trillions of microorganisms and that 99% of our genes are microbial. Understanding the microbiome is crucial for medicine as shifts in the microbial ecology can be linked to various diseases. The lecturer discusses his own efforts to track biomarkers and microbiome data over time, revealing how perturbations correlated with disease symptoms and weight changes. Precision approaches analyzing large cohorts will be needed to unravel microbiome dynamics in health and illness.
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.
Exploring Our Inner Universe Using Supercomputers and Gene SequencersLarry Smarr
This document summarizes a talk given by Dr. Larry Smarr on his research exploring the human microbiome using supercomputers and gene sequencers. He began by researching astrophysics but has recently applied those methods to study the microbes within the human body. Through deep genome sequencing of his own stool samples over time and large-scale computational analysis, he was able to map changes in his gut microbiome that provided insights into an undiagnosed autoimmune disease. His research demonstrates how quantitative analysis of the microbiome using advanced technologies can lead to new understandings of health and disease.
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My Remembrances of Mike Norman Over The Last 45 YearsLarry Smarr
Mike Norman has been a leader in computational astrophysics for over 45 years. Some of his influential work includes:
- Cosmic jet simulations in the early 1980s which helped explain phenomena from galactic centers.
- Pioneering the use of adaptive mesh refinement in the 1990s to achieve dynamic load balancing on supercomputers.
- Massive cosmology simulations in the late 2000s with over 100 trillion particles using thousands of processors across multiple supercomputing sites, producing petabytes of data.
- Developing end-to-end workflows in the 2000s to couple supercomputers, high-speed networks, and large visualization systems to enable real-time analysis of extremely large astrophysics simulations.
Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019Larry Smarr
Larry Smarr discusses quantifying his body and health over time through extensive self-tracking. He measures various biomarkers through regular blood tests and analyzes his gut microbiome by sequencing stool samples. This revealed issues like chronic inflammation and an unhealthy microbiome. Smarr then took steps like a restricted eating window and increasing plant diversity in his diet, which reversed metabolic syndrome issues and correlated with shifts in his microbiome ecology. His goal is to continue precisely measuring factors like toxins, hormones, gut permeability and food/supplement impacts to further optimize his health.
Panel: Reaching More Minority Serving InstitutionsLarry Smarr
This document discusses engaging more minority serving institutions (MSIs) in cyberinfrastructure development through regional networks. It provides data showing the importance of MSIs like historically black colleges and universities (HBCUs) in educating underrepresented minority students in STEM fields. Regional networks can help equalize opportunities by assisting MSIs in overcoming barriers to resources through training, networking infrastructure support, and helping institutions obtain necessary staffing and funding. Strategies mentioned include collaborating with MSIs on grants and addressing issues identified in surveys like lack of vision for data use beyond compliance. The goal is to broaden participation in STEAM fields by leveraging the success MSIs have shown in supporting underrepresented students.
Global Network Advancement Group - Next Generation Network-Integrated SystemsLarry Smarr
This document summarizes a presentation on global petascale to exascale workflows for data intensive sciences. It discusses a partnership convened by the GNA-G Data Intensive Sciences Working Group with the mission of meeting challenges faced by data-intensive science programs. Cornerstone concepts that will be demonstrated include integrated network and site resource management, model-driven frameworks for resource orchestration, end-to-end monitoring with machine learning-optimized data transfers, and integrating Qualcomm's GradientGraph with network services to optimize applications and science workflows.
Wireless FasterData and Distributed Open Compute Opportunities and (some) Us...Larry Smarr
This document discusses opportunities for ESnet to support wireless edge computing through developing a strategy around self-guided field laboratories (SGFL). It outlines several potential science use cases that could benefit from wireless and distributed computing capabilities, both in the short term through technologies like 5G, LoRa and Starlink, and longer term through the vision of automated SGFL. The document proposes some initial ideas for deploying and testing wireless edge computing technologies through existing projects to help enable the SGFL vision and further scientific opportunities. It emphasizes that exploring these emerging areas could help drive new science possibilities if done at a reasonable scale.
The Asia Pacific and Korea Research Platforms: An Overview Jeonghoon MoonLarry Smarr
This document provides an overview of Asia Pacific and Korea research platforms. It discusses the Asia Pacific Research Platform working group in APAN, including its objectives to promote HPC ecosystems and engage members. It describes the Asi@Connect project which provides high-capacity internet connectivity for research across Asia-Pacific. It also discusses the Korea Research Platform and efforts to expand it to 25 national research institutes in Korea. New related projects on smart hospitals, agriculture, and environment are mentioned. The conclusion discusses enhancing APAN and the Korea Research Platform and expanding into new areas like disaster and AI education.
Panel: Reaching More Minority Serving InstitutionsLarry Smarr
This document discusses engaging more minority serving institutions (MSIs) in the National Research Platform (NRP). It provides data showing that MSIs serve a disproportionate number of underrepresented minority students and are important producers of STEM graduates from these groups. The NRP can help broaden participation in STEAM fields by providing MSIs access to advanced cyberinfrastructure resources, new learning modalities, and opportunities for collaborative research between MSIs and other institutions. Regional networks also have a role to play in helping MSIs overcome barriers and attracting them to collaborative grants. The goal is to tear down walls between research and teaching and reinvent the university experience for more inclusive learning and innovation.
Panel: The Global Research Platform: An OverviewLarry Smarr
The document provides an overview of the Global Research Platform (GRP), an international collaborative partnership creating a distributed environment for data-intensive global science. The GRP facilitates high-performance data gathering, analytics, transport up to terabits per second, computing, and storage to support large-scale global science cyberinfrastructure ecosystems. It aims to orchestrate research across multiple domains using international testbeds for investigating new technologies related to data-intensive science. Examples of instruments generating exabytes of data that would benefit include the Korea Superconducting Tokamak, the High Luminosity LHC, genomics, the SKA radio telescope, and the Vera Rubin Observatory.
Panel: Future Wireless Extensions of Regional Optical NetworksLarry Smarr
CENIC is a non-profit organization that operates an 8,000+ mile fiber optic network connecting over 12,000 sites across California, including K-12 schools, universities, libraries, and research organizations. It has over 750 private sector partners and contributes over $100 million annually to the California economy. CENIC's network enables research and education collaborations, innovation, and economic growth statewide. It also operates a wireless research network called PRP that connects wireless sensors to supercomputers, supporting applications like wildfire modeling.
Global Research Platform Workshops - Maxine BrownLarry Smarr
The document announces a workshop on global research platforms that will be held virtually in 2021 and in Salt Lake City in 2022, with topics including large-scale science, next-generation platforms, data transport, and international testbeds. It also announces the 4th Global Research Platform Workshop to be held in October 2023 in Limassol, Cyprus co-located with the IEEE eScience 2023 conference.
EPOC and NetSage provide engagement and network monitoring services to support research and education. NetSage collects anonymized network flow data to help understand traffic patterns and troubleshoot performance issues. It provides dashboards and analysis to answer common questions from network engineers and end users. Examples of NetSage deployments and use cases were shown for the CENIC network, including top sources and destinations of traffic, debugging slow flows, and analyzing international traffic patterns by country over time.
The document discusses accelerating science discovery with AI inference-as-a-service. It describes showcases using this approach for high energy physics and gravitational wave experiments. It outlines the vision of the A3D3 institute to unite domain scientists, computer scientists, and engineers to achieve real-time AI and transform science. Examples are provided of using AI inference-as-a-service to accelerate workflows for CMS, ProtoDUNE, LIGO, and other experiments.
Democratizing Science through Cyberinfrastructure - Manish ParasharLarry Smarr
This document summarizes a presentation by Manish Parashar on democratizing science through cyberinfrastructure. The key points are:
1) Broad, fair, and equitable access to advanced cyberinfrastructure is essential for democratizing 21st century science, but there are significant barriers related to knowledge, technical issues, social factors, and balancing capabilities.
2) An advanced cyberinfrastructure ecosystem for all requires integrated portals, access to local and national resources through high-speed networks, diverse allocation modes, embedded expertise networks, and broad training.
3) Realizing this vision will require a scalable federated ecosystem with diverse capabilities and incentives for partnerships to meet growing needs for cyberinfrastructure and
Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;Larry Smarr
This document summarizes a panel discussion on building the National Research Platform ecosystem with regional networks. The panelists discussed how their regional networks are connecting to and using the Nautilus nodes of the NRP. Examples included using NRP for deep learning and computer vision research at the University of Missouri, challenges of adoption in Nevada and potential solutions, and Georgia Tech's new involvement through the Southern Crossroads regional network. The regional networks see opportunities to expand NRP access and training to enable more researchers in their regions to take advantage of the platform.
Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...Larry Smarr
The document discusses Open Force Field (OpenFF), an open-source project that enables rapid development of molecular force fields through automated infrastructure, open data and software, and an open science approach. OpenFF provides access to large quantum chemical datasets, runs quantum chemistry calculations on pre-emptible cloud resources with minimal human intervention, and facilitates easy iteration and testing of new force field hypotheses through an open development model.
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, when they may be suitable to use, and how tools like CloudBank and Kubernetes can help facilitate science users' access to cloud resources.
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, noting they provide huge capacity and variety but are very expensive for regular use. Facilitating science users on clouds requires services like CloudBank and Kubernetes federation.
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, noting they provide huge capacity and variety but are very expensive for regular use. Facilitating science users on clouds requires tools for account management, documentation, and integrating cloud resources through HTCondor and Kubernetes.
Frank Würthwein - NRP and the Path forwardLarry Smarr
NRP will replace PRP and aims to democratize access to national research cyberinfrastructure. The long term vision is to create an open national cyberinfrastructure by federating resources across research institutions. Key innovations include an innovative network fabric, application libraries for FPGAs, a "bring your own resource" model, and innovative scheduling and data infrastructure. The NSF has funded the Prototype National Research Platform project to support NRP for the next 5 years. NRP aims to grow resources, introduce new capabilities, and be driven by the research community.
Local Advanced Lung Cancer: Artificial Intelligence, Synergetics, Complex Sys...Oleg Kshivets
Overall life span (LS) was 1671.7±1721.6 days and cumulative 5YS reached 62.4%, 10 years – 50.4%, 20 years – 44.6%. 94 LCP lived more than 5 years without cancer (LS=2958.6±1723.6 days), 22 – more than 10 years (LS=5571±1841.8 days). 67 LCP died because of LC (LS=471.9±344 days). AT significantly improved 5YS (68% vs. 53.7%) (P=0.028 by log-rank test). Cox modeling displayed that 5YS of LCP significantly depended on: N0-N12, T3-4, blood cell circuit, cell ratio factors (ratio between cancer cells-CC and blood cells subpopulations), LC cell dynamics, recalcification time, heparin tolerance, prothrombin index, protein, AT, procedure type (P=0.000-0.031). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and N0-12 (rank=1), thrombocytes/CC (rank=2), segmented neutrophils/CC (3), eosinophils/CC (4), erythrocytes/CC (5), healthy cells/CC (6), lymphocytes/CC (7), stick neutrophils/CC (8), leucocytes/CC (9), monocytes/CC (10). Correct prediction of 5YS was 100% by neural networks computing (error=0.000; area under ROC curve=1.0).
These lecture slides, by Dr Sidra Arshad, offer a simplified look into the mechanisms involved in the regulation of respiration:
Learning objectives:
1. Describe the organisation of respiratory center
2. Describe the nervous control of inspiration and respiratory rhythm
3. Describe the functions of the dorsal and respiratory groups of neurons
4. Describe the influences of the Pneumotaxic and Apneustic centers
5. Explain the role of Hering-Breur inflation reflex in regulation of inspiration
6. Explain the role of central chemoreceptors in regulation of respiration
7. Explain the role of peripheral chemoreceptors in regulation of respiration
8. Explain the regulation of respiration during exercise
9. Integrate the respiratory regulatory mechanisms
10. Describe the Cheyne-Stokes breathing
Study Resources:
1. Chapter 42, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 36, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 13, Human Physiology by Lauralee Sherwood, 9th edition
Cell Therapy Expansion and Challenges in Autoimmune DiseaseHealth Advances
There is increasing confidence that cell therapies will soon play a role in the treatment of autoimmune disorders, but the extent of this impact remains to be seen. Early readouts on autologous CAR-Ts in lupus are encouraging, but manufacturing and cost limitations are likely to restrict access to highly refractory patients. Allogeneic CAR-Ts have the potential to broaden access to earlier lines of treatment due to their inherent cost benefits, however they will need to demonstrate comparable or improved efficacy to established modalities.
In addition to infrastructure and capacity constraints, CAR-Ts face a very different risk-benefit dynamic in autoimmune compared to oncology, highlighting the need for tolerable therapies with low adverse event risk. CAR-NK and Treg-based therapies are also being developed in certain autoimmune disorders and may demonstrate favorable safety profiles. Several novel non-cell therapies such as bispecific antibodies, nanobodies, and RNAi drugs, may also offer future alternative competitive solutions with variable value propositions.
Widespread adoption of cell therapies will not only require strong efficacy and safety data, but also adapted pricing and access strategies. At oncology-based price points, CAR-Ts are unlikely to achieve broad market access in autoimmune disorders, with eligible patient populations that are potentially orders of magnitude greater than the number of currently addressable cancer patients. Developers have made strides towards reducing cell therapy COGS while improving manufacturing efficiency, but payors will inevitably restrict access until more sustainable pricing is achieved.
Despite these headwinds, industry leaders and investors remain confident that cell therapies are poised to address significant unmet need in patients suffering from autoimmune disorders. However, the extent of this impact on the treatment landscape remains to be seen, as the industry rapidly approaches an inflection point.
Rasamanikya is a excellent preparation in the field of Rasashastra, it is used in various Kushtha Roga, Shwasa, Vicharchika, Bhagandara, Vatarakta, and Phiranga Roga. In this article Preparation& Comparative analytical profile for both Formulationon i.e Rasamanikya prepared by Kushmanda swarasa & Churnodhaka Shodita Haratala. The study aims to provide insights into the comparative efficacy and analytical aspects of these formulations for enhanced therapeutic outcomes.
- Video recording of this lecture in English language: https://youtu.be/Pt1nA32sdHQ
- Video recording of this lecture in Arabic language: https://youtu.be/uFdc9F0rlP0
- 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
Observing the Dynamics of the Human Immune System Coupled to the Microbiome in Health and Disease
1. “Observing the Dynamics of the Human Immune System
Coupled to the Microbiome in Health and Disease”
CASIS Workshop on Biomedical Research Aboard the ISS
Columbia University
New York City, NY
May 28, 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. Visualizing 5-10 Year Time Series of 150 Blood & Stool
Variables Led Me to Discover a Chronic Disease
Calit2 64 megapixel VROOM
3. Only One of My Blood Measurements
Was Far Out of Range--Indicating Chronic Inflammation
Normal Range
<1 mg/L
27x Upper Limit
Normal
Episodic Peaks in Inflammation
Followed by Spontaneous Drops
Complex Reactive Protein (CRP) is a Blood Biomarker
for Detecting Presence of Inflammation
4. But by Using Stool Analysis Time Series, I Discovered
I Had Oscillating Immune Variables Far Above Normal
Typical
Lactoferrin
Value for
Active
IBD
Normal Range
<7.3 μg/mL
124x Upper Limit
Lactoferrin is a Protein Shed from Neutrophils -
An Immune System Antibacterial that Sequesters Iron
5. The Natural Partner in the Oscillating Immune System
Would Be The Gut Microbiome Ecology
Your Body Has 10 Times
As Many Microbe Cells As Human Cells
99% of Your
DNA Genes
Are in Microbe Cells
Not Human Cells
Inclusion of the Microbiome
Will Radically Change Medicine
6. 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
7. We Downloaded Additional Gut Microbiomes
from NIH HMP For Comparative Analysis
From Sequences to Bacterial Species Relative Abundance
Required 25 CPU-Years at San Diego Supercomputer Center
IBD Patients
2 Ulcerative Colitis Patients,
6 Points in Time
5 Ileal Crohn’s Patients,
3 Points in Time
“Healthy” Individuals
250 Subjects
1 Point in Time Larry Smarr
6 Points in Time
Total of 27 Billion Reads
Or 2.7 Trillion Bases
Source: Jerry Sheehan, Calit2
Weizhong Li, Sitao Wu, CRBS, UCSD
8. Using Scalable Visualization Allows Comparison of
the Relative Abundance of 200 Gut Microbe Species
Comparing 3 LS Time Snapshots (Left)
with Healthy, Crohn’s, UC (Right Top to Bottom)
Calit2 VROOM-FuturePatient Expedition
9. We Found Major Shifts in Microbial Ecology
Between Healthy and Two Forms of IBD
Collapse of
Bacteroidetes
Explosion of
Proteobacteria On the IBD Spectrum
10. Comparing Changes in Gut Microbiome Ecology with
Oscillations of the Innate and Adaptive Immune System
LS Data from Yourfuturehealth.com Stool Tests
Normal
Innate Immune System
Adaptive Immune System
Normal
Time Points of
Metagenomic
Sequencing
of LS Stool Samples
Therapy: 1 Month Antibiotics
+2 Month Prednisone
11. Time Series Reveals Autoimmune Dynamics
of Gut Microbiome by Phyla
Therapy
Six Metagenomic Time Samples Over 16 Months
13. Inexpensive 16S Time Series of Microbiome
Now Possible Through Ubiome
Data source: LS (Yellow Lines Stool Samples);
Sequencing and Analysis Ubiome
14. What Might We Learn?
Zero G as a Selection Pressure on Human Microbiome
"Space flight alters cellular and physiological responses
in astronauts including the immune response,"
said ASU's Cheryl Nickerson,
who led a project aboard NASA's space shuttle.
"However, relatively little was known about
microbial changes to infectious disease risk
in response to space flight."
Slide Presented by LS to NAC July 2013
From NAC Information Technology Infrastructure Committee