Global Telepresence in Support of Global Public HealthLarry Smarr
08.04.17
Briefing
University of California School of Global Health
All Campuses Planning Committee
Calit2@UCSD
Title: Global Telepresence in Support of Global Public Health
La Jolla, CA
How will our children, grand children and great grand children be living? What policies, research and investments do they need us to make today to make their lives better tomorrow? A team of over 50 scientists and business analysts in CSIRO identified five megatrends, several megashocks and two scenarios for the next 20 years. A megatrend is a pattern of environmental, social and/or economic activity with profound implications for how we live. Megashocks are sudden, hard to predict, single events. Scenarios are a mix of science fiction and science fact and explore how the trends and shocks might play out into an uncertain future.
Global Telepresence in Support of Global Public HealthLarry Smarr
08.04.17
Briefing
University of California School of Global Health
All Campuses Planning Committee
Calit2@UCSD
Title: Global Telepresence in Support of Global Public Health
La Jolla, CA
How will our children, grand children and great grand children be living? What policies, research and investments do they need us to make today to make their lives better tomorrow? A team of over 50 scientists and business analysts in CSIRO identified five megatrends, several megashocks and two scenarios for the next 20 years. A megatrend is a pattern of environmental, social and/or economic activity with profound implications for how we live. Megashocks are sudden, hard to predict, single events. Scenarios are a mix of science fiction and science fact and explore how the trends and shocks might play out into an uncertain future.
Thrive:Timely Health Indicators Using Remote Sensing & innovation for the Vit...US-Ignite
Prevention is better than a cure, so a timely alert could preclude a trip to the ER for the 25 million Americans who have Asthma. This technology could benefit all people with environmentally triggered health conditions and supply forecasts to ER and walk in clinic managers, David Lary, University of Texas at Dallas and York Eggleston, Machine Data Learning.
The Singularity: Toward a Post-Human RealityLarry Smarr
06.02.13
Talk to UCSD's Sixth College
Honor's Course on Kurzweil's The Singularity is Near
Title: The Singularity: Toward a Post-Human Reality
La Jolla, CA
Smart metering technologies allow for gathering high resolution water demand data in the residential sector, opening up new opportunities for the development of models describing water consumers’ behaviors. Yet, gathering such accurate water demand data at the end-use level is limited by metering intrusiveness, costs, and privacy issues. In this paper, we contribute a stochastic simulation model for synthetically generating high-resolution time series of water use at the end-use level. Each water end-use fixture in our model is characterized by its signature (i.e., its typical single-use pattern), as well as frequency distributions of its number of uses per day, single use duration, time of use during the day, and contribution to the total household water demand. The model relies on statistical data from a real-world metering campaign across 9 cities in the US. Showcasing our model outputs, we demonstrate the potential usability of this model for characterizing the water end-use demands of different communities, as well as for analyzing the major components of peak demand and performing scenario analysis.
Reducing Bacterial Contamination In WaterwaysJason Schroeder
Presentation at the River Network "River Rally" conference in Baltimore, Maryland May 29th - June 1st. Our workshop discussed Milwaukee Riverkeeper\'s IDDE program specifically focused on bacteria monitoring for human sewage, using genetic testing to determine the presence of Bacteroides, a specific human marker for human sewage.
We discuss how many stormwater outfalls we found containing human sewage, our documentation of the data, the use of GIS and Google Maps and Google Earth for displaying the data and how to move forward to fix this serious human health risk and pollution problem.
Cheryl Nenn and I co-presented this presentation/workshop. Slides 11 - 32 were presented by me, while Cheryl presented slides 2 - 10 and 33 - 34.
Supporting epidemic intelligence, personalised and public health with advance...Joao Pita Costa
Today, our everyday access to technology permits a health monitoring that can complement the traditional methods in Healthcare and Public Health. In this paper, we present some of this available technology, with a particular focus on disease detection, topological data analysis, and media monitoring tools, made available by the AILAB at the JSI and the ISI Foundation. This technology is ready to be adapted to research and commercial problems in the context of health systems.
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
“Data for Development – the value of data for research and society” by Dr. Ma...LEARN Project
“Data for Development – the value of data for research and society”, Dr. Martin Hilbert, University of California - presented at the 4th LEARN RDM Workshop in Santiago, Chile: http://learn-rdm.eu/
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Thrive:Timely Health Indicators Using Remote Sensing & innovation for the Vit...US-Ignite
Prevention is better than a cure, so a timely alert could preclude a trip to the ER for the 25 million Americans who have Asthma. This technology could benefit all people with environmentally triggered health conditions and supply forecasts to ER and walk in clinic managers, David Lary, University of Texas at Dallas and York Eggleston, Machine Data Learning.
The Singularity: Toward a Post-Human RealityLarry Smarr
06.02.13
Talk to UCSD's Sixth College
Honor's Course on Kurzweil's The Singularity is Near
Title: The Singularity: Toward a Post-Human Reality
La Jolla, CA
Smart metering technologies allow for gathering high resolution water demand data in the residential sector, opening up new opportunities for the development of models describing water consumers’ behaviors. Yet, gathering such accurate water demand data at the end-use level is limited by metering intrusiveness, costs, and privacy issues. In this paper, we contribute a stochastic simulation model for synthetically generating high-resolution time series of water use at the end-use level. Each water end-use fixture in our model is characterized by its signature (i.e., its typical single-use pattern), as well as frequency distributions of its number of uses per day, single use duration, time of use during the day, and contribution to the total household water demand. The model relies on statistical data from a real-world metering campaign across 9 cities in the US. Showcasing our model outputs, we demonstrate the potential usability of this model for characterizing the water end-use demands of different communities, as well as for analyzing the major components of peak demand and performing scenario analysis.
Reducing Bacterial Contamination In WaterwaysJason Schroeder
Presentation at the River Network "River Rally" conference in Baltimore, Maryland May 29th - June 1st. Our workshop discussed Milwaukee Riverkeeper\'s IDDE program specifically focused on bacteria monitoring for human sewage, using genetic testing to determine the presence of Bacteroides, a specific human marker for human sewage.
We discuss how many stormwater outfalls we found containing human sewage, our documentation of the data, the use of GIS and Google Maps and Google Earth for displaying the data and how to move forward to fix this serious human health risk and pollution problem.
Cheryl Nenn and I co-presented this presentation/workshop. Slides 11 - 32 were presented by me, while Cheryl presented slides 2 - 10 and 33 - 34.
Supporting epidemic intelligence, personalised and public health with advance...Joao Pita Costa
Today, our everyday access to technology permits a health monitoring that can complement the traditional methods in Healthcare and Public Health. In this paper, we present some of this available technology, with a particular focus on disease detection, topological data analysis, and media monitoring tools, made available by the AILAB at the JSI and the ISI Foundation. This technology is ready to be adapted to research and commercial problems in the context of health systems.
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
“Data for Development – the value of data for research and society” by Dr. Ma...LEARN Project
“Data for Development – the value of data for research and society”, Dr. Martin Hilbert, University of California - presented at the 4th LEARN RDM Workshop in Santiago, Chile: http://learn-rdm.eu/
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
In silico drugs analogue design: novobiocin analogues.pptx
Almaden may 6th 2014 gilbert
1. Sequencing Chicago: Mapping Urban
Metabolism
Jack A Gilbert
@gilbertjacka
www.americangut.org
www.microbial-models.com
www.homemicrobiome.com
www.earthmicrobiome.org
www.hospitalmicrobiome.com
2. 400million city dwellers
China will add
221Chinese cities will have 1M
or more people.
And by 2030...
Rapid Urbanization in Developing Economies
of Chinese people will live in
cities with 1M or more people.
In 2025:
70%
....requiring the
construction of one New
York City every year for
several decades
Source: Foreign Policy Magazine, Sep/Oct
2010, “Megacities,” Richard Dobbs (McKinsey
Global Institute)
Landsat images of the Pearl River Delta in 1980 and 2005,
illustrating the impact of urbanization on the planet.
Between now and 2020, the Guangdong province will invest
$229B in 202 ongoing and 258 new transport infrastructure
projects to create a single 50M person city.
3. Produced by: S. Jiang, J. Ferreira, M. Gonzalez (2011) | Data Source: CMAP Travel Tracker Data, 2008.
Reference: Jiang, S., J. Ferreira, and M. González. 2012. Clustering Daily Patterns of Human Activities in the City. Data Mining and
Knowledge Discovery. Volume 25, Number 3, Pages 478-510
Mapping Megadata for Human Activity Patterns: survey data for 10,000
Chicago households on two weekdays in 2008
4. Crowd Funded Human Microbiome – American Gut
4
>$800,000
8450 56
www.americangut.org
5.
6. House 1 Dynamic Bayesian Network
Predicting Interactions between people and
surfaces
7. Adding dogs into the mix make the interaction
space more complex.
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
House 4 Dynamic Bayesian Network
8. We can forensically identify physical
connections between people
Young Couple living with a lodger
- you can identify the ‘relationship’ from the microbiome
- you can also tell which parts of the house the lodger uses.
A young family (parents with 2 young boys) shows no such
delineation.
9. University of Chicago: Kim Handley, Simon Lax,
Daniel Smith, Kristen Starkey, John Alverdy,
Emily Landon, Jack Gilbert, etc.
Illinois Institute of Technology: Tiffanie Ramos,
Brent Stephens
University of Toronto: Jeff Siegel
Building science data summary
• 84 variables measured continuously every 5 minutes
• 100,000+ data points per variable
• 8.4 million+ data points collected
• over 8500+ hours of active data collection per variable
Microbial Community Analysis
• Bacterial, Fungal diversity and function over
12,000 samples
• Patients, Staff, Air, Water, Surfaces
Patient Records
• Age, Sex, disease burden, antibiotics, admission,
stay, blood tests, surgery, anesthesia, etc.
10. The Hospital Microbiome shifts towards a human
microbiome following arrival of patients and staff
11. -3 -2 -1 0 1 2
-2-1012
CCA1
CCA2
-101
F
DO
ALKALINITY
w_102
w_36
w_73
w_96
W_36, W_73
W_112, W_96
Chicago Area Waterways Project
112 36 96 73
0%
10%
20%
30%
40%
50%
60%
70%
fish mucus
human feces
Goose feces
Bird associated
Cat feces
mammal feces
animal skin
May June july Aug. Sept. May June July Aug. Sept. May Aug. Sept. May June July Aug. Sept.
Some samples were dominated by goose, human and animal feca
microbiota
• City Municipal
Water reclamation
Department Study
• $4M over 7 years
• Tracking sources of
impact
• Tracking impact of
water management
strategies
12. Mapping human and building microbiota
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
13. Mapping human and building microbiota
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Homes,
Offices,
Hospitals,
Public Restrooms
Gyms,
Sports Stadiums,
Retail
14. Mapping air, water and green-site microbiota
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
15. Mapping air, water and green-site microbiota
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Array
of
Things
16. Array of Things – Air Microbiome
Temperature
Humidity
Light
Sound
CO2
IR
Motion
Ultrasonic (proximity)
Precipitation
Anemometer
...
17. Array of Things – Air Microbiome
Temperature
Humidity
Light
Sound
CO2
IR
Motion
Ultrasonic (proximity)
Precipitation
Anemometer
...
Microbial community
Temperature
Carbon Dioxide
Carbon Monoxide
NOx
Humidity
Weather events
Wind speed
Wind direction
Bluetooth signals
Visibility
Noise level
Air quality
Air density
Local tweet mining
18. Current 30 node prototype
A 30-node
prototype is
being
developed for
deployment in
summer 2014
with internal
funding from
Argonne
National
Laboratory.