The document discusses new opportunities and responsibilities that have arisen from advances in generating large amounts of human biological data through omics technologies. These advances allow emerging network modeling approaches for disease and open collaborative problem solving using cloud computing infrastructure. A nascent movement is described where patients can control sensitive health information to enable sharing. Open social media is said to allow citizens and experts to collaboratively solve problems through gaming approaches.
A sponsored supplement produced for Jisc on how researchers can cope with the data deluge of modern research techniques. Published by Times Higher Education on 25 November 2009
This talk provides a review of the current status of research related to self-assembling DNA nanotechnology (particularly DNA nanostructures, synthetic biology, and DNA origami scaffolding structures) and how the self-assembly of artificial systems might be applied in the context of neuro-nanomedicine. One application of self-assembling DNA nanotechnology might be new forms of brain-computer interfaces (BCIs) that are less invasive than current computer chip-based hardware solutions. Another application of self-assembling DNA nanotechnology might be high-resolution neocortical recording devices where synthetic molecules would assemble a DNA signature every time a neuron was fired.
In this deck from the 2014 HPC User Forum in Seattle, Jack Collins from the National Cancer Institute presents: Genomes to Structures to Function: The Role of HPC.
Watch the video presentation: http://wp.me/p3RLHQ-d28
A sponsored supplement produced for Jisc on how researchers can cope with the data deluge of modern research techniques. Published by Times Higher Education on 25 November 2009
This talk provides a review of the current status of research related to self-assembling DNA nanotechnology (particularly DNA nanostructures, synthetic biology, and DNA origami scaffolding structures) and how the self-assembly of artificial systems might be applied in the context of neuro-nanomedicine. One application of self-assembling DNA nanotechnology might be new forms of brain-computer interfaces (BCIs) that are less invasive than current computer chip-based hardware solutions. Another application of self-assembling DNA nanotechnology might be high-resolution neocortical recording devices where synthetic molecules would assemble a DNA signature every time a neuron was fired.
In this deck from the 2014 HPC User Forum in Seattle, Jack Collins from the National Cancer Institute presents: Genomes to Structures to Function: The Role of HPC.
Watch the video presentation: http://wp.me/p3RLHQ-d28
High Performance Cyberinfrastructure to Support Data-Intensive Biomedical Res...Larry Smarr
08.06.16
Invited Talk
Association of University Research Parks BioParks 2008
"From Discovery to Innovation"
Salk Institute
Title: High Performance Cyberinfrastructure to Support Data-Intensive Biomedical Research Instruments
La Jolla, CA
High Performance Cyberinfrastructure to Support Data-Intensive Biomedical Res...Larry Smarr
08.06.16
Invited Talk
Association of University Research Parks BioParks 2008
"From Discovery to Innovation"
Salk Institute
Title: High Performance Cyberinfrastructure to Support Data-Intensive Biomedical Research Instruments
La Jolla, CA
Using KnetMiner to search and visualise the knowledge network of genes involved in neurodegenerative diseases such as Alzheimer, Parkinson and Huntington.
Gene Wiki and Mark2Cure update for BD2KBenjamin Good
An introduction to the Gene Wiki project with an emphasis on the use of the new WikiData project. Also describes mark2cure, a citizen science initiative oriented on biomedical text mining.
Presentation given at Health Informatics and Knowledge Management conference
(http://publichealth.curtin.edu.au/HIKM/), as part of Australasian Computer Science Week 2012.
http://www.cs.rmit.edu.au/acsw2012/
Building a Network of Interoperable and Independently Produced Linked and Ope...Michel Dumontier
Over 15 years ago, Sir Tim Berners Lee proclaimed the founding of an exciting new future involving intelligent agents operating over smarter data in order to perform complex tasks at the behest of their human controllers. At the heart of this vision lies an uneasy alliance between tedious formal knowledge representations and powerful analytics over big, but often messy data. Bio2RDF, our decade old open source project to create Linked Data for the life sciences, has weaved emergent Semantic Web technologies such as ontologies and Linked Data to generate FAIR - Findable, Accessible, Interoperable, and Reusable - data in the form of billions of machine accessible statements for use in downstream biomedical discovery.
This revolution in data publication has been strengthened by action from global bioinformatics institutions such as the NCBI, NCBO, EBI, and DBCLS. Notably, NCBI's PubChem has successfully coupled large scale data integration with community-based standards to offer a remakable biochemical knowledge resource amenable to data hungry discovery tools. Yet, in the face of increasing pressure from researchers, funders, and publishers, will these approaches be sufficient for growing and maintaining a comprehensive knowledge graph that is inclusive of all biomedical research?
Ozempic: Preoperative Management of Patients on GLP-1 Receptor Agonists Saeid Safari
Preoperative Management of Patients on GLP-1 Receptor Agonists like Ozempic and Semiglutide
ASA GUIDELINE
NYSORA Guideline
2 Case Reports of Gastric Ultrasound
NVBDCP.pptx Nation vector borne disease control programSapna Thakur
NVBDCP was launched in 2003-2004 . Vector-Borne Disease: Disease that results from an infection transmitted to humans and other animals by blood-feeding arthropods, such as mosquitoes, ticks, and fleas. Examples of vector-borne diseases include Dengue fever, West Nile Virus, Lyme disease, and malaria.
Basavarajeeyam is an important text for ayurvedic physician belonging to andhra pradehs. It is a popular compendium in various parts of our country as well as in andhra pradesh. The content of the text was presented in sanskrit and telugu language (Bilingual). One of the most famous book in ayurvedic pharmaceutics and therapeutics. This book contains 25 chapters called as prakaranas. Many rasaoushadis were explained, pioneer of dhatu druti, nadi pareeksha, mutra pareeksha etc. Belongs to the period of 15-16 century. New diseases like upadamsha, phiranga rogas are explained.
micro teaching on communication m.sc nursing.pdfAnurag Sharma
Microteaching is a unique model of practice teaching. It is a viable instrument for the. desired change in the teaching behavior or the behavior potential which, in specified types of real. classroom situations, tends to facilitate the achievement of specified types of objectives.
Flu Vaccine Alert in Bangalore Karnatakaaddon Scans
As flu season approaches, health officials in Bangalore, Karnataka, are urging residents to get their flu vaccinations. The seasonal flu, while common, can lead to severe health complications, particularly for vulnerable populations such as young children, the elderly, and those with underlying health conditions.
Dr. Vidisha Kumari, a leading epidemiologist in Bangalore, emphasizes the importance of getting vaccinated. "The flu vaccine is our best defense against the influenza virus. It not only protects individuals but also helps prevent the spread of the virus in our communities," he says.
This year, the flu season is expected to coincide with a potential increase in other respiratory illnesses. The Karnataka Health Department has launched an awareness campaign highlighting the significance of flu vaccinations. They have set up multiple vaccination centers across Bangalore, making it convenient for residents to receive their shots.
To encourage widespread vaccination, the government is also collaborating with local schools, workplaces, and community centers to facilitate vaccination drives. Special attention is being given to ensuring that the vaccine is accessible to all, including marginalized communities who may have limited access to healthcare.
Residents are reminded that the flu vaccine is safe and effective. Common side effects are mild and may include soreness at the injection site, mild fever, or muscle aches. These side effects are generally short-lived and far less severe than the flu itself.
Healthcare providers are also stressing the importance of continuing COVID-19 precautions. Wearing masks, practicing good hand hygiene, and maintaining social distancing are still crucial, especially in crowded places.
Protect yourself and your loved ones by getting vaccinated. Together, we can help keep Bangalore healthy and safe this flu season. For more information on vaccination centers and schedules, residents can visit the Karnataka Health Department’s official website or follow their social media pages.
Stay informed, stay safe, and get your flu shot today!
Knee anatomy and clinical tests 2024.pdfvimalpl1234
This includes all relevant anatomy and clinical tests compiled from standard textbooks, Campbell,netter etc..It is comprehensive and best suited for orthopaedicians and orthopaedic residents.
- Video recording of this lecture in English language: https://youtu.be/lK81BzxMqdo
- Video recording of this lecture in Arabic language: https://youtu.be/Ve4P0COk9OI
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
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Explore natural remedies for syphilis treatment in Singapore. Discover alternative therapies, herbal remedies, and lifestyle changes that may complement conventional treatments. Learn about holistic approaches to managing syphilis symptoms and supporting overall health.
Ethanol (CH3CH2OH), or beverage alcohol, is a two-carbon alcohol
that is rapidly distributed in the body and brain. Ethanol alters many
neurochemical systems and has rewarding and addictive properties. It
is the oldest recreational drug and likely contributes to more morbidity,
mortality, and public health costs than all illicit drugs combined. The
5th edition of the Diagnostic and Statistical Manual of Mental Disorders
(DSM-5) integrates alcohol abuse and alcohol dependence into a single
disorder called alcohol use disorder (AUD), with mild, moderate,
and severe subclassifications (American Psychiatric Association, 2013).
In the DSM-5, all types of substance abuse and dependence have been
combined into a single substance use disorder (SUD) on a continuum
from mild to severe. A diagnosis of AUD requires that at least two of
the 11 DSM-5 behaviors be present within a 12-month period (mild
AUD: 2–3 criteria; moderate AUD: 4–5 criteria; severe AUD: 6–11 criteria).
The four main behavioral effects of AUD are impaired control over
drinking, negative social consequences, risky use, and altered physiological
effects (tolerance, withdrawal). This chapter presents an overview
of the prevalence and harmful consequences of AUD in the U.S.,
the systemic nature of the disease, neurocircuitry and stages of AUD,
comorbidities, fetal alcohol spectrum disorders, genetic risk factors, and
pharmacotherapies for AUD.
Title: Sense of Taste
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
6. Open Social Media allows citizens and experts to use gaming to solve problems
7. 1- Now possible to generate massive amount of human “omic’s” data
2-Network Modeling Approaches for Diseases are emerging
3- IT Infrastructure and Cloud compute capacity allows
a generative open approach to biomedical problem solving
4-Nascent Movement for patients to Control Sensitive information
allowing sharing
5- Open Social Media allows citizens and experts to use gaming to
solve problems
A HUGE OPPORTUNITY -- A HUGE RESPONSIBILITY
8.
9.
10.
11.
12.
13. ENVIRONMENT
Non-coding RNA network
BRAIN
HEART
ENVIRONMENT
GI TRACT
protein network
KIDNEY
ENVIRONMENT
metabolite network
IMMUNE SYSTEM
VASCULATURE
transcriptional network
ENVIRONMENT
24. BUILDING PRECISION MEDICINE
Extensions of Current Institutions
Proprietary Short term Solutions
Open Systems of Sharing in a Commons
25. An Alternative
Biomedicine
Information
Commons
Commons are resources that are owned in common or shared among
communities.
-David Bollier
26. Why Sage Bionetworks?
We believe in a world where biomedical research has changed. It
will be conducted in an open, collaborative way where all parties
can contribute to making better, faster, relevant discoveries
We activate/We challenge We enable others
• Diverse collaborations with • Developing platforms for
individuals/researchers and collaboration and
institutions to collectively engagement – Synapse,
grow the biomedical BRIDGE
Commons • Defining governance
• Crowdsourcing approaches to approaches– PLC
challenge the communities
We research
• Leading biomedical modeling
research
• Novel training doctoral and
internship programs
28. Governance
Technology Platform
Impactful Models
Better Models of
Disease:
INFORMATION
COMMONS
Challenges
29. Two recurring problems in Alzheimer’s disease research
Ambiguous pathology
Are disease-associated molecular systems &
genes destructive, adaptive, or both?
Bottom line: We need to identify causal factors
vs correlative or adaptive features of disease.
Diverse mechanisms
How do diverse mutations and environmental
factors combine into a core pathology?
Bottom line: There is no rigorous / consistent global
framework that integrates diverse disease factors.
29
30. Identifying key disease systems and genes- Gaiteri et al.
1.) Identify groups of genes that move together – coexpressed “modules”
- correlated expression of multiple genes across many patients
- coexpression calculated separately for Disease/healthy groups
- these gene groups are often coherent cellular subsystems, enriched in one or
more GO functions
Example “modules” of coexpressed genes, color-coded
31. Identifying key disease systems and genes
1.) Identify groups of genes that move together – coexpressed “modules”
2.) Prioritize the disease-relevance of the modules by clinical and network measures
Prioritize modules through expression
synchrony with clinical measures or
tendency too reconfigure themselves in
disease
vs
32. Identifying key disease systems and genes
1.) Identify groups of genes that move together – coexpressed “modules”
2.) Prioritize the disease-relevance of the modules by clinical and network measures
3.) Incorporate genetic information to find directed relationships between genes
Infer directed/causal relationships
Prioritize modules through expression
and clear hierarchical structure by
synchrony with clinical measures or tendency
too reconfigure themselves in disease incorporating eSNP information
(no hair-balls here)
vs
33. Example network finding: microglia activation in AD
Module selection – what identifies these modules as relevant to Alzheimer’s disease?
The eigengene of a module of ~400 probes correlates with Braak score, age, cognitive disease severity
and cortical atrophy. Members of this module are on average differentially expressed (both up- and
down-regulated).
Evidence these modules are related to microglia function
The members of this module are enriched with GO categories (p<.001) such as “response to biotic
stimulus” that are indicative of immunologic function for this module.
The microglia markers CD68 and CD11b/ITGAM are contained in the module (this is rare – even when a
module appears to represent a specific cell-type, the histological markers may be lacking).
Numerous key drivers (SYK, TREM2, DAP12, FC1R, TLR2) are important elements of microglia signaling .
Alzgene hits found in co-regulated microglia module:
34. Figure key:
Five main immunologic families
found in Alzheimer’s-associated
module
Square nodes in surrounding network
denote literature-supported nodes.
Node size is proportional to
connectivity in the full module.
Core family members are shaded.
(Interior circle) Width of
connections between 5
immune families are
linearly scaled to the
number of inter-family
connections.
Labeled nodes are either highly
connected in the original network,
implicated by at least 2 papers as
associated with Alzheimer’s disease,
or core members of one of the 5
immune families.
37. Design-stage AD projects at Sage
Fusing our expertise in… Gene regulatory networks
Diffusion Spectrum Imaging
Feedback
Microcircuits &
neuronal diversity
Join us in uniting genes, circuits and regions
to build multi-scale biophysical disease models.
Contact chris.gaiteri@sagebase.org
38. Tool: PORTABLE LEGAL CONSENT
Control of Private information by Citizens allows sharing
weconsent.us
John Wilbanks
John Wilbanks • Online educational wizard
TED Talk • Tutorial video
• Legal Informed Consent Document
“Let’s pool our medical data” • Profile registration
weconsent.us • Data upload
39. two approaches to building common
scientific and technical knowledge
Every code change versioned
Every issue tracked
Text summary of the completed project Every project the starting point for new work
Assembled after the fact All evolving and accessible in real time
Social Coding
40. Synapse is GitHub for Biomedical Data
• Every code change versioned
• Every issue tracked
• Every project the starting point for new work
• Data and code versioned • Social/Interactive Coding
• Analysis history captured in real time
• Work anywhere, and share the results with anyone
• Social/Interactive Science
41. Data Analysis with Synapse
Run Any Tool
On Any Platform
Record in Synapse
Share with Anyone
42. “Synapse is a compute platform
for transparent, reproducible, and
modular collaborative research.”
44. Download analysis and meta-analysis
Download another Cluster Result Download Evaluation and view more stats
• Perform Model averaging
• Compare/contrast models
• Find consensus clusters
• Visualize in Cytoscape
46. Objective assessment of factors influencing model
performance (>1 million predictions evaluated)
Sanger CCLE
Cross validation prediction accuracy (R2)
Prediction accuracy
improved by…
Not discretizing
data
Including
expression data
Elastic net
regression
130 compounds In Sock Jang 24 compounds
50. Sage-DREAM Breast Cancer Prognosis Challenge
one month of building better disease models together
Caldos/Aparicio
breast cancer data
154 participants; 27 countries
334 participants; >35 countries
Sep 26 Status
Challenge Launch: July 17
>500 models posted to Leaderboard
Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge Phase 2 Best Performing Te
51. Sage Bionetworks-DREAM Breast Cancer Prognosis
Challenge
Phase 2 Best Performing Team: Attractor Metagenes
Team Members: Wei-Yi Cheng, Tai-Hsien Ou Yang, and
Dimitris Anastassiou
Affiliation: Center for Computational Biology and
Bioinformatics and Department of Electrical Engineering,
Columbia University
52. How to disrupt the System?
Build a way for the patients actively to engage their
insights in real-time around what is happening to
them ( their state of wellness or disease) where their
narratives, samples, data, insights, and funds are
shown to enable decision making in what they should
do, what treatments they need
53.
54. BRIDGE Seed Projects
Fanconi Diabetes
Melanoma
Anemia Activated
Hunt Community
Project
Breast
Real Names
Cancer
Parkinson’s
Genomic
Project
Research
54
55. BREAST CANCER GENOMIC RESEARCH: CURRENT APPROACHES
1. Isloated
breast cancer
cohorts
2. Many funders,
many disparate
objectives
Funded researchers 3. Data
is siloed
4. Clinical/genomic
data are accessible
but minimally
useable
5. Little incentive to
annotate data and curate
for other scientists
6. Limited impact of 7. Many published
today’s fragmented breast cancer
data on standard-of- prognosis models
care improvements but little consensus
for breast cancer
patients 55
56. BRIDGE APPROACH: BREAST CANCER PROGNOSIS “CO-OPETITIONS”
TO BUILD BETTER DISEASE MODELS TOGETHER
2. Core/surgical
biopsy
Path lab
Clinical
informatics
1. Activated
8. Field-test best models
breast cancer
in clinic and hospital
patients
3. Aggregate
BC patient Com 7. Give back education
Findings
data via and risk assessment to
muni
Citizen citizens
BRIDGE portal
ty
Portal
5. Open community-
Foru based “co-opetitions”
ms forge new computational
models
4. BC data 6. “Cco-opetitions”
curated, open leaderboard allows
and supported researchers to work
by analysis tools together
56
57. MELANOMA Screening – Could it be better?
Education is derived Best accuracy of
from top-down clinical diagnosis =
experiential 64%
knowledge (Grin, 1990)
160k new cases/year
48k deaths in 2012
in US
HPI
ABCDE Both intra- and
“ugly duckling” inter- institutional
MD Dermoscopy
Pathology
data are siloed
Molecular
?Photos
There is no standard
screening program for
skin lesions; seeing an
MD is self directed
57
58.
59. Initial focus on building the data needed
Novel Data collection
4. Give back risk-
+ Usage assessment & education
to the citizens
1.Activated citizens
take skin pictures
virtual cycle:
continuous
2. Store aggregation of data
tons of data!
enriching the model
3. Run
algorithmic
cChallenges in
the compute
space 59
60. Now possible to generate massive amount of human “omic’s”
data
Network Modeling for Diseases are emerging
IT Infrastructure and Cloud compute capacity allows
a generative open approach to biomedical problem solving
Nascent Movement for patients to Control Private information
allowing sharing
Open Social Media allowing citizens and experts to use gaming
to solve problems
THESE FIVE TRENDS CAN ENABLE AN OPEN COMMUNITY OF
IMPATIENT CITIZENS-- AS PATIENTS/RESEARCHERS/FUNDERS
61. DYNAMIC MULTI-SCALE PATIENT COMMUNITIES
ENABLING REAL TIME LEARNING
USING OPEN APPROACHES
DRIVEN BY “INFINITE CHALLENGES”
64. CORRUPTION OF DENIAL
Complexity of systems
Proximity of Solutions
Sufficiency of current phenotypic data and
appropriateness of role of patients
Effectiveness of how we work with big Data
65. " #$$%&'! Bob Young
Top Hat
my Jane McConigal
gene IoF
my Wadah Khanfar
Al Jazeera
dat a
Patrick Meier
m y
paper
Ushhidi
Jennifer Pahlka
Code for America
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Keyn ot e Sp eak er s: Law r en ce Lessi g – author “The future of ideas” &“Remix”
Jam i e Heyw ood – patients like me Lan ce Ar m st r on g – LiveStrong Davi d Hau ssl er - UCSC
Genome Browser Jam es Boyl e – Duke Law School Ad r i en Tr eu ille –Foldit
Sage Commons Congress – San Francisco April 19-20
! " #$%'$( ) *+% -" .*/&
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TenCong r ess i n SF!
Ear n one of t en t r i p s t o Com m ons
Young Investigator Awards
– t o ap p l y vi si t h t t p :/ / b i t .l y/ 2012YIA!