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PLENARY KEYNOTE PRESENTATIONS: THURSDAY, MAY 1 | 8:00 – 10:00 AM @ BioIT World, April 29 – May 1, 2014 Seaport World Trade Center, Boston, MA

 

Reporter: Aviva Lev-Ari, PhD, RN

 

Keynote Introduction: Sponsored by Fred Lee, M.D., MPH, Director, Healthcare Strategy and Business Development, Oracle Health Sciences

Heather Dewey-Hagborg

Artist, Ph.D. Student, Rensselaer Polytechnic Institute

Heather Dewey-Hagborg is an interdisciplinary artist, programmer and educator who explores art as research and public inquiry. She recreates identity from strands of human hair in an entirely different way. Collecting hairs she finds in random public places – bathrooms, libraries, and subway seats – she uses a battery of newly developing technologies to create physical, life-sized portraits of the owners of these hairs. Her fixation with a single hair leads her to controversial art projects and the study of genetics. Traversing media ranging from algorithms to DNA, her work seeks to question fundamental assumptions underpinning perceptions of human nature, technology and the environment. Examining culture through the lens of information, Heather creates situations and objects embodying concepts, probes for reflection and discussion. Her work has been featured in print, television, radio, and online. Heather has a BA in Information Arts from Bennington College and a Masters degree from the Interactive Telecommunications Program at Tisch School of the Arts, New York University. She is currently a Ph.D. student in Electronic Arts at Rensselaer Polytechnic Institute.

 

Yaniv Erlich, Ph.D.

Principal Investigator and Whitehead Fellow, Whitehead Institute for Biomedical Research

 

Dr. Yaniv Erlich is Andria and Paul Heafy Family Fellow and Principal Investigator at the Whitehead Institute for Biomedical Research. He received a bachelor’s degree from Tel-Aviv University, Israel and a PhD from the Watson School of Biological Sciences at Cold Spring Harbor Laboratory in 2010. Dr. Erlich’s research interests are computational human genetics. Dr. Erlich is the recipient of the Burroughs Wellcome Career Award (2013), Harold M. Weintraub award (2010), the IEEE/ACM-CS HPC award (2008), and he was selected as one of 2010 Tomorrow’s PIs team of Genome Technology.

 

Isaac Samuel Kohane, M.D., Ph.D.

Henderson Professor of Health Sciences and Technology, Children’s Hospital and Harvard Medical School;

Director, Countway Library of Medicine; Director, i2b2 National Center for Biomedical Computing;

Co-Director, HMS Center for Biomedical Informatics

 

Isaac Kohane, MD, PhD, co-directs the Center for Biomedical Informatics at Harvard Medical School. He applies computational techniques, whole genome analysis, and functional genomics to study human diseases through the developmental lens, and particularly through the use of animal model systems. Kohane has led the use of whole healthcare systems, notably in the i2b2 project, as “living laboratories” to drive discovery research in disease genomics (with a focus on autism) and pharmacovigilance

(including providing evidence for the cardiovascular risk of hypoglycemic agents which ultimately contributed to “black box”ing by the FDA) and comparative effectiveness with software and methods adopted in over 84 academic health centers internationally. Dr. Kohane has published over 200 papers in the medical literature and authored a widely used book on Microarrays for an Integrative Genomics. He has been elected to multiple honor societies including the American Society for Clinical Investigation, the American College of Medical Informatics, and the Institute of Medicine. He leads a doctoral program in genomics and bioinformatics within the Division of Medical Science at Harvard University. He is also an occasionally practicing pediatric endocrinologist.

 

#SachsBioinvestchat, #bioinvestchat

#Sachs14thBEF

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Track 5 Next-Gen Sequencing Informatics: Advances in Analysis and Interpretation of NGS Data @ BioIT World, April 29 – May 1, 2014 Seaport World Trade Center, Boston, MA

Reporter: Aviva Lev-Ari, PhD, RN

 

NGS Bioinformatics Marketplace: Emerging Trends and Predictions

10:50 Chairperson’s Remarks

Narges Baniasadi, Ph.D., Founder & CEO, Bina Technologies, Inc.

11:00 Global Next-Generation Sequencing Informatics Markets: Inflated Expectations in an Emerging Market

Greg Caressi, Senior Vice President, Healthcare and Life Sciences, Frost & Sullivan

This presentation evaluates the global next-generation sequencing (NGS) informatics markets from 2012 to 2018. Learn key market drivers and restraints,

key highlights for many of the leading NGS informatics services providers and vendors, revenue forecasts, and the important trends and predictions that

affect market growth.

Organizational Approaches to NGS Informatics

11:30 High-Performance Databases to Manage and Analyze NGS Data

Joseph Szustakowski, Ph.D., Head, Bioinformatics, Biomarker Development,

Novartis Institutes for Biomedical Research

The size, scale, and complexity of NGS data sets call for new data management and analysis strategies. High-performance database systems

combine the advantages of both established and cutting edge technologies. We are using high performance database systems to manage and analyze NGS, clinical, pathway, and phenotypic data with great success. We will describe our approach and concrete success stories that demonstrate its efficiency and effectiveness.

12:00 pm Taming Big Science Data Growth with Converged Infrastructure

Aaron D. Gardner, Senior Scientific Consultant,

BioTeam, Inc.

Many of the largest NGS sites have identified IO bottlenecks as their number one concern in growing their infrastructure to support current and projected

data growth rates. In this talk Aaron D. Gardner, Senior Scientific Consultant, BioTeam, Inc. will share real-world strategies and implementation details

for building converged storage infrastructure to support the performance, scalability and collaborative requirements of today’s NGS workflows.

12:15 Next Generation Sequencing:  Workflow Overview from a High-Performance Computing Point of View

Carlos P. Sosa, Ph.D., Applications Engineer, HPC Lead,

Cray, Inc.

Next Generation Sequencing (NGS) allows for the analysis of genetic material with unprecedented speed and efficiency. NGS increasingly shifts the burden

from chemistry done in a laboratory to a string manipulation problem, well suited to High- Performance Computing. We explore the impact of the NGS

workflow in the design of IT infrastructures. We also present Cray’s most recent solutions for NGS workflow.

SOSA in REAL TIME

Bioinformatics and BIG DATA – NGS @ CRAY i 2014

I/O moving, storage data – UNIFIED solution by Cray

  • Data access
  • Fast Access
  • Storage
  • manage high performance computinf; NGS work flow, multiple human genomes 61 then 240 sequentiallt, with high performance in 51 hours, 140 genomes in simultaneous

Architecture @Cray for Genomics

  • sequensors
  • Galaxy
  • servers for analysis
  •  workstation: Illumina, galaxy, CRAY does the integration of 3rd party SW using a workflow LEVERAGING the network, the fastest in the World, network useding NPI for scaling and i/O
  • Compute blades, reserves formI?O nodes, the Fastest interconnet in the industry
  • scale of capacity and capability, link interconnect in the file System: lustre
  • optimization of bottle neck: capability, capacity, file structure for super fast I/O

12:40 Luncheon Presentation I

Erasing the Data Analysis Bottleneck with BaseSpace

Jordan Stockton, Ph.D., Marketing Director,

Enterprise Informatics, Illumina, Inc.

Since the inception of next generation sequencing, great attention has been paid to challenges such as storage, alignment, and variant calling. We believe

that this narrow focus has distracted many biologists from higher-level scientific goals, and that simplifying this process will expedite the discovery

process in the field of applied genomics. In this talk we will show that applications in BaseSpace can empower a new class of researcher to go from

sample to answer quickly, and can allow software developers to make their tools accessible to a vast and receptive audience.

1:10 Luncheon Presentation II: Sponsored by

The Empowered Genome Community: First Insights from Shareable Joint Interpretation of Personal Genomes for Research

Nathan Pearson, Ph.D. Principal Genome Scientist,

QIAGEN

Genome sequencing is becoming prevalent however understanding each genome requires comparing many genomes. We launched the Empowered Genome Community, consisting of people from programs such as the Personal Genome Project (PGP) and Illumina’s Understand Your Genome. Using Ingenuity Variant Analysis, members have identified proof of principle insights on a common complex disease (here,myopia) derived by open collaborative analysis of PGP genomes.

Pearson in REAL TIME

One Genome vs. population of Genomes

IF one Genome:

  1. ancestry
  2. family health
  3. less about drug and mirrors
  4. health is complex

CHallenges

1. mine genome

2. what all genome swill do for Humanity not what my genome can do for me

3. Cohort analysis, rich for variance

4. Ingenuity Variant Analysis – secure environment

5. comparison of genomes, a sequence, reference matching

6. phynogenum, statistical analysis as Population geneticists do

Open, collabrative myopia analysis GENES rare leading to myuopia – 111 genomes

– first-pass finding highlight 12 plausibly myopia-relevant genes: variants in cases vs control

– refine finding and analysis, statistical association, common variance

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Track 4 Bioinformatics: Utilizing Massive Quantities of –omic Information across Research Initiatives @ BioIT World, April 29 – May 1, 2014 Seaport World Trade Center, Boston, MA

Reporter: Aviva Lev-Ari, PhD, RN

 

Bioinformatics for Big Data

10:50 Chairperson’s Remarks

Les Mara, Founder, Databiology, Ltd.

 

11:00 Data Management Best Practices for Genomics Service Providers

Vas Vasiliadis, Director, Products, Computation Institute,

University of Chicago and Argonne National Laboratory

Genomics research teams in academia and industry are increasingly limited at all stages of their work by large and unwieldy datasets, poor integration between the computing facilities they use for analysis, and difficulty in sharing analysis results with their customers and collaborators. We will discuss issues with current approaches and describe emerging best practices for managing genomics data through its lifecycle.

Vas in REAL TIME

Computation Institute @ University of Chicago solutions to non profit entities, scale and make available in an affordable way “I have nothing to say on Big Data”, 57.7% survey by NAS, average time researcher spend on research, it will get worse, research data management morphed into better ways, industrial robust way, commercial start ups are role model. All functions of an enterprise now available as applications for small business.

  • Highly scaleable, invisible
  • high performance
  • In Genomics, tools – shipping hard drive new ways to develop research infrastructure:
  • dropbox, does not scale Amazon’s Webservices is the cloud
  • security in sharing across campuses, InCommon – cross domains sw access constrains are mitigated.
  • identity provision for multiple identity – identity Hub, one time association done, Group Hubs, i.e., ci connect – UChicago, access to systems at other campuses – connecting science to cycles of data, network not utilizied efficiently – tools not design for that, FTP, Firewalls are designed for data not Big data.
  • Science DMZ – carve realestate for Science data transfer, monitoring the transfer
  • Reproducibility, Provenance, Public mandates
  • Data publication Service: VIVO, fisshare, Fedora, duracloud, doi, identification, store, preserve,, curation workflow
  • Search for discovery: Faceted Search. browse distributed, access locally – automation required, outsourcing, delivery throufg SaaS
  • We are all on cloud

11:30 NGS Analysis to Drug Discovery: Impact of High-Performance Computing in Life Sciences

Bhanu Rekepalli, Ph.D., Assistant Professor and Research Scientist, Joint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory

We are working with small-cluster-based applications most widely used by the scientific community on the world’s premier supercomputers. We incorporated these parallel applications into science gateways with user-friendly, web-based portals. Learn how the research at UTK-ORNL will help to bridge the gap between the rate of big data generation in life sciences and the speed and ease at which biologists and pharmacists can study this data.

Bhanu in REAL TIME

Cost per Genome does down, 2011 from $100,000 to $1,000

  • Solutions:
  • architecture
  • parallel informatics
  • SW modules
  • web-based gateway
  • XSEDE.org sponsured by NSF at all sponsored research by NSF
  • LCF – applications: Astrophysics, Bioinfo, CFD, highly scalable wrappers for the analysis Blast scaling results in Biology
  • Next generation super computers: Xeon/Phi

NICS Informatics Science gateway – PoPLAR Portal for Parallel Scaling Life Sciences Applications & Research

  • automated workflows
  • Smithsonian Institute, generate genomes fro all life entities in the universe: BGI
  • Titan Genomic Data analysis –   Everglade ecosystem, sequenced
  • Univ S. Carolina great computing infrastructure
  • Super computer: KRAKEN
  • 5-10 proteins modeling on supercomputers for novel drug discovery
  • Vascular Tree system for Heart transplant – visualization and modeling

12:00 pm The Future of Biobank Informatics

Bruce Pharr, Vice President, Product Marketing, Laboratory Systems, Remedy Informatics

As biobanks become increasingly essential to basic, translational, and clinical research for genetic studies and personalized medicine, biobank informatics must address areas from biospecimen tracking, privacy protection, and quality management to pre-analytical and clinical collection/identification of study data elements. This presentation will examine specific requirements for third-generation biobanks and how biobank informatics will meet those requirements.

Bruce Pharr in REAL TIME

Flexible Standartization

BioBank use of informatics in the1980s – bio specimens. 1999 RAND research 307 M biospecimens in US biobanks growing at 20M per year.

2nd – Gen Bioband

2005 – 3rd-Gen Biobanks – 15000 studies on Cancer, biospecimen, Consent of donors is a must.

Biobank – PAtion , Procedure, specimen acquistion, storage, processing, distribution, analysis

Building Registries – Mosaic Platform

  • Specimen Track BMS,
  • Mosaic Ontology:  application and Engine

1. standardize specimen requirement

Registries set up the storage: administrator dashboard vs user bashboard

2. Interoperability

3. Quality analysis

4. Informed Consent

 

12:15 Learn How YarcData’s Graph Analytics Appliance Makes It Easy to Use Big Data in Life Sciences

Ted Slater, Senior Solutions Architect, Life Sciences, YarcData, a division of Cray

YarcData, a division of Cray, offers high performance solutions for big data graph analytics at scale, finally giving researchers the power to leverage all the data they need to stratify patients, discover new drug targets, accelerate NGS analysis, predict biomarkers, and better understand diseases and their treatments.

12:40 Luncheon Presentation I

The Role of Portals for Managing Biostatistics Projects at a CRO

Les Jordan, Director, Life Sciences IT Consulting, Quintiles

This session will focus on how portals and other tools are used within Quintiles and at other pharmas to manage projects within the biostatistics department.

1:10 Luncheon Presentation II (Sponsorship Opportunity Available) or Lunch on Your Own

1:50 Chairperson’s Remarks

Michael Liebman, Ph.D., Managing Director, IPQ Analytics, LLC

Sabrina Molinaro, Ph.D., Head of Epidemiology, Institute of ClinicalPhysiology, National Research Council –

CNR Italy

1:55 Integration of Multi-Omic Data Using Linked Data Technologies

Aleksandar Milosavljevic, Ph.D., Professor, Human Genetics; Co-Director,

Program in Structural & Computational Biology and Molecular Biophysics;

Co-Director, Computational and Integrative Biomedical Research Center,

Baylor College of Medicine

By virtue of programmatic interoperability (uniform REST APIs), Genboree servers enable virtual integration of multi-omic data that is distributed across multiple physical locations. Linked Data technologies of the Semantic Web provide an additional “logical” layer of integration by enabling distributed queries across the distributed data and by bringing multi-omic data into the context of pathways and other background knowledge required for data interpretation.

2:25 Building Open Source Semantic Web-Based Biomedical Content Repositories to Facilitate and Speed Up Discovery and Research

Bhanu Bahl, Ph.D., Director, Clinical and Translational Science Centre,

Harvard Medical School

Douglas MacFadden, CIO, Harvard Catalyst at Harvard Medical School

Eagle-i open source network at Harvard provides a state-of-the-art informatics

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AWARDS: Best of Show Awards, Best Practices Awards and 2014 Benjamin Franklin Award  @ BioIT World, April 29 – May 1, 2014 Seaport World Trade Center, Boston, MA

Reorter: Aviva Lev-Ari, PhD, RN

 

Best of Show Awards

The Best of Show Awards offer exhibitors an opportunity to distinguish their products from the competition. Judged by a team of leading industry experts and Bio-IT World editors, this award identifies exceptional innovation in technologies used by life science professionals today. Judging and the announcement of winners is conducted live in the Exhibit Hall. Winners will be announced on Wednesday, April 30 at 5:30pm. The deadline for product submissions is February 21, 2014. To learn more about this program, contact Ryan Kirrane at 781-972-1354 or email rkirrane@healthtech.com.

2014 WINNER(s) are announced in Real Time

2014 – Five categories

1. Clinical ad Health IT – Astazeneca with Tessella – Real Time Analytics for Clinical Trial (RTACT) – engine for innovations

2. Research and Drug Discovery: U-bioPRED with the TranSMART Foundation – Open Source  – Emperial College – Biomarkers for Asthma,  hospitals, 340 universities, 34 Pharmas

3. Informatics: Pistoia Alliance – HELM – Pfizer, released data for HELM Project

4. Knowledge Management Finalists: GENENTECH – Genentech Cell Line Resource

5. IT Infrastructure/HPC Winner:

Baylor College of Medicine with DNAnexus –

 

2014 Judges’Prize – UK for Patient Data Intgration

2014 Editors’ Choice Award: Mount Sinai – Rethinking Type 2 Diabetes through Data Informatics

2014 Benjamin Franklin Award

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by the Bioinformatics Organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. Nominations are now being accepted!

The winner will be announced in the Ampitheater at 9:00am on Wednesday, April 30 during the Plenary Keynote and Awards Program, WEDNESDAY, APRIL 30 | 8:00 – 9:45 AM.

Full details including previous laureates and entry forms are available at www.bioinformatics.org/franklin.

2014 WINNER is:

Helen Berman, Ph.D.

Board of Governors Professor of Chemistry and Chemical Biology, Rutgers University;

Founding Member, Worldwide Protein Data Bank (wwPDB); Director, Research Collaboratory for Structural Bioinformatics PDB (RCSB PDB)

Helen: ACCEPTANCE AWARD SPEECH

Proteins: Synthesis, enzymes, Health & Disease

PDB depositors: 850 new entries / month, 468 Miliions downloads & views, PDB Access

History of sharing the databank on protein

J.D. Bernl – 1944 crystalied Pepsin with Dorothy Hodgkin Oxford, manyWomen Distingushed

1960 – Early structure of proteins: Myoglobin, hemoglobin

1970

1980

1990

2000  Ribosomes

2010s: macromolecule machines

  • Science of protein structure
  • Technology: electromicroscopy,  Structure Genomics – data driven science Hybrid methods at Present for 3D structure identification

COMMUNITY ATTITUDE –  1971 PDB archive established at Cold Spring Harbor, Walter Hamilton, petition to have an Open DB of Protein, Brookhaven Labs, to be shared with UK, Nature New Biology: Seven Structures to the DB

1982 – AIDs epidemic – NIH – requested data to be Open, community set its own rules on data organization Fred Richards, Yale, requested on moral ground, DB to be Open.

1993 – mandatory to sahre dat linked to publication, no Journal will accet  an article id data was not in PDB.

1996 – dictionary put together

2008: experimental data madatory to be put in PDB, Validation

2011: PDBx  definition of X-Ray, NMR, and 3DEM, small-angle Scattering

Collaboration with to enable: self storage, structure based drug design

SCIENCE in ther IMPORTANT to be put there, IT evolved, changes to data

global organization collaboration

Communities to work together

L.D>Bernal – SOcial function of Science, 1939

Elenor Ostrom 2009 Nobel Prize in Economics – Community collaboration by rules

Best Practices Awards

Add value to your Conference & Expo attendance, sponsorship or exhibit package, and further heighten your visibility with the creative positioning offered as a Best Practices participant. Winners will be selected by a peer review expert panel in early 2014.

Bio-IT World will present the Awards in the Amphitheater at 9:30am on Wednesday, April 30 during the Plenary Keynote and Awards Program, WEDNESDAY, APRIL 30 | 8:00 – 9:45 AM

Early bird deadline (no fee) for entry is December 16, 2013 and final deadline (fee) for entry is February 10, 2014. Full details including previous winners and entry forms are available at Bio-ITWorldExpo.com.

2014 WINNER(s) are:

 

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Track 6 Systems Pharmacology: Pathways to Patient Response @ BioIT World, April 29 – May 1, 2014 Seaport World Trade Center, Boston, MA

Reporter: Aviva Lev-Ari, PhD, RN

April 30, 2014

Modeling: Novel Tools

10:50 Chairperson’s Remarks

Avi Ma’ayan, Ph.D., Associate Professor, Pharmacology and Systems

Therapeutics, Icahn School of Medicine at Mount Sinai

11:00 The Human Avatar: Quantitative Systems Pharmacology to Support Physician Decision Making in Neurology and Psychiatry

Hugo Geerts, Ph.D., MBA, BA, CSO, In Silico Biosciences;

Adjunct Associate Professor, Perelman School of Medicine, University of Pennsylvania

CNS Quantitative Systems Pharmacology uses computer-based mechanistic modeling integrating brain network neurophysiology, functional imaging of

genetics, pharmacology of drug-receptor interactions and parameterization with clinical data. A patient model (“human avatar”) can be developed

accounting for polypharmacy and life history of traumatic events to help identify optimal treatments.

 

11:30 VisANT: An Integrative Network Platform to Connect Genes, Drugs, Diseases and Therapies

Zhenjun Hu, Ph.D., Research Associate Professor, Center for Advanced Genomic Technology,

Bioinformatics Program, Boston University

With the rapid accumulation of our knowledge on diseases, disease-related genes and drug targets, network-based analysis plays an increasingly

important role in systems biology, systems pharmacology and translational science. The new release of VisANT aims to provide new functions to facilitate

the convenient network analysis of diseases, therapies, genes and drugs.

12:00 pm Selected Oral Poster Presentation: Individualized PK/PD Biosimulations for Precision Drug Dosing: Diabetes Mellitus

Clyde Phelix, Ph.D., Associate Professor, Biology,

University of Texas San Antonio

Individualized biosimulations offer many advantages to precision medicine. Using one’s transcriptome to determine parameters of kinetic models of metabolism reanimates that individual for in silico testing. The Transcriptome-To-Metabolome™ Model is multiorgan and multicompartmental, including over 30 primary and secondary metabolic pathways and transport processes. Thus pharmacokinetics/pharmacodynamics studies can be performed in silico before treating each patient.

12:40 Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

Modeling: Cancer

1:50 Chairperson’s Remarks

Hugo Geerts, Ph.D., MBA, BA, CSO, In Silico Biosciences; Adjunct Associate Professor, Perelman School of Medicine, University of Pennsylvania

In REAL TIME

»»1:55 FEATURED PRESENTATION

Identifying Drug Targets from Drug-Induced Changes in Genome-Wide mRNA Expression

Avi Ma’ayan, Ph.D., Associate Professor, Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai

We collected and organized publicly available genome-wide gene expression data where hundreds of drugs were used to treat mammalian cells and changes in expression were compared to a control. We then developed computational methods that try to find the drug targets from the expression changes. We show that different steps in the analysis can contribute to approaching the right answer.

In REAL TIME

System biology and drug related by phynotypes, drugs causes diseasespatient and side effects

Networs,

Gene-set Libraries stored in Gene Matrix Transpose(GMT) files, KEGG Example

Drug-set Libraries

Drug-Drug similarity data, SIDER 2 Side Effect Resource, FDA adverse effect Report data

Connactivity Map: Broad  Institute, L1000 cell lines microarray, different  drug dose, DRUG effect on GENES

  • develop new compondts,
  • measure toxicity

LINC-L1000 data overview, Drug-drug similarity structure, connversion

for Vector side effect

LINCS Canvas Browser

Cell-Line/Drug Browser

New method for clustering patient by outcomes, survival analysis

http://www/maayanlab.net/LINCS/LCB/

Drug interact with target drug vs transcription factors, over expression

Over expression of transcription factors vs knock out for validation

2:25 Infrastructure for Comparison of Systematically Generated Cancer Networks vs. Literature Models

Dexter Pratt, Project Director,

NDEx, Cytoscape Consortium

Cancer subtype genetic networks can be generated by systematic analysis of patient somatic mutation data. Comparison to existing models of cancer

mechanisms is an important step in investigating these data-derived models. Recent work on Network Based Stratification (NBS) at the Ideker Lab will be

described along with tools for network comparison under development in the NDEx project.

In REAL TIME

Network based classification, unsupervised methoods

Ovarian cancer- sparse mutations, no two patients share same mutation, clustering by expression profile – can be cause, gene – gene interaction, smooth knowlede,

Reference networks, Common Entity identification system used, started at UCSD. overlap of curated PATHWAYS, query, neighborhoods in the reference network,

Using mapping tables to mapp identifiers for entity correspondence

Complex Reference Networks N:1 and 1:N

Transcriptionalcontrol motif, extract motifs mapp data to motifs, concordence,  and other metrics to be computed fromreferenced data,

Boundaries of Pathways – Reaction chain,  Differentially expressed genes –>> enzymes –>>> reactions  (differentilly regulated) –>> smaoll molecules

CONCLUTIONS

Cliniccal relevance, hypothesis motifs and interactions.

MAY 1, 2014

Modeling: Drug/Dose Response

1:55 Chairperson’s Remarks

Birgit Schoeberl, Ph.D., Vice President, Research, Merrimack Pharmaceuticals

»»2:00 FEATURED PRESENTATION

Systems Approaches to Risk Assessment

Lawrence J. Lesko, Ph.D., FCP, Clinical Professor and Director, Center for Pharmacometrics and Systems Pharmacology, University of Florida

“Idiosyncratic” adverse drug events (ADEs) are a substantial societal burden in terms of morbidity, mortality and healthcare costs. Predicting who

will suffer ADEs from what medications is extremely difficult with current observational or surveillance approaches. A new mechanistic approach to

drug safety science is sorely needed. Systems approaches may address this unmet medical need.

2:30 Pharmacodynamic Characterization of Compounds in Drug Discovery

Rui-Ru Ji, Ph.D., Principal Scientist, Genomics, Bristol-Myers Squibb

The transcriptome reacts in a dose-dependent manner to compound treatment. We will present methodology and will discuss multiple applications of dose

response profiling of the whole transcriptome.

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PLENARY KEYNOTE PRESENTATIONS: TUESDAY, APRIL 29 | 4:00 – 5:00 PM @ BioIT World, April 29 – May 1, 2014 Seaport World Trade Center, Boston, MA

 

Reporter: Aviva Lev-Ari, PhD, RN

 

PLENARY KEYNOTE PRESENTATIONS:

TUESDAY, APRIL 29 | 4:00 – 5:00 PM

Keynote Introduction: Sponsored by Dave Wilson, Senior Director, Business Development Manager, Global Channels, Hitachi Data Systems

John Quackenbush, Ph.D.

CEO, GenoSpace; Professor, Dana-Farber

Cancer Institute and Harvard School of Public Health

John Quackenbush received his Ph.D. in 1990 in theoretical physics from UCLA working on string theory models. Following two years as a postdoctoral fellow in physics, Dr. Quackenbush applied for and received a Special Emphasis Research Career Award from the National Center for Human Genome Research to work on the Human Genome Project. He spent two years at the Salk Institute and two years at Stanford University working at the interface of genomics and computational biology. In 1997 he joined the faculty of The Institute for Genomic Research (TIGR) where his focus began to shift to understanding what was encoded within the human genome. Since joining the faculties of the Dana-Farber Cancer Institute and the Harvard School of Public Health in 2005, his work has focused on decoding and modeling the networks of interacting genes that drive disease. In 2011 he and partner Mick Correll launched GenoSpace to facilitate genomic data analysis and interpretation, focused on accelerating research and delivering relevant and actionable solutions for personalized medicine.

IN REAL TIME FROM THE AMPHITHEATER of World BioIT2014

Twitter

#BioIT14

2900 attendees 140 exhibitor, 250 Speakers, Best of Show Awart, Best Practices Award, Franklin Award, Memorial to Pat McGovern ex-CEO and Chairman of IDG and launcher of BioIT, McGovern Institute for Brain Research @MIT his gift $350 million, [Broad’s gift to MIT was $650million]

Hitachi Data Perspective

Cloud and Aanlytics

John Quackenbush about Precision Medicine

Desire to use an information ecosystem for mediicine

The DRIVER is DATA – access t data Data that drives innovations in BioMedical

IT

  • Cloud Computing data, information and STORAGE of Data, data access, integration,
  • iPhone – applications for needs,

Bio – anniversary of DNA discovery structure in 1953

Genome Sequence – Transforming Medicine: Big Data: Volume, Velocity, Variety

Genomic Medicine – data for interpretation of Symptoms: diet, exercise

Cost of generation of data drops clinical relevance of data – sequencing now $1000 pay with credit card

Cost of the Analysis – $100,000 – Research number the genes translational, identify biomarkers to better achieve efficacy in segments of the population.

Diagnosis – Clinical Medicine

Reimbursement – few $ to identify VARIANCE relevant to treat disease

Cloud – secure the infrastructure – same dat looked by different parties to answer different questions.

GenoSpace for Research – N= many patients

GenoSpace for Clinical Care – N=1

GenoSpace for Patient Community – N=many individual patients

Patient CONSENT

  • Secure storage data
  • analytics and visualization
  • diverse data
  • share dat securely

data in transit to be secure,  consumption of data

R&D Context

1000 Patients

50 Clinical site

large complex data

MMRF’s COMMPASS Study @Dana Farber – Multiple Myeloma Research Foundation

PORTAL design – to make data analysis of Cohort of Patioets, attribute analyzer, tools to find properties of cohort, compare across cohorts

Data analysis made easy – Precision Medicine based on Prediction

Population level data

end stage treatment

clincal trial

Translational Research – Pharma targets patients 

MMRF – gateway to the Community, interface for Patients to provide information during the course of Treatment, PATIENTS share, 1000 patients signed up to share data

  • Patient Reported outcomes
  • data integration
  • clinical trial recruitment
  • biomarker discovery

HOW to deliver data to POINT of CARE: Cancer more data Clinical (Pathology/Lab)

BioPoetry: Story what the data analysis MEANS

CURATION OF DATA – GenoSpace – for Clinical Labs

  • Pathology Group: Sequencing
  • Application development for REPORTS: FullView – meta data GEnoSpace 
  • Look at the assay for standard of Care
  • PDF format to scan and place in EMR, language suggestive,
  • MD’s Portal, giving access to Patients to add data

 

Thomson Reuter – Annotate

An OS for Precision Medicin

Genomics and integration with Clinical data

how to create system for all parties involved. Use of data for multiple needs that overlap

Information management – patient at the center

Precision Medicine is the FUTURE – Digital Architects for Precision Mediicne

 

 

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LPBI Repository of HashTags for Scientific Conferences

Reporter: Aviva Lev-Ari, PhD, RN

BioIT World, April 29 – May 1, 2014, Seaport World Trade Center, Boston, MA

http://www.bio-itworldexpo.com/uploadedFiles/Bio-IT_World_Expo/Agenda/14/2014-BIT-Brochure.pdf

http://pharmaceuticalintelligence.com/2014/04/09/bioit-world-april-29-may-1-2014-seaport-world-trade-center-boston-ma/

Searches by Dr. Stephen  J Williams

Hashtags that get more than 3000 views and @sites that have at least 3000 followers

#pharmaIT
#BIOIT
#technews
#curation
#pharmanews
#mobilehealth
#mhealth
#science
#science2_0

2014 Bio-IT World Twitter feed @bioitworld

#healtcare
#BIOIT14
#Boston   —-NOTE that #city has alot of appeal now

Twitter Feeds

@Biotech News
@MhealthForAll
@mHealthAlliance
@HCtrends
@mobilehealth360
@science 2_0
Brian Dolan@mobilehealth    —- has 4000 followers

,,,,

14th ANNUAL BIOTECH IN EUROPE FORUM For Global Partnering & Investment

30th September – 1st October 2014 • Congress Center Basel

SACHS Associates, London

http://www.sachsforum.com/zurich14/index.html

http://pharmaceuticalintelligence.com/2014/03/25/14th-annual-biotech-in-europe-forum-for-global-partnering-investment-930-1012014-•-congress-center-basel-sachs-associates-london/

 

NOT LISTED YET


We need to establish for our business, I.e.,

#CancerImmunoTherapy@pharma_BI
#TranslationalMedicine@pharma_BI
#CardiovascularPharmacoGenomics@pharma_BI
#CancerChemo-RT@pharma_BI
#BioMed-MedicalDevices@Pharma_BI

Open Access OnLine Scientific Journal
BioMed-MedTech Venture
Scientific Conference Press Coverage

25 characters for each #______

How about the following

#pharma_BiandBioMed
#pharma_e-Seriesande-Books
#pharma_ ScientificConferencePress 

 

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John Rinn - Genomic Garbage Man

John Rinn – Genomic Garbage Man (Photo credit: ChimpLearnGood)

DNA: One man’s trash is another man’s treasure, but there is no JUNK after all

Author: Demet Sag, PhD

One man’s trash is another man’s treasure, but there is no JUNK after all:

The JUNK has a meaning

 

Long non-coding RNAs recognized after transcriptome sequencing and studied more closely recently thanks to genomic tiling arrays, cDNA sequencing and RNA-Seq, which they have provided initial insights into the extent and depth of transcribed sequence across human and other genomes. How many are there in the genome? What are their mechanisms? How can we use them in molecular diagnostics and targeted therapies?  How do they effect the function in a disease? Is it possible to modulate gene expression at the level of stem cell to redirect the cell differentiation? These are the main questions that we are looking for.

In early 90s actually first lincRNA was described, Xist. The main function was dosage compensation. Then in 2000s FANTOM consortium project changed the perspective on these long transcripts. Then they are called natural antisense transcripts (NATs), because very large number of these transcripts is overlapping with, and is transcribed in the antisense direction, to protein-coding genes.  As a result of this study 11000 lincRNA discovered from full length cDNAs in mice. Later, yet another shift occur since these transcribed units are solely located in the introns or within “junk” DNA of protein-coding genes.  Another independent study quantified that about 40% of protein-coding genes express NATs. Proven that there is nothing junk about DNA. Then, it was found that there are 8000 lincRNAs and among these 4000 are determined since they provide cell identity with multi-exogenic, polyadenylated, capped, ether in the cytoplasm or in the nucleus. However, even more recent studies show that there are about 20,000 lincRNAs.  Furthermore, lincRNAs are classified under three distinct class: 1. Long-non-coding RNAs away from protein-coding genes, 2 NATs transcribed from the opposite strand of protein-coding genes, 3. Intronic lincRNAs expressed from within the introns of protein coding genes.

 

English: The human genome, categorized by func...

The human genome, categorized by function of each gene product, given both as number of genes and as percentage of all genes. (Photo credit: Wikipedia)

Their function is under study. However, keep in mind that they are redundant, so deleting or creating null mutations may or may not answer specific development questions. On the other hand, epigenetics, gene imprinting, and pathologies can be the best resource to identify their specific roles in biological functions and interactions.  Distinct gene regulation either as a cis or trans element, gene imprinting, modulating alternative splicing, nuclear organization, determining a chromatin structure are under study.  This will allow us to relate genome structure and function in health and disease better.  Identification of their function during biological responses require a long way to be completed due to complexity since lincRNAs also regulate microRNAs.  Regardless of many obstacles there is a progress.  Disregulation of these lincRNA mainly observed in several cancer types, prostate, breast, hepatocellular carcinoma, colorectal, glioma and melanoma, possibly more. Most of the studies are done in vitro. However, there are many great model organism work as well, such as mice, zebra fish, and worm.

It was also not surprising that their regulation possibly under control of hormones based on circadian clock of our body. So better to sleep eight hour a day is not a cliché.

 

Next topic will include understanding of lincRNA mechanisms and epigenetics followed by lincRNAs during disease and cellular genesis.

 

Mechanism, Genome and Genetics:

Long non-coding RNAs: insights into functions. Mercer TR, Dinger ME, Mattick JS Nat. Rev. Genet. 2009;10:155159. http://www.ncbi.nlm.nih.gov/pubmed/19188922

 

Long Noncoding RNAs: Past, Present, and Future” Genetics 1 March 2013: 651-669. http://www.genetics.org/content/193/3/651.abstract

 

“RNA-protein analysis using a conditional CRISPR nuclease” Proc. Natl. Acad. Sci. USA 2 April 2013: 5416-5421. http://www.pnas.org/content/110/14/5416.abstract

“Noncoding RNA and Polycomb recruitment” RNA 1 April 2013: 429-442. http://rnajournal.cshlp.org/content/19/4/429.abstract

 

“Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs” Nucleic Acids Res 1 August 2012: 6391-6400. http://nar.oxfordjournals.org/content/40/14/6391.abstract

 

 

“Long noncoding RNAs regulate adipogenesis” Proc. Natl. Acad. Sci. USA 26 February 2013: 3387-3392. http://www.pnas.org/content/110/9/3387.abstract

 

“Circadian changes in long noncoding RNAs in the pineal gland” Proc. Natl. Acad. Sci. USA 14 August 2012: 13319-13324. http://www.pnas.org/content/109/33/13319.abstract

Animal and Development:

“Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis” Genome Res 1 March 2012: 577-591. http://genome.cshlp.org/content/22/3/577.abstract

 

“Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm” Genome Res 1 April 2011: 578-589. http://genome.cshlp.org/content/21/4/578.abstract

Long noncoding RNAs in C. elegans” Genome Res 1 December 2012: 2529-2540. http://genome.cshlp.org/content/22/12/2529.abstract

A spatial and temporal map of C. elegans gene expression” Genome Res 1 February 2011: 325-341. http://genome.cshlp.org/content/21/2/325.abstract

 

“SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors” Genes Dev. 1 April 2013: 749-766. http://genesdev.cshlp.org/content/27/7/749.abstract

Other related articles published on this Open Access Online Scientific Journal include the following:

…  therapies in a variety of animal models and contributed to regulatory CMC and IND-enabling safety and toxicology studies for inclusion in …  sequences sort a-cardiac and b-cytoplasmic actin messenger RNAs to different cytoplasmic compartments. J. Cell. Biol., …

…  and posttranscriptional mechanisms contributing to the regulatory network. We examined proinflammatory gene regulation in …  articles What about Circular RNAs? (pharmaceuticalintelligence.com) How Genes Function …

…  due to their broad scope and non-specificity in the human genome. “I am extremely pro-patent, but I simply believe that people …  believe that individuals have an innate right to their own genome, or to allow their doctor to look at that genome, just like the lungs or …

…  Intelligence http://pharmaceuticalintelligence.com/2013/03/02/genome-sequenc…of-the-healthy/ ‎ Key Issues in Genome Sequencing of Healthy Individuals Eric Topol, MD, Genomic Medicine I …  touching on important controversies in the use of whole genome …

6 February 2013  by Dr. Sudipta Saha on Pharmaceutical Intelligence
…  of recombination is highly uneven across the human genome, as in all studied organisms. Substantial recombination active regions …  this variation would require comparison of recombination genome-wide among many single genomes. Whole-genome amplification (WGA) of …

…  Lev-Ari, PhD, RN and Pnina G. Abir-Am, PhD Putting Genome Interpretation to the Test 01/30/2013 Ashley Yeager How well do methods for interpreting genome variation work? Ashley Yeager takes a look at a community experiment that is trying to assess just how useful genome interpretation tools in real-world situations. At the American …

…  genomes — through the end of this year, National Human Genome Research Institute estimates indicate. And in his book, The Creative …  the interpretation of an apparently healthy person’s genome and that of an individual who is already affected by a disease, whether …
Topics: Cardiovascular Pharmaceutical Genomics, Personalized Medicine & Genomic Research, Pharmaceutical R&D investment, CANCER BIOLOGY & Innovations in Cancer Therapy, Chemical Genetics, Cell Biology, Signaling & Cell Circuits, Computational Biology/Systems and Bioinformatics, Medical and Population Genetics, genome biology, Biological Networks, Gene Regulation and Evolution, Population Health Management, Genetics & Pharmaceut, human genome, National Institutes of Health, Scripps Research Institute, Proteomics, Bio Instrumentation in Experimental Life Sciences Resea, Massachusetts General Hospital, DNA, FDA Regulatory Affairs, Clinical Trials and IRB related issues, Biomarkers & Medical Diagnostics, metabolomics, Molecular Genetics & Pharmaceutical, Genomic Testing: Methodology for Diagnosis, Technology Transfer: Biotech and Pharmaceutical, Health Law & Patient Safety, Eric Topol, national human genome research institute, Encode, NIST

…  scary findings: the tale of John Lauerman’s whole genome sequencing FEBRUARY 15, 2012 Joe Thakuria draws John Lauerman’s blood for whole genome sequencing. By Madeleine Price Ball, licensed under …  scary findings: the tale of John Lauerman’s whole genome sequencing » Joe Thakuria draws John …

…  2: LEADERS in the Competitive Space of Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in …  Treatment http://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic-drug-selection-in-cancer- …
Topics: Personalized Medicine & Genomic Research, Pharmaceutical R&D investment, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Medical and Population Genetics, genome biology, Disease Biology, Small Molecules in Development of Ther, Population Health Management, Genetics & Pharmaceut, Cancer, Foundation Medicine, Proteomics, DNA, DNA Sequencing, Biomarkers & Medical Diagnostics, metabolomics, AstraZeneca, Molecular Genetics & Pharmaceutical, Nature Medicine, Stem Cells for Regenerative Medicine, Genomic Testing: Methodology for Diagnosis, Technology Transfer: Biotech and Pharmaceutical, Full genome sequencing, Genomic Endocrinology, Preimplantation Genetic Diagnosi, Interviews with Scientific Leaders, Pharmacogenomics, Drug Delivery Platform Technology, Digene, Yuri Milner

3 February 2013  by sjwilliamspa on Pharmaceutical Intelligence
Genome-Wide Detection of Single-Nucleotide and Copy-Number Variation of a Single …  of DNA replication and the ability to amplify a whole genome.  The amplicons are then sequenced either by whole-genome sequencing methods using Sanger-sequencing to verify any single …

…  Aviva Lev-Ari, RN Genome Biol. 2012 Dec 13;13(12):R115. [Epub ahead of print] Whole-genome reconstruction and mutational signatures in gastric cancer. Nagarajan …  read and DNA-PET sequencing to present the first whole-genome analysis of two gastric adenocarcinomas, one with chromosomal …

1 September 2012  by pkandala on Pharmaceutical Intelligence
…  by interpreting the mathematical patterns in the cancer genome. Researchers at the University of Oslo, Norway (UiO) have developed a …  Hospital and UiO. Finds the changed patterns in the genome There is much talk about finding the special cancer gene. In reality, …

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Mobilizing Scientific Societies: Editorial by Science Editor-in-Chief Dr. Bruce Alberts

Reporter: Stephen J. Williams, Ph.D

This image has an empty alt attribute; its file name is ArticleID-28.png

WordCloud Image Produced by Adam Tubman

In a weekly editorial, Dr. Bruce Alberts, Editor-in –Chief of the journal Science discussed issues pertaining to science education in the United States[1].  He suggests the US science education system may need to be more flexible in its approach to science education in grade and high school.  He considers the one major problem is the “broad coverage of each subject, which kills student interest and makes genuine comprehension impossible.  Dr. Alberts suggest that state-based textbooks and the inability of the scientific community to understand teacher’s needs is driving this inadvertent problem.  The current textbooks used for scientific education focus more on memorization of a multitude of scientific terms than on concept development, experimentation and inquisition, and conclusion.  Materials are desperately needed for teachers to guide students to confront the overall concept, and working in teams, design potential methods to further explore these concepts.  He suggest this style of teaching would require close partnerships between top-notch teachers , educational  experts and scientific societies in order to research the effect of current curriculum materials but also develop  new Web-based  curriculum.

In a recent interview in the March 2013 issue of Wired magazine with Clayton Christensen, Ph.D. the author of the famed book The innovator’s Dilemma,  Dr. Christensen forwqarns the impending changes in higher education due to increased availability of online learning.  As he states, universities are on the precipice of a collapse in the future and those which survive will evolve hybrid models of education, part online and part classroom but will provide more specialized offerings to fit current needs.  Indeed, as listed below these changes and suggestions in science education may well be underway.  Below is a brief listing of scientific societies who have undertaken these challenges and formed extensive programs in STEM education.

FASEB (Federation of American Societies for Experimental Biology) programs such as:

Resources for Faculty and K-12 Teachers

APS Frontiers in Physiology Program – Provides professional development for middle and high school teachers by providing them with tools and resources and connecting them with researchers on-line and through workshops.

APS Physiology Understanding Week – Fosters relationships among teachers, students, and physiologists. PhUn Week encourages member physiologists across the nation to volunteer and work with teachers in their local community to visit a classroom during the first week in November.

Leap to the Top in Science Classes  from AAAS found at:

http://news.aaas.org/2013_annual_meeting/0214leap-to-the-top-in-science-classes.shtml

A progress report from the 2013 AAAS meeting follows:

Often, in the daily grind of slogging through a difficult science class, students see fully formed scientists and their discoveries as a distant blur. Remote men and women somehow make advanced science happen.

New efforts aim to bring students face to face with creative, imaginative scientists right in their classroom.

With a lifetime of scientific contributions at their back, many retired scientists, engineers, and physicians are returning to school, not as pupils or as instructors, but as classroom volunteers in public elementary, middle, and high schools.

This week over 400 teachers and scientists gathered in Boston for the first International Teacher-Scientist Partnership Conference, organized by AAAS Education and Human Resources and the University of California, San Francisco Science & Health Education Partnership, sponsored by the National Science Foundation. Presenters are scheduled to share a range of partnership models over three days, from scientists generating digital education tools, to teachers participating in research.

Throughout the first day of the conference, the conversation turned to the idea of bringing scientists into the classroom to work directly with the students.

Virginia Shepherd from Vanderbilt University shared a comprehensive analysis of the university’s nearly 20-year-old Graduate STEM Fellows in K-12 Education program. Presentation attendees duly applauded the success of the program but said that they had trouble establishing similar programs in their state for lack of funding.

A handful of organizations represented at the conference have found that an affordable way to bring scientists into the classroom is to recruit retired scientists.

Volunteers at Northeastern University’s Retirees Enhancing Science Education through Experiments and Demonstrations program, or RE-SEED, spend at least one day a week in an elementary, middle, or high school classroom in Massachusetts helping students conduct experiments as part of the existing curriculum.

“Retired scientists and engineers have a lot of experience from a lifetime of working in laboratories. They can make what the students are learning relevant,” said Christos Zahopoulos, a professor of education and engineering at Northeastern University.

Since founding RE-SEED in 1991, Zahopoulos has helped to start similar programs in 15 states, conducting on-site trainings for volunteers. While such programs start out strong, many of them have since faded, with only a handful remaining, he said.

Even though retirees are offering a free service to the schools, getting them trained and placed takes a certain amount of funding, Zahopoulos says. He has been fortunate to fund RE-SEED with private donations. Many programs were not so lucky.

AAAS’ Senior Scientists and Engineers (SSE), a service-oriented organization for retired scientists and engineers, has managed to sustain a similar program for seven years. In 2005, Zahopoulos helped SSE establish its own volunteer program.

Donald Rea, a former research chemist for NASA’s Jet Propulsion Laboratory and SSE volunteer coordinator for Virginia, hopes that helping to reinforce science education will enhance the public understanding of science in years to come.

“If you want to have an influence on science literacy, you want to get [kids] while they are young. So we work in classrooms as young as second grade,” Rea said.

This kind of investment takes many years to fully mature. So, how do Rea and Zahopoulos measure success? They look to their teachers, volunteers, and students.

Rea said he measures success by the eagerness of schools and teachers to participate year after year.

For Zahopoulos, hints of success sometimes come in the mail. He says one student wrote in to RE-SEED upon graduating from high school, several years after any contact with a RE-SEED volunteer, to say that she had decided to major in biology and had enrolled in a pre-medicine program.

Both Rea and Zahopoulos said they have been amazed at the dedication and eagerness of volunteers.

“When we first started, we asked volunteers to commit to one day a week for one year. Now we have volunteers who have been with us for 18 years and some volunteer as many as 4 times per week,” Zahopoulos said.

Ron McKnight, a former Department of Energy physicists and SSE volunteer has recently taken on the task of coordinating volunteers living in Montgomery County, Md. He still volunteers in middle school science classrooms and is considering taking on another assignment.

When asked what he loves about volunteering, he replied, “Whenever a kid I’m working with asks a really good question, that’s when I have a really good day.”

National Science Foundation (NSF) Research on Learning in Formal and Informal Settings (DRL)

Information can be found at http://www.nsf.gov/div/index.jsp?div=DRL

DRL invests in projects to improve the effectiveness of STEM learning for people of all ages. Its mission includes promoting innovative research, development, and evaluation of learning and teaching across all STEM disciplines by advancing cutting-edge knowledge and practices in both formal and informal learning settings. DRL also promotes the broadening and deepening of capacity and impact in the educational sciences by encouraging the participation of scientists, engineers, and educators from the range of disciplines represented at NSF. Therefore, DRL’s role in the larger context of Federal support for education research and evaluation is to be a catalyst for change—advancing theory, method, measurement, development, and application in STEM education. The Division seeks to advance both early, promising innovations as well as larger-scale adoptions of proven educational innovations. In doing so, it challenges the field to create the ideas, resources, and human capacity to bring about the needed transformation of STEM education for the 21st century.

Society of Toxicology K-12 Educational Outreach for Scientists

http://www.toxicology.org/ai/k12o/k-12scientists.asp

This sites contains multiple .pdf  files on volunteering and mentoring topics including

  • Scientist Mentor Ideas
  • Links to Other Mentoring Sites
  • Resources for toxicologists to use in K-12 Outreach
  • Regional Chapter K-12 Outreach

References:

1.         Alberts B: Mobilizing scientific societies. Science 2012, 338(6113):1396.

for high school teachers please see https://www.teachercertificationdegrees.com/top-blogs/science-teacher/

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New development in measuring mechanical properties of tissue

Author – Writer: Dror Nir, PhD

Measuring the effects induced onto imaging by the mechanical properties of tissue is a common approach to differentiate tissue abnormalities. In previous posts I discussed the applicability of imaging applications that visualize variations in tissue stiffness; e.g. ultrasound-elastography and MRI-elastography as aid in the diagnosis workflow of cancer. Today, I would like to report on a recent publication made in SPIE Newsroom describing an optical-imaging system to measure tissue stiffness at high resolution. I think that such emerging technologies should be followed up as they bear promise to bridge deficiencies of the traditional modalities currently in use.

Reporting on: Optical elastography probes mechanical properties of tissue at high resolution

By: David Sampson, Kelsey Kennedy, Robert McLaughlin and Brendan Kennedy

Information published at: SPIE Newsroom – Biomedical Optics & Medical Imaging

Probing the micro-mechanical properties of tissue using optical imaging might offer new surgical tools that enable improved differentiation of tissue pathologies, such as cancer or atherosclerosis.

11 January 2013, SPIE Newsroom. DOI: 10.1117/2.1201212.004605

Elastography is an emerging branch of medical imaging that uses mechanical contrast to better characterize tissue pathology than can be achieved with structural imaging alone. It achieves this by imaging a tissue’s response to mechanical loading. Although commercial products based on ultrasonography and magnetic resonance imaging (MRI) have been available for several years, these new modalities offer superior tissue differentiation deep in the human body. However, elastography is limited by its low resolution compared with the length scales relevant to many diseases. Increasing the resolution with optical techniques might offer new opportunities for elastography in medical imaging and surgical guidance.

An elastography system requires a means of loading the tissue to cause deformation and an imaging system with sufficient sensitivity and range to capture this deformation. Implicit in these requirements is access to the tissue of interest. Optical elastography has previously been largely based on schemes that suit small tissue samples rather than intact tissue in living humans. Additionally, such schemes have not had the sensitivity or range to produce high-fidelity images of mechanical properties. We have addressed both these issues in our recent work, developing the means to access tissues in vivo and improve the sensitivity and range of optical elastography using phase-sensitive optical coherence tomography as the underlying modality. The use of optical coherence tomography to perform elastography has come to be referred to as optical coherence elastography.1

To make optical coherence elastography on human subjects feasible, we designed an annular piezoelectric loading transducer (see Figure 1), through which we could simultaneously image, enabling the first in vivo dynamic optical coherence elastography on human subjects.2 We were subsequently able to extend this to three dimensions (see Figure 2), in collaboration with Stephen Boppart’s group at the University of Illinois at Urbana-Champaign.3 This extension took advantage of the high speed of spectral-domain optical coherence tomography, and the maturity of phase-sensitive detection techniques originally developed for Doppler flowmetry and microangiography.

Figure 1. Schematic (left) and photograph (right) of the annular load transducer and imaging optics for in vivo optical coherence elastography.

 

Figure 2. 2D images of in vivo human skin selected from 3D stacks. (a) Optical coherence tomography image and (b) the same image overlaid by the 2D dynamic elastogram recorded at 125Hz load frequency, highlighting the greater strain in the epidermis. Reprinted in modified form with permission.3

For general access to tissues in the body, optical coherence elastography faces two basic limitations. The free-space probe requires miniaturization for versatile access to tissue in confined or convoluted geometries. We addressed this in studies of the elastic properties of human airways using catheter-based anatomical optical coherence tomography.4

 

Figure 3. (a) Schematic diagram of needle optical coherence elastography. The phase difference Δφ=φ1– φ2 determines the displacement, d, when scaled by the wavelength, λ, and refractive index, n. (b) Needle and pig trachea. (c) Local displacement versus distance, with tissue boundaries indicated by red stars. (d) Representative histology. Reprinted in modified form with permission.6

More fundamentally, optical coherence tomography can only penetrate, at best, 1–2mm into most tissues, limiting it to superficial applications. To address this issue, we combined optical coherence elastography with needle probes, an active research area in our group (see Figure 3).5 We conveniently use the needle probe itself to deform the tissue during insertion.6 The deformation ahead of the needle tip depends on the mechanical properties of the tissue encountered, as well as on the nearby tissue environment, particularly on any interfaces ahead of it. We measure the local sub-micrometer displacement of the tissue between two positions of the moving needle probe. We plot this displacement versus distance ahead of the probe: see Figure 3(c). The slope of the displacement at location z is a measure of the local strain. A change in slope signifies a change in tissue stiffness; the steeper the slope, the softer the tissue (other things being equal). Figure 3 highlights this effect in a layered sample of pig trachea. The positions of the changes in slope correlate well with the tissue interfaces shown in the accompanying histology: see Figure 3(d).

The other key area of improvement we have focused on is lowering the optical coherence elastography noise floor by increasing the detection sensitivity, which is vital to make clinical imaging practical. We firstly showed that Gaussian-smoothed, weighted-least squares strain estimation improved the sensitivity of estimates by up to 12dB over conventional finite-difference methods.7 Next, we showed that performance could be further improved at low optical coherence tomo- graphy signal-to-noise ratios (and, therefore, at greater depths in tissue) by employing a 2D Fourier transform technique.8Combined with other system refinements, these improvements have enabled us to reach a displacement sensitivity of 300pm for typical optical coherence tomography signal-to-noise ratios in tissue, with room for improvement.

The Young’s modulus of soft tissue varies from kPa to tens of MPa, whereas the scattering coefficient of such tissues—which is largely responsible for determining the contrast of optical coherence tomography—is typically in the range 2–20mm−1. This apparent native advantage in mechanical over optical contrast (see the example in Figure 4), combined with the maturation of optical coherence elastography methods, bodes well for the future. In our group, we are pursuing tumor-margin identification using elastography; others have begun to consider corneal elastography,9, 10 and still others are examining shear wave schemes with the aim of probing Young’s modulus much deeper in tissues.11,12

 

Figure 4. Optical coherence tomography (a) and optical coherence elastography (b) images of the same phantom with two inclusions visible, showing enhanced mechanical over scattering contrast.

Optical elastography currently sits at a similar stage of development as ultrasound elastography did in 1999. Based on a similar trajectory, this field will rapidly expand over the next decade. Our recent results point to the first convincing applications of optical elastography being just around the corner.

We acknowledge funding for this work from Perpetual Trustees, the Raine Medical Research Foundation, the Cancer Council of Western Australia, the Australian Research Council, the National Health and Medical Research Council (Australia), and the National Breast Cancer Foundation (Australia).


David Sampson

Optical+Biomedical Engineering Laboratory
School of Electrical, Electronic and Computer Engineering

and
Centre for Microscopy, Characterisation and Analysis
The University of Western Australia

 

Perth, Australia
Kelsey Kennedy, Robert McLaughlin, Brendan Kennedy

Optical+Biomedical Engineering Laboratory
School of Electrical, Electronic and Computer Engineering
The University of Western Australia

Perth, Australia

References:
1. J. Schmitt, OCT elastography: imaging microscopic deformation and strain of tissue, Opt. Express 3(6), p. 199-211, 1998.doi:10.1364/OE.3.000199
2. B. F. Kennedy, T. R. Hillman, R. A. McLaughlin, B. C. Quirk, D. D. Sampson, In vivo dynamic optical coherence elastography using a ring actuator, Opt. Express 17(24), p. 21762-21772, 2009.doi:10.1364/OE.17.021762
3. B. F. Kennedy, X. Liang, S. G. Adie, D. K. Gerstmann, B. C. Quirk, S. A. Boppart, D. D. Sampson, In vivo three-dimensional optical coherence elastography, Opt. Express 19(7), p. 6623-6634, 2011.doi:10.1364/OE.19.006623
4. J. P. Williamson, R. A. McLaughlin, W. J. Noffsingerl, A. L. James, V. A. Baker, A. Curatolo, J. J. Armstrong, Elastic properties of the central airways in obstructive lung diseases measured using anatomical optical coherence tomography, Am. J. Resp. Crit. Care 183(5), p. 612-619, 2011.doi:10.1164/rccm.201002-0178OC
5. R. A. McLaughlin, B. C. Quirk, A. Curatolo, R. W. Kirk, L. Scolaro, D. Lorenser, P. D. Robbins, B. A. Wood, C. M. Saunders, D. D. Sampson, Imaging of breast cancer with optical coherence tomography needle probes: Feasibility and initial results, IEEE J. Sel. Topics Quantum Electron. 18(3), p. 1184-1191, 2012. doi:10.1109/JSTQE.2011.2166757
6. K. M. Kennedy, B. F. Kennedy, R. A. McLaughlin, D. D. Sampson, Needle optical coherence elastography for tissue boundary detection, Opt. Lett. 37(12), p. 2310-2312, 2012. doi:10.1364/OL.37.002310
7. B. F. Kennedy, S. H. Koh, R. A. McLaughlin, K. M. Kennedy, P. R. T. Munro, D. D. Sampson, Strain estimation in phase-sensitive optical coherence elastography, Biomed. Opt. Express 3(8), p. 1865-1879, 2012.doi:10.1364/BOE.3.001865
8. B. F. Kennedy, M. Wojtkowski, M. Szkulmowski, K. M. Kennedy, K. Karnowski, D. D. Sampson, Improved measurement of vibration amplitude in dynamic optical coherence elastography, Biomed. Opt. Express 3(12), p. 3138-3152, 2012. doi:10.1364/BOE.3.003138
9. R. K. Manapuram, S. R. Aglyamov, F. M. Monediado, M. Mashiatulla, J. Li, S. Y. Emelianov, K. V. Larin, In vivo estimation of elastic wave parameters using phase-stabilized swept source optical coherence elastography, J. Biomed. Opt. 17(10), p. 100501, 2012.doi:10.1117/1.JBO.17.10.100501
10. W. Qi, R. Chen, L. Chou, G. Liu, J. Zhang, Q. Zhou, Z. Chen, Phase-resolved acoustic radiation force optical coherence elastography, J. Biomed. Opt. 17(11), p. 110505, 2012. doi:10.1117/1.JBO.17.11.110505
11. C. Li, G. Guan, S. Li, Z. Huang, R. K. Wang, Evaluating elastic properties of heterogeneous soft tissue by surface acoustic waves detected by phase-sensitive optical coherence tomography, J. Biomed. Opt. 17(5), p. 057002, 2012. doi:10.1117/1.JBO.17.5.057002
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