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Patent Information Users Group, Inc.

The International Society for Patent Information Professionals

PIUG 2007 Boston Biotechnology Meeting

Main | Program | Presentations (members only) | Accommodations | Travel

Monday, February 12, 2007 – 9:00 a.m.-5:00 p.m.
Amgen, One Kendall Square, Bldg. 1000, Cambridge, MA

Final Program

Session 1: Where to Search?

8:00-8:30 am BREAKFAST Sponsored by BizInt
8:30-8:45 am Introduction Suzanne Robins
8:45-9:15 am A Brief History of Patent Sequence Elyse Turner, Merck & Co., Inc.
9:15-9:45 am GENESEQ – Guidelines and policies Colin Williams, Thomson Scientific
9:45-10:15 am CAS’ Coverage of Sequences in REGISTRY Barbara Vieira, CAS
10:15-10:45 am BREAK Sponsored by GeneIT
10:45-11:10 am All about WIPO - A Comparative Review of Sources of WIPO Sequence Data Robert Austin, FIZ Karlsruhe
11:10-11:35 am To PSIPS and Beyond - Exploring the Content and Utility of USGENE Robert Austin, FIZ Karlsruhe
11:35-12:00 am Uses of PatGenDB an Automated Compilation of Patent Genomic Data Hugo Villar, PatentInformatics
   
12:00-1:00 pm LUNCH
   

Session 2: How to, What to, and Why to Search?

1:00-1:20 pm The Role That Sequence Searches Play in Patent Prosecution and FTO Analysis Mario Cloutier, Millennium Pharmaceuticals, Inc.
1:20-1:40 pm Search Strategies for Oligonucleotides and Proteins Gregory E. Roland
1:40-2:00 pm Patent Analysis of Short Sequence Dr. Kamalakar Gulukota, Gene-IT, Inc.
2:00-2:20 pm Which Date? Finding the Publicly Accessible Date in a Sequence Prior Art Search Kenneth L. Hoppe, Pfizer Inc
2:20-2:30 pm BREAK Sponsored by Gene-IT
2:30-2:50 pm Understanding and Editing of Genomic Repetitive Sequences within Nucleic Acid Strings Steve Chappell Mitchell, Technology & Patent Research International, Inc.
2:50-3:10 pm Freedom-To-Operate Patent Searches for Selecting Sequences of Drug Targets Heahyun Yoo, Bristol Myers Squibb Company
3:10-3:30 pm CAS Registry BLAST® Tips and Tricks Lora Burgess, CAS
3:30-4:30 pm Questions and Discussion

Meeting Abstracts

A Brief History of Patent Sequences

Abstract

There has been an explosion of interest and developments in the area of patent sequence databases. Biotechnology and pharmaceutical companies are filing for hundreds of thousands of sequences. New products and tools are being introduced to help not only scientists, but patent attorneys and patent searchers manage and use this information. Patent attorneys and searchers need to evaluate the sequences to answer legal questions concerning patentability and freedom to operate.

In evaluating the sequence database it is important to understand the data and where it originates from. This understanding leads to an assessment of the reliability and completeness of the databases. This discussion will highlight the commercial players providing patent sequence databases and database tools. Focus of the discussion will be on what information is and is not being provided by the Patent Offices.

Elyse D. Robinson Turner
Manager Patent Information
Patent Department
Merck & Co., Inc.
P.O. Box 2000
Rahway, NJ 07065
732-594-6418

Biography

Elyse Turner is a founding member of PIUG and one of the members who originated the local meeting in the northeast. She wrote the original constitution and bylaws for PIUG and chaired the Bylaws Committee. She served as PIUG Secretary 1994-1996, PIUG Vice-Chair 2002-2004, PIUG Chair 2004-2006 and currently serves as PIUG Past Chair 2006-2008. The Electronic Communications committee was established by Elyse. She initiated and maintained the PIUG/PATMG DIALMAIL Bulletin Board then worked with Sandra Unger and Derwent to migrate and maintain communications on an internet discussion list sponsored by Derwent. She also worked with Sharon Peterson to create the PIUG web pages and with Tommy Ebe for CAS to provide the server for the web pages. In 1999, she became the PIUG webmaster. In 2000, she received an Award of Appreciation for 12 years of championing and facilitating electronic communications within PIUG. She took on the planning for the 2001 PIUG NE Workshop and continued with planning for the 2002 and 2003. She spearheaded planning for the PIUG 2003 and 2004 Annual Conferences. She currently acts as Board Liaison to the Vendor/Producer Committee.

Elyse served on the Questel-Orbit Advisory Council 1996-2004. She has been searching patents at Merck & Co., Inc since 1987. Before joining Merck, she was an intern at Bell Laboratories while completing her MLS at Rutgers University. She has been a member of SLA since 1985. She received her undergraduate degree in Biological Sciences from the University of Chicago in 1983.

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GENESEQ – Guidelines and policies

Abstract

The effective, and accurate, retrieval of biological sequence information is crucial to users of patent databases. GENESEQ, provided by Thomson Scientific, is one such database covering nucleotide and amino acid sequences disclosed in patents from 41 patent issuing authorities with coverage back to 1981.

The methods and guidelines for the selection of relevant patents, and the sequences contained within, will be described and will include the assignment of basic/equivalent status from the major patent issuing authorities. From here the creation of the two GENESEQ products will be discussed, and will include where the sequences are sourced from. Following this there will be an explanation of how GENESEQ indexing is applied, focussing mainly on keywording and organism assignment. This will include a description of the links between the Derwent World Patent Index (DWPI) and GENESEQ and their relative coverage of sequence information.

Colin Williams,
Editorial & Content manager,
Genomics,
Thomson Scientific
Tel: +44 (0)20 7424 2163
Fax: +44 (0)20 7344 2911
Email: colin.williams @ thomson.com
Address: 14 Gt. Queen St., London, WC2B 5DF

Biography

Colin Williams is the Editorial and Content manager for GENESEQ and GENESEQ FASTAlert at Thomson Scientific. He studied Biochemistry at the University of Sheffield before completing a PhD in protein X-ray crystallography. Following post doctoral work he moved to ASM Scientific, a start-up biotechnology company in Cambridge UK. Here, as part of a team of three, he developed a novel isothermal DNA amplification technology for use in point of care pathogen detection and contributed towards patent applications for the technology. Subsequent to this he joined Thomson Scientific as GENESEQ manager in November 2005. Here he is responsible for optimising production in terms of timeliness and quality, but also examining potential content changes and additions to the product.

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CAS’ Coverage of Sequences in REGISTRY

Abstract

CAS sequence coverage in Registry has grown significantly since 1988. This presentation covers features and benefits of CAS’ sequence data including types of sequences in Registry, sources of that data, and timeliness of coverage. The presentation will describe basic selection and indexing criteria such as assignment of claimed and unclaimed sequences, sequence naming practices, handling of GenBank nucleotides and translates, and curation of modified and ambiguous sequences. It will highlight significant indexing adjustments that have occurred over time.

Barbara Vieira
Sr Product Development Manager
CAS
2540 Olentangy River Rd
Columbus OH 43202
USA
614-447-3600

Biography

Dr. Barbara Vieira is a Senior Product Development Manager at CAS. She has been with CAS for 16 years primarily in database building and SciFinder development. Dr. Vieira holds a Ph.D. in biochemistry and managed the CAS Department of Molecular Biology & Genetics, Editorial Operations, prior to moving to New Product Development in 2005. Her current focus is on new product initiatives in the life science area.

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All about WIPO - a Comparative Review of Sources of WIPO Sequence Data

Abstract

A thorough patent sequence search should ideally include a complete collection of WIPO international patent application publication sequences. But does such a collection really exist? This talk will explore and place into context the various sources of WIPO sequence data currently available to diligent patent sequence searchers. Particular focus will be given on what is and is not included WIPO's "Published Nucleotide and/or Amino Acid Sequence Listings Contained in Published PCT Applications" sequence download service, which is the basis of the PCTGEN database on STN.

Robert Austin
Regional Sales Manager
FIZ Karlsruhe Inc
376 Carter Road
Princeton, NJ 08540-7422
Tel: 609 333 1466
Email: robert.austin @ fiz-k.com
www.fiz-k.com

Biography

Robert Austin has been the U.S. representative for FIZ Karlsruhe, the European partner of the Scientific and Technical Information Network (STN), since January 2001. In this role he specializes in technical training for STN patent databases throughout the United States, including the Derwent World Patents Index, GENESEQ (DGENE) and INPADOC. Prior to working for FIZ Karlsruhe he worked for 9 years at Derwent Information Ltd (now Thomson Scientific) in the United Kingdom consecutively in three roles: Pharmaceutical Patent Indexer, European Customer Trainer, and Product Manager for Derwent World Patents Index on Dialog, Questel.Orbit and STN. He graduated from Huddersfield University (UK) with a bachelors degree in Applied Chemistry in 1991, and has been searching and teaching STN since 1996.

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To PSIPS and Beyond - Exploring the Content and Utility of USGENE

Abstract

Organizations who wish to effectively establish, protect and commercially exploit their biotechnological intellectual property, need the most comprehensive, reliable and up-to-date source of USPTO patent sequence information. The USPTO Genetic Sequence Database (USGENE), provided by the SequenceBase Corporation, is a new resource encompassing all nucleotide and amino acid sequences available from relevant USPTO issued (granted) patents and published applications, with coverage dating back to 1982. USGENE will bring together the disparate sources of USPTO sequence data with key elements of bibliographic and full-text data, to provide a unified platform where patent searchers can seamlessly combine sequence, date and patent claims text searching. The methodology and sources for creating USGENE will be outlined, along with some examples of how this invaluable resource can be best utilized by patent information professionals.

Robert Austin
Regional Sales Manager
FIZ Karlsruhe Inc
376 Carter Road
Princeton, NJ 08540-7422
Tel: 609 333 1466
Email: robert.austin @ fiz-k.com
www.fiz-k.com

Biography

Robert Austin has been the U.S. representative for FIZ Karlsruhe, the European partner of the Scientific and Technical Information Network (STN), since January 2001. In this role he specializes in technical training for STN patent databases throughout the United States, including the Derwent World Patents Index, GENESEQ (DGENE) and INPADOC. Prior to working for FIZ Karlsruhe he worked for 9 years at Derwent Information Ltd (now Thomson Scientific) in the United Kingdom consecutively in three roles: Pharmaceutical Patent Indexer, European Customer Trainer, and Product Manager for Derwent World Patents Index on Dialog, Questel.Orbit and STN. He graduated from Huddersfield University (UK) with a bachelors degree in Applied Chemistry in 1991, and has been
searching and teaching STN since 1996.

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Uses of PatGenDB - an Automated Compilation of Patent Genomic Data

Abstract

Genetic patent information can be useful for multiple purposes. For example, legal aids can use the information to assess patentability and freedom to operate, technology managers can use it for intellectual property valuation, while scientists can use patents as valuable sources of scientific information to be combined with other sources to effect research and development. Each situation has different constrains. We have carried out an automated compilation of genetic patent data of both nucleic acid and amino acid sequence data from five major sources (EBI, NCBI, DDBJ, PSIPS, WIPO). The information was placed in a non-redundant searchable relational database, PatGenDB. We will describe how the database was assembled and we will provide a detailed analysis of the unique content in each database.

Hugo O Villar
PatentInformatics, An Altoris, Inc. Project.
11575 Sorrento Valley Rd – Suite 214
San Diego, CA 92121
Email: hugo @ altoris.com
Phone: (858)259-8161

Biography

Hugo Villar founded Altoris, Inc in 2003 to provide new informatics tools for the life sciences. He oversees commercial and technical aspects of the organization and its projects, ChemApps (www.chemapps.com) and PatentInformatics (www.patentinformatics.com).
He was VicePresident of Chemoproteomics at Triad Therapeutics, a San Diego biotechnology company, from 2001 until 2004, where he developed drug discovery technologies, including patented bioinformatics techniques. From 1992 until 2001 he held several positions at Telik, Inc., a company focused on the development of oncological products, ultimately being Vice President of Discovery Technologies. Dr Villar worked at IBM, SRI International and the Molecular Research Institute, where he stills serves in its board of directors. His technical interest has been in the application of computers to diverse problems in the life sciences. As a result he has published over 80 technical peer-review publications and holds over 18 patents in different aspects of drug discovery.
Dr Villar holds a Ph.D. in Chemistry from the Universidad Nacional de La Plata (Argentina) and a Masters in Business Administration, with emphasis on Health Care and Pharmaceutical Management from the University of Colorado.

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The Role That Sequence Searches Play in Patent Prosecution and FTO Analysis

Abstract

Sequence searches play an integral part of genomics based patent applications. From drafting the application throughout prosecution of the application, patent practitioners as well as patent examiners perform sequence searches to assess patentability of the molecule(s). This presentation discusses some of the reasons why sequence searches are performed during patent prosecution and how the information obtained is key to establishing novelty and (potentially) utility of the molecule. The presentation will also cover the evolution of genomics based patent applications, from the gold rush days of the late 1990’s until today. The discussion will also include the utility and written description guidelines established by the United States Patent Office and the Inventive Step Requirements established by the European Patent Office and the effect that such guidelines/requirements have had on the prosecution of genomics based patent applications.

Mario Cloutier
Patent Agent
Millennium Pharmaceuticals, Inc.
40 Landsdowne St
Cambridge, MA 02139
Phone: 617-577-3522
e-mail: cloutier @ mpi.com

Biography

Mario Cloutier is a Patent Agent at Millennium Pharmaceuticals, Inc. in Cambridge, Massachusetts. He has been part of Millennium’s Intellectual Property department since January 2000 and he specializes in the prosecution of biotechnology patent applications and freedom to operate analyses. Prior to joining Millennium’s Intellectual Property department, Mario headed the laboratory portion of Millennium’s transcription profiling core facility. Prior to joining Millennium, Mario obtained a Master’s degree in Biochemistry, then worked at Genetics Institute (now Wyeth Pharmaceuticals).

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Uses of PatGenDB an Automated Compilation of Patent Genomic Data

Abstract

Genetic patent information can be useful for multiple purposes. For example, legal aids can use the information to assess patentability and freedom to operate, technology managers can use it for intellectual property valuation, while scientists can use patents as valuable sources of scientific information to be combined with other sources to effect research and development. Each situation has different constrains. We have carried out an automated compilation of genetic patent data of both nucleic acid and amino acid sequence data from five major sources (EBI, NCBI, DDBJ, PSIPS, WIPO). The information was placed in a non-redundant searchable relational database, PatGenDB. We will describe how the database was assembled and we will provide a detailed analysis of the unique content in each database.

Hugo O Villar
PatentInformatics, An Altoris, Inc. Project.
11575 Sorrento Valley Rd – Suite 214
San Diego, CA 92121
Email: hugo @ altoris.com
Phone: (858)259-8161

Biography

Hugo Villar founded Altoris, Inc in 2003 to provide new informatics tools for the life sciences. He oversees commercial and technical aspects of the organization and its projects, ChemApps (www.chemapps.com) and PatentInformatics (www.patentinformatics.com).
He was VicePresident of Chemoproteomics at Triad Therapeutics, a San Diego biotechnology company, from 2001 until 2004, where he developed drug discovery technologies, including patented bioinformatics techniques. From 1992 until 2001 he held several positions at Telik, Inc., a company focused on the development of oncological products, ultimately being Vice President of Discovery Technologies. Dr Villar worked at IBM, SRI International and the Molecular Research Institute, where he stills serves in its board of directors. His technical interest has been in the application of computers to diverse problems in the life sciences. As a result he has published over 80 technical peer-review publications and holds over 18 patents in different aspects of drug discovery.
Dr Villar holds a Ph.D. in Chemistry from the Universidad Nacional de La Plata (Argentina) and a Masters in Business Administration, with emphasis on Health Care and Pharmaceutical Management from the University of Colorado.

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Search Strategies for Oligonucleotides and Proteins

Abstract

The pharmaceutical industry has begun to explore the use of oligonucleotides such as aptamers, siRNA, and spiegelmers along with proteins (antibodies and peptides) in drug design, target validation and as possible therapeutics. The relative short length (<100 residues) along with target specific regions of these innovative molecules present challenges to the information professional when it comes to searching for information. When developing a strategy to search these short sequences, the information professional needs to consider altering standard BLAST parameters in order to find relevant results. Based on editorial policies, indexing and system limitations, the presentation will explore methods on how to search short sequences and proteins from both a sequence based as well as keyword perspective.

Gregory E. Roland
Sr. Manager, Intellectual Property
GLIST- Global Legal Information Science Team
Pfizer Corporate Legal Patent Department
2800 Plymouth Rd
Ann Arbor, MI 48178
734/622-1570
Email: Gregory.Roland @ Pfizer.com

Biography

After spending 10 years as a research scientist evaluating the mechanism of action of novel antibacterial compounds through in vivo and in vitro studies, Greg Roland joined the then Parke-Davis Information Management group in 1999. Working with a team of attorneys and research scientists, Greg’s primary responsibility was to provide biotechnology information including Freedom to Operate search reports on sequence based research tools. After Parke-Davis was acquired by Pfizer in 2000, Greg continued in his biotechnology support role while managing a team of local information professionals. During this time, Greg worked with a team of Biopatent information professionals in developing an in house Biopatent BLAST application for the submission of sequences and viewing of BLAST related results. To complement the Biopatent BLAST tool, the team developed a comprehensive sequence and keyword based search protocol that combined search results from multiple platforms into a single report. Beginning in October of 2003, Greg joined the newly created Global Legal Information Science Team (GLIST) in the Pfizer Legal department where he manages information professionals at multiple sites while continuing to support Pfizer’s biotechnology information needs.

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Patent Analysis of Short Sequences

Abstract

Searching for short sequences is particularly challenging since it often brings up too many results. Furthermore, there are heuristic limitations of standard methods like Blast that are particularly acute for short sequences.

I will use as example, the case of finding patented diagnostic primers specific to the genome of the human papillomavirus. Primary challenges (and solutions) I will highlight include:

(1) Limitations of Blast and use of a percent identity method to solve some of them.
(2) How do you deal with a large number of results? What specific filters can be applied? How can they be applied? And
(3) Collaborative sharing of results with colleagues.

Dr. Kamalakar Gulukota ("Gulu")
Director of Content Development
Gene-IT, Inc.
1700 West Park Drive, Suite 260
Westborough, MA 01581
Tel: (508) 616-0100
Fax: (508) 616-0110
Email: gulukota @ gene-it.com

Biography

Dr Gulukota is a trained physician turned scientist entrepreneur. He has more than a 12 years experience in drug discovery in the big pharma, academic, and contract research settings. Throughout his career, he has been applying in-silico methods to improve the productivity of drug discovery. He brings a unique combination of medical, scientific and business acumen to bear on this particularly thorny problem.

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Which Date? Finding the Publicly Accessible Date in a Sequence Prior Art Search

Abstract

In a prior art search, the date the information was “publicly accessible” needs to be located. In some sequence databases the entry date into the public domain from that database is easily found but in others it is not a straightforward process, e.g. GENBANK. Another issue to be aware of is the sequence version in the database relative to the release date. I will review prior art sequence database resources, some database history, sequence version issues, and where to locate the public release data.

Kenneth L. Hoppe
Patent Department
Pfizer Inc
Groton CT 06340
(860) 715-0348
Email: kenneth.L.hoppe @ pfizer.com

Biography

Ken Hoppe has a BS and MS in Biology. He has ten years laboratory experience in molecular biology working at the University of Connecticut Medical Center’s Department of Biochemistry, Harvard Medical School at Beth Israel and Children’s Hospitals in Boston, and in Pfizer’s Groton Connecticut research laboratories working in the area of atherosclerosis. For the last five years, Ken has worked in the biotechnology patent searching field in Pfizer’s Information Management and Patent Departments. In this role, Ken helped manage the development of an in-house software application that helps post-process results from in-house biosequence patent databases.

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Understanding and Editing of Genomic Repetitive Sequences within Nucleic Acid Strings

Abstract

Biotechnology commercial intelligence requires the development of an evolved information service program in genetics and molecular biology. Important, defining concepts affecting this specialized work include an understanding of genetic repetitive elements within nucleic acid sequence strings. Suggested approaches will be introduced, which feature use of tools and aspects of rules for editing DNA. A typical question regarding the use and targeting of genetic markers will be discussed within a hypothetical search.

Steve Chappell Mitchell
Technology & Patent Research International, Inc.
17055 Via Del Campo, Suite 200
San Diego, CA 92127
USA
Tel: +1 858 592 9084
Fax: +1 858 592 0045
Email: searches @ TPRInternational.com
www.TPRInternational.com

Biography

Steve Chappell Mitchell has extensive of professional experience in patents and non-patent literature for Genomics-based Intellectual Property protection, specializing in Genetics, Cancer, and Immunology. Steve developed expertise as a patent information professional with specialized leadership experience at top companies. At Abbott, Steve received awards with letters of commendation from company chief executives, which included the Administrative Services Award of Excellence and the President's Award. Currently at Technology & Patent Research (TPR) International, his intellectual property patent work involves Freedom to Operate, Validity, Patentability, and Litigation support. Steve has specialist knowledge for in-depth technical searching in the biotechnology areas of genetics, comparative genomics, immunology, cancer, antibodies, and molecular biology.

He holds numerous patent inventorships granted from his 20-year career in scientific discovery and development while managing laboratories in Cancer Medicine, Heart Disease, and Immunology. His discovery institutions include:
  • California Institute of Technology for the Human Genome Project
  • Harvard University for Immunology, Class II gene regulation
  • Cedars Sinai/UCLA for Genomics, Cloning of the Heart Disease Region
  • University of Arizona for Human Tumor Cloning and Diabetes
  • UroGenesys/Agensys for Cancer Medicine and Molecular Biology

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Freedom-To-Operate Patent Searches for Selecting Sequences of Drug Targets

Abstract

The number of sequence claimed as intellectual properties has been dramatically increased in the past several years. Therefore, the target validation step of drug discovery processes should include the clearance of freedom-to-operate (FTO) issues over using sequences of potential drug targets in order to avoid infringing patents claiming such sequences. This presentation discusses some of the challenges, search scopes/criteria of sequence searches, and suggests ways to alleviate difficulties in conducting sequence-based patent information searches associated with freedom-to-operate issues.

Heahyun Yoo
Information and Knowledge Integration, Pharmaceutical Research Institute Informatics,
Bristol Myers Squibb Company
(609) 818-3246
Email: heahyun.yoo @ bms.com or heahyunyoo @ yahoo.com

Biography

Heahyun Yoo is a senior patent analyst I at the Bristol Myers Squibb’s Information & Knowledge Integration Informatics. She has been specialized in biotech patent information searching for ~10 years with expertise in sequence analysis based searches. With this background, she lead a microbial genome sequence annotation projects during her employment in DuPont Central R&D. Heahyun has a Ph.D. in chemistry with dissertation on biochemical studies. Her academic and industrial research experiences include biochemical and molecular biological works in the fields of oncology and neurosciences.

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CAS Registry BLAST® Tips and Tricks

Abstract

The CAS Registry BLAST is an easy to use search interface that offers a variety of choices for running a BLAST search in the Registry file. This talk will address what some of the options are, and the effect they have on the BLAST results.

Lora Burgess
Senior Applications Specialist

Biography

Lora Burgess has been working as an STN trainer at Chemical Abstracts Service since December 2000. Prior to her work at CAS, she spent 4 years as an Information Technology Resource Provider at the US Patent and Trademark Office, training patent examiners on commercial search systems, PTO in-house systems, and chemical structure searching. She has been searching on STN since 1991, when she began using STN for her graduate studies in chemistry. She holds a Master's degree in Chemistry from John's Hopkins University and has trained clients in Europe and the United States.

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Last update: 7 February 2007 / Ric Snead-Qin Meng
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