Petrelis Files

March 14, 2005

Catherine Mathis
The New York Times
Corporate Communication

Dear Ms. Mathis:

I've sifted through the U.S. Patent and Trade Office's search engines and learned Dr. David Ho, director of the Aaron Diamond AIDS Research Center, is listed below as the inventor of six HIV tests, herbal extracts or agents.

Of particular interest to me, which I want the Times to pay attention to, is item number five on my list, "Defensins: as an antiviral agent," on the list below.

Dr. Ho's abstract to the patent office stated: "The invention further relates to methods for identifying and using agents, including small molecule chemical compositions, antibodies, peptides, nucleic acids, antisense nucleic acids, and ribozymes, that increase naturally occurring defensin expression or activity, thereby inhibiting HIV in a cell; as well as to the use of expression profiles and compositions in diagnosis and prophylaxis, and therapy related to HIV infection and related disease states such as AIDS."

Ho and his co-inventors filed the patent claim on May 30, 2003.

In a January 23, 2004, story by Andrew Pollack, headlined "AIDS Researcher Partly Retracts Study that Caused Stir," the Times reported how Ho and his colleagues made mistakes in an experiment with defensins.

However, the Times did not report that the test involved in the experiment is partly patented by Ho. I believe the paper should have informed readers of Ho's competing interests in this matter.

Now would be a good time to revisit what Pollack wrote, especially his omission of public information about the patent owners of the test used in the failed experiment.

If the Times feels it could have done a better job of delivering all the facts to the reader in this AIDS-specific story, a note to readers about Ho possessing the patent on the test would be appropriate.

Furthermore, as you see below, I've attached information from the patent office on all six of the patents that list Ho as an inventor, and four patents listing his laboratory, the Aaron Diamond AIDS Research Center, as the assignee for an invention.

Some of the inventions may have been used in analyzing specimens from the gay male patient in New York with a drug-resistant strain of HIV, extensively reported on in the Times. I say may have been used because I am not sure how many tests and of what sort were performed on the patient, or if Ho or his research center has patents on any of the tests.

If any of the tests used in the New York mutant HIV strain case are patented by either Ho or his laboratory, then I think the Times has a responsibility to tell readers these facts.

I suggest you determine if any Ho or Aaron Diamond AIDS Research Center patented tests were used in that case, to make sure the Times' coverage was as fully informed and accurate about transparency as possible.

I respectfully request a reply.

Sincerely,
Michael Petrelis
San Francisco, CA


^^^

U.S. PATENT AND TRADE OFFICE
http://www.uspto.gov/patft/index.html

SIX PATENTS THAT LIST DR. DAVID HO AS AN INVENTOR

1.
Chinese herbal extracts in the treatment of HIV related disease in vitro

Abstract
The invention features herbal extracts from ten (10) Chinese Herbal Medicines demonstrating significant in vitro and ex vivo anti-HIV activity and their use for the diagnosis and treatment of HIV and HIV-related disease.

Inventors: Ho; David D. (Chapqua, NY); Li; Xiling S. (Alhambra, CA)

Assignee: Cedars-Sinai Medical Center (Los Angeles, CA)

Appl. No.: 712062

Filed: June 7, 1991


2.
Immunoreagents reactive with a conserved epitope of human immunodeficiency virus type I (HIV-1) gp120 and methods of use

Abstract
The invention features immunoreagents which neutralize the Human Immunodeficiency Virus Type 1 (HIV-1) by binding to a novel conserved epitope of the HIV-1 gp120. These immunoreagents exhibit a broad neutralizing effect upon HIV attachment to host cells, and are therefore useful in the detection, prevention, amelioration and treatment of HIV disease, primarily AIDS (Acquired Immunodeficiency Syndrome) and ARC (AIDS Related Complex). More particularly, the invention relates to novel human monoclonal antibodies selectively reactive to a conserved conformation dependent determinant of the HIV-1 gp120, derivatives thereof, cell lines that produce these antibodies, and the use of the monoclonal antibodies and their derivatives for the detection, prevention, amelioration and treatment of HIV related disease.

Inventors: Ho; David D. (Capaqua, NY); Robinson; James E. (New Orleans, LA)

Assignee: Cedars-Sinai Medical Center (Los Angeles, CA); Louisiana State University and Agricultural and Mechanical College (New Orleans, LA)

Appl. No.: 870531

Filed: June 6, 1997


3.
Methods for identifying genomic equivalent markers and their use in quantitating cells and polynucleotide sequences therein


Abstract
Methods for identifying genetic sequences useful as genomic equivalent markers for organisms are described. The method involves determining the ratio of the absolute number of copies of wild type and mutant amplicons in a number of samples from organisms heterozygous for the mutation. After establishing the number of copies of a particular genetic sequence per genome, the sequence may be used as a measure of the number of genomes per sample, in order to normalize the analysis of another target sequence to abundance per cell. By way of example, the CCR5 gene was shown to be present at 2 copies per genome.

Inventors: Zhang; Linqi (New York, NY); Lewin; Sharon R. (Armadale, AU); Kostrikis; Leondios (New York, NY); Ho; David D. (Chappaqua, NY)
Assignee: The Rockefeller University (New York, NY)
Appl. No.: 481288
Filed: January 11, 2000



4.
Vaccination of hiv infected persons following highly active antiretrovial therapy

Abstract
The present invention provides a method of permitting cessation of antiviral therapy on HIV-infected subjects without virus rebound or with at least a delayed virus rebound or a decreased post rebound set-point. The method comprises the re-induction of HIV-specific immune responses using a vaccination strategy to induce both humoral and cell-mediated immunity. The present invention achieves an immunological control of persistent infectious virus after discontinuation of antiviral therapy. The vaccine strategy according to the invention is both safe and immunogenic in the subject HIV-infected patient population.

Inventors: Ho, David; (New York, NY) ; Markowitz, Martin; (New York, NY) ; KLEIN, MICHEL; (LYON CEDEX, FR) ; HABIB, RAPHAELLE EL; (LYON CEDEX, FR)
Correspondence Name and Address: MCDONNELL BOEHNEN HULBERT & BERGHOFF
300 SOUTH WACKER DRIVE
SUITE 3200
CHICAGO
IL
60606
US


Serial No.: 182067
Series Code: 10
Filed: October 9, 2002


5.
Defensins: use as antiviral agents


Abstract
The present invention relates to inhibition of viruses, e.g., HIV, using defensins. The invention further relates to methods for identifying and using agents, including small molecule chemical compositions, antibodies, peptides, nucleic acids, antisense nucleic acids, and ribozymes, that increase naturally occurring defensin expression or activity, thereby inhibiting HIV in a cell; as well as to the use of expression profiles and compositions in diagnosis and prophylaxis, and therapy related to HIV infection and related disease states such as AIDS.

Inventors: Zhang, Linqi; (Rochelle Park, NJ) ; Ho, David D.; (Chappaqua, NY) ; Caffrey, Rebecca E.; (Redwood City, CA) ; Dalmasso, Enrique A.; (Fremont, CA) ; Mei, Jianfeng; (Guilford, CT)
Correspondence Name and Address: TOWNSEND AND TOWNSEND AND CREW, LLP
TWO EMBARCADERO CENTER
EIGHTH FLOOR
SAN FRANCISCO
CA
94111-3834
US


Assignee Name and Adress: Aaron Diamond AIDS Research Center
New York
NY

The Rockefeller University
Fremont
CA

Ciphergen Biosystems, Inc.
Serial No.: 452763
Series Code: 10
Filed: May 30, 2003




6.

Comparative proteomics of progressor and nonprogressor populations

Abstract
The invention identifies polypeptide biomarkers of disease progression or nonprogression by comparative protein profiling of samples from progressors and nonprogressors subpopulations of a population exposed to the pathogen or sharing a risk facto causing the disease. The polypeptides, their ligands, and modulators find use as diagnostic, prognostic, and therapeutic agents.

Inventors: Rich, William E.; (Redwood Shores, CA) ; Ho, David D.; (Chappaqua, NY) ; Zhang, Linqi; (Rochelle Park, NJ)
Correspondence Name and Address: TOWNSEND AND TOWNSEND AND CREW, LLP
TWO EMBARCADERO CENTER
EIGHTH FLOOR
SAN FRANCISCO
CA
94111-3834
US


Assignee Name and Adress: Ciphergen Biosystems, Inc.
Fremont
CA

Aaron Diamond AIDS Research Center
New York
NY

The Rockefeller University
New York
NY
Serial No.: 452666
Series Code: 10
Filed: May 30, 2003




FOUR PATENTS THAT LIST THE AARON DIAMOND AIDS RESEARCH CENTER AS THE ASSIGNEE

1.
G-coupled receptors associated with macrophage-trophic HIV, and diagnostic and therapeutic uses thereof


Abstract
Entry of HIV-1 into target cells requires cell surface CD4 as well as additional host cell cofactors. A cofactor required for infection with virus adapted for growth in transformed T cell lines was recently identified and named fusin. Fusin, however, does not promote entry of macrophage-tropic viruses that are believed to be the key pathogenic strains in vivo. It has now been determined that the principal cofactor for entry mediated by the envelope glycoproteins of primary macrophage-tropic strains of HIV-1 is CC-CKR5, a receptor for the .beta.-chemokines RANTES, MIP-1.alpha., and MIP-1.beta..


Assignee: New York University (New York, NY); The Aaron Diamond Aids Research Center (New York, NY)
Appl. No.: 666020
Filed: June 19, 1996



2.
Sulfated CCR5 peptides for HIV-1 infection


Abstract
This invention provides a compound comprising the structure: .theta..alpha.YDINYYTSE.beta..lambda. wherein each T represents a threonine, each S represents a serine, each E represents a glutamic acid, each Y represents a tyrosine; each D represents an aspartic acid, each I represents an isoleucine; and each N represents an asparagine; wherein .alpha. represents from 0 to 9 amino acids, with the proviso that if there are more than 2 amino acids, they are joined by peptide bonds in consecutive order and have a sequence identical to the sequence set forth in SEQ ID.

Inventors: Dragic; Tatjana (Scarsdale, NY); Olson; William C. (Ossining, NY)
Assignee: Progenics Pharmaceuticals, Inc. (Tarrytown, NY); Aaron Diamond AIDS Research Centre (New York, NY)
Appl. No.: 796202
Filed: February 28, 2001




3.

Uses of a chemokine receptor for inhibiting HIV-1 infection

Abstract
This invention provides a polypeptide comprising a fragment of a chemokine receptor capable of inhibiting HIV-1 infection. In an embodiment, the chemokine receptor is C--C CKR-5. In another embodiment, the fragment comprises at least one extracellular domain of the chemokine receptor C--C CKR-5. This invention further provides different uses of the chemokine receptor for inhibiting HIV-1 infection.

Correspondence Name and Address: John P. White
Cooper & Dunham LLP
1185 Avenue of the Americas
New York
NY
10036
US


Assignee Name and Adress: Progenics Pharmaceuticals, Inc.

Aaron Diamond AIDS Research Centre (ADARC)


Serial No.: 852238
Series Code: 09
Filed: May 9, 2001



4.
Stabilized viral envelope proteins and uses thereof


Abstract
This invention provides an isolated nucleic acid which comprises a nucleotide segment having a sequence encoding a viral envelope protein comprising a viral surface protein and a corresponding viral transmembrane protein wherein the viral envelope protein contains one or more mutations in amino acid sequence that enhance the stability of the complex formed between the viral surface protein and transmembrane protein. This invention also provides a viral envelope protein comprising a viral surface protein and a corresponding viral transmembrane protein wherein the viral envelope protein contains one or more mutations in amino acid sequence that enhance the stability of the complex formed between the viral surface protein and transmembrane protein. This invention further provides methods of treating HIV-1 infection.

Correspondence Name and Address:

John P. White
Cooper & Dunham LLP
1185 Avenue of the Americas
New York
NY
10036
US

Assignee Name and Adress: Progenics Pharmaceuticals, Inc.

Aaron Diamond AIDS Research Centre

Serial No.: 780993

Series Code: 10

Filed: February 18, 2004