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[bioontology-support] NCBO annotator web service

Trish Whetzel whetzel at stanford.edu
Tue Aug 17 10:32:56 PDT 2010


Sure, the attachment did not come through. Can you re-send?

Trish


On Aug 17, 2010, at 10:21 AM, Lorena Carlo wrote:

> Hi Trish,
>
> I am getting the following error from the web service:
>
> 502
> <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
> <html><head>
> <title>502 Proxy Error</title>
> </head><body>
> <h1>Proxy Error</h1>
> <p>The proxy server received an invalid
> response from an upstream server.<br />
> The proxy server could not handle the request <em><a href="/obs/ 
> annotator/submit
> /mlc2200 at columbia.edu">POST /obs/annotator/submit/mlc2200 at columbia.edu 
> </a><
> /em>.<p>
> Reason: <strong>Error reading from remote server</strong></p></p>
> <hr>
> <address>Apache/2.2.13 (Red Hat) Server at rest.bioontology.org Port  
> 80</address
> >
> </body></html>
>
> I am attaching the file I am using. Can you help me checking this.  
> Thanks.
>
> Best,
> Lorena
>
> Trish Whetzel wrote:
>> We do not yet have an absolute requirement for the email address.  
>> However, our funders are very interested to know who and how people  
>> are using the Web services that we provide.
>>
>> Thanks,
>> Trish
>>
>>
>> On Aug 10, 2010, at 1:08 AM, Lorena Carlo wrote:
>>
>>> Hi Trish,
>>>
>>> Ok, no problem I will change it, thanks. I would like to ask why  
>>> is the email address required?. Thanks.
>>>
>>> Best regards,
>>> Lorena
>>>
>>> Trish Whetzel wrote:
>>>> Hi Lorena and Ying,
>>>> Can you replace the following line in the Python code to access  
>>>> the Annotator:
>>>> # Submit job
>>>> submitUrl = annotatorUrl + '/submit'
>>>> with
>>>> # Submit job
>>>> submitUrl = annotatorUrl + '/submit/example at your_email.com'
>>>> and include your email address?
>>>>
>>>> Thanks,
>>>> Trish
>>>>
>>>>
>>>>
>>>> On Aug 4, 2010, at 12:20 PM, Trish Whetzel wrote:
>>>>
>>>>> I also wanted to mention that we have a NCBO Annotator Google  
>>>>> group (http://groups.google.com/group/annotator-discuss)  
>>>>> intended to be a space where Annotator users can discuss their  
>>>>> use cases for the Annotator and choice of ontologies,  
>>>>> parameters, etc.
>>>>>
>>>>> Trish
>>>>>
>>>>>
>>>>> On Aug 4, 2010, at 9:48 AM, Lorena Carlo wrote:
>>>>>
>>>>>> Dear Trish,
>>>>>>
>>>>>> Thanks for your email. I am copying this email to Ying, she is  
>>>>>> a student here at Columbia and will be using the annotator  
>>>>>> service with python too. Thanks.
>>>>>>
>>>>>> Best regards,
>>>>>> Lorena
>>>>>>
>>>>>> Trish Whetzel wrote:
>>>>>>> I'm not aware of anyone using the Annotator Web service in  
>>>>>>> Python, however attached is an Annotator client example in  
>>>>>>> Python.
>>>>>>>
>>>>>>> Trish
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Aug 3, 2010, at 1:48 PM, Lorena Carlo wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Hi Trish, Thanks for your email. I would like to know if  
>>>>>>>> there is people in the community using python and the  
>>>>>>>> annotator web service?. If so can you redirect me to the  
>>>>>>>> resources that will help me to use this web service in  
>>>>>>>> python?. Thanks!. Best regards, Lorena Trish Whetzel wrote:
>>>>>>>>> Hi Lorena, Let me know if you have any questions about  
>>>>>>>>> accessing the Annotator via the REST Web service. Also, if  
>>>>>>>>> you are able to share information on your use case for the  
>>>>>>>>> Annotator with our Google group that would be wonderful: http://groups.google.com/group/annotator-discuss 
>>>>>>>>> . Best regards, Trish On Aug 3, 2010, at 12:45 PM, Clement  
>>>>>>>>> Marie Jonquet wrote:
>>>>>>>>>> Dear Lorena, There is unfortunately no SOAP web services  
>>>>>>>>>> for the Annotator. This is only deployed as a REST service  
>>>>>>>>>> and HTML, Java, Perl and Ruby on rails client are  
>>>>>>>>>> available: http://www.bioontology.org/wiki/index.php/Annotator_Web_service 
>>>>>>>>>>  Hope you will still use it. We will let you know if this  
>>>>>>>>>> situation change in the future. Please follow up  
>>>>>>>>>> conversation with Trish Whetzel (CC), as I will not be at  
>>>>>>>>>> Stanford any time soon. Clement  
>>>>>>>>>> -------------------------------------------------------------------------- ------------------------- Dr 
>>>>>>>>>> . Clement JONQUET  -  PhD in Informatics  -  Postdoctoral  
>>>>>>>>>> Research Fellow jonquet at stanford.edu <mailto:jonquet at stanford.edu 
>>>>>>>>>> > http://www.stanford.edu/~jonquet <http://www.stanford.edu/%7Ejonquet 
>>>>>>>>>> > Stanford Center for Biomedical Informatics Research  
>>>>>>>>>> (BMIR) Medical School Office Building, Room X-215 251  
>>>>>>>>>> Campus Drive Stanford, CA 94305-5479 USA Tel:        +1 650  
>>>>>>>>>> 724-0388 Fax:       +1  650 725-7944 Skype:  clementpro http://bmir.stanford.edu/ 
>>>>>>>>>>   
>>>>>>>>>> -------------------------------------------------------------------------- ------------------------- -----Original 
>>>>>>>>>>  Message----- From: Lorena Carlo [mailto:lorena.carlo at dbmi.columbia.edu 
>>>>>>>>>> ] Sent: Tuesday, August 03, 2010 11:38 AM To: jonquet at stanford.edu 
>>>>>>>>>>  <mailto:jonquet at stanford.edu> Subject: NCBO annotator web  
>>>>>>>>>> service Dear Clement Jonquet, I am interested in using the  
>>>>>>>>>> NCBO annotator  web service in an python application. I  
>>>>>>>>>> don't find the web service wsdl. Can you send me the wsdl  
>>>>>>>>>> URL?.  Thanks. Best regards, Lorena Carlo PhD student in  
>>>>>>>>>> Biomedical Informatics Columbia University
>>>>>>>>> Trish Whetzel, PhD Outreach Coordinator The National Center  
>>>>>>>>> for Biomedical Ontology Ph: 650-721-2378  
>>>>>>>>> whetzel at stanford.edu <mailto:whetzel at stanford.edu> http://www.bioontology.org
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
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> At least 1 regimen must have contained a platinum agent (i.e.,  
> carboplatin or cisplatin).
> Presenting for a well-woman visit, annual Pap smear, or family  
> planning.
> First episode of sight-threatening CMV retinitis.
> Known hormone receptor status.
> Medications known to cause gastrointestinal irritation or alteration  
> of gastrointestinal motility or absorption should be avoided if  
> possible.
> Variegate porphyria and hereditary coproporphyria eligible but  
> analyzed separately.
> Gastrointestinal (GI) or genitourinary (GU) bleeding of clinical  
> significance within 6 weeks prior to randomization.
> Oxygen saturation at least 90% on room air.
> Are participating in a clinical trial of any investigational drug.
> Primary testicular androgen suppression (e.g., LHRH agonist or DES)  
> continues during study.
> Known or documented brain metastases.
> Topical, oral, and systemic corticosteroids.
> Alkaline phosphatase less than 2.5 times ULN (for patients with  
> documented benign disease).
> Mixed malignant glioma.
> Use of neuroleptics or narcotic analgesics within 4 weeks prior to  
> screening.
> Diagnosis of idiopathic myelofibrosis or other myeloproliferative  
> disorder with myelofibrosis.
> Proof of HIV infection.
> Under 366 days at diagnosis.
> Chemotherapy, hormonal therapy, or other immunotherapy.
> Bone marrow aspiration and biopsy within the past 42 days.
> Metastatic disease with documented progression.
> Measurable or evaluable indicator lesion.
> Are at least 13 years old. (Need consent of parent or guardian if  
> under 18.).
> Patients who have received any investigational agent within 4 weeks  
> of enrollment.
> More than 6 months since prior radiotherapy for head and neck cancer.
> Zidovudine (AZT) for > 6 months.
> Receiving a transplant from a living related donor who is ABO (blood  
> type) compatible and haploidentical (3,4, or 5 antigen match by  
> serologic typing).
> No hypocellular bone marrow (no greater than 15% cellularity) or  
> marked decrease in 1 or more hematopoietic precursors.
> Must weigh at least 50 kilogram.
> Bone marrow blasts greater than 5% of nucleated cells.
> No concurrent immunomodulating agent.
> NNRTI therapy prior to study entry (with the exception of Group D).
> Myelotoxic agents for malignancy or other condition.
> Alkaline phosphatase less than 2 times ULN* NOTE: * Less than 5  
> times ULN if documented liver disease.
> Any investigational drug during the 4 weeks prior to randomization.
> Current neoplasm other than Kaposi's sarcoma.
> Any immunomodulator therapy within 30 days prior to entry.
> Grades I, II, or III.
> Patients who have undergone prior resection of recurrent or  
> progressive tumor require evaluable disease only.
> Positive PPD.
> Rifampin, rifabutin, astemizole, loratadine, or terfenadine within  
> 21 days prior to initial study drug dose.
> Shortening fraction or ejection fraction greater than 40% of normal  
> value for age by echocardiogram or radionuclide scan.
> Tanner Stage of Development: Stage 1.
> FSP less than 40.
> Histologically confirmed refractory solid tumor and/or lymphoma.
> Unable to participate in 5 lifestyle intervention meetings occurring  
> over a one year period.
> CMV serology (IgG) positive (CMV bDNA cohort and CMV-virology cohort).
> Written informed consent.
> Hypertrophic cardiomyopathy (obstructive or non-obstructive).
> Prophylactic therapy for Pneumocystis carinii pneumonia.
> No other major medical illness or psychiatric impairment that would  
> preclude study compliance.
> Are receiving anti-HIV medications at study entry.
> No concurrent drugs that would preclude absorption of oral topotecan.
> Evidence of evolution to AML (e.g., refractory anemia with excess  
> blasts (RAEB) or RAEB in transformation).
> Other: No prior cancer therapy that would preclude study.
> Concurrent chemotherapy allowed after surgery and before vaccination.
> Temperature more than 38 degrees and/or drenching night sweats for  
> more than 1 month; watery diarrhea for 2 or more weeks; weight loss  
> of more than 10 percent.
> Intact, unbroken skin over the painful area(s) to be treated.
> Have taken drugs that might affect the immune system, within 4 weeks  
> prior to study entry.
> History of grade 2 or worse liver abnormality.
> A stable dosage of non-excluded medications for at least 2 weeks  
> prior to the Screening Visit.
> Willingness and ability to complete interviews.
> No concurrent sulfonylurea agent for diabetes or antiarrhythmic  
> agents.
> Amyloidosis.
> Naproxen.
> Also eligible after two to four cycles of conventional dose salvage  
> chemotherapy, regardless of response.
> Biologic response modifiers (alpha interferon, IL-2, immune  
> modulators). Required:.
> No prior imatinib mesylate (stratum II).
> Active immunization within 21 days prior to study entry.
> No prior ipsilateral or contralateral invasive breast cancer.
> No concurrent investigational ancillary therapy.
> At V1, the subject must demonstrate a baseline FEV1 within >45% and  
> <75% of predicted for their height, age, gender, and race.
> No other concurrent immune modulators.
> Hepatic: Serum bilirubin < 2.0 mg/dL; AST and ALT < 2 x ULN w/o  
> liver metastases or <5 x ULN w/liver metastases.
> Comatose.
> No grade 2 or greater neuropathy.
> Unwilling to comply with study design. Concurrent Medication:  
> Excluded:.
> No impending spinal cord compression.
> Platelet count at least 50,000/mm3.
> Liver enzymes no greater than upper limit of normal.
> Interferon or interleukin.
> In second or greater relapse.
> Hematopoietic progenitor cell transplant subjects with chronic or  
> Grade II-IV acute GVHD being treated with high dose  
> immunosuppressive therapy.
> More than 4 weeks since prior systemic therapies for prostate cancer.
> Alcoholism or drug abuse within 12 months of study entry.
> Sciatica persisting 3 or more months after physician visit.
> Ejection fraction of at least 40% by radionuclide angiogram  
> echocardiogram.
> Erythropoietin, G-CSF or GM-CSF within 30 days prior to entry.
> Alkaline phosphatase no greater than 4 times ULN if AST/ALT less  
> than ULN.
> Have a disease affecting the red blood cells.
> Have a fever or chronic diarrhea within 30 days of study entry.
> Have phenotypic sensitivity to atazanavir and LPV/RTV.
> No known brain metastases or primary brain tumors.
> Active opportunistic infection or febrile illness with temperature  
> >= 38.5 C within 3 days prior to study entry.
> Prior use of the combined treatment of the 2 study drugs used in  
> this study.
> Positive syphilis serology.
> Must be negative for BR96 antibodies in serum.
> No clinical immunodeficiency.
> Women age 18 years or older.
> At least 1 week since prior hormonal therapy for this disease.
> No clinically serious active infection.
> Histological confirmation waived for brain stem gliomas.
> Are a woman and are pregnant or breastfeeding, intend to become  
> pregnant within the next 2 years or a woman not using effective  
> birth control.
> No prior mediastinal irradiation.
> ADAS-cog score of at least 12 and MMSE score of 10 to 26.
> Karnofsky Performance Rating Scale below 50 or physical limitations  
> or illness severity sufficient to preclude participation in  
> outpatient group psychotherapy.
> Agree to avoid becoming pregnant or causing someone to become  
> pregnant while participating in the study.
> Prior prostatic radiotherapy allowed.
> HIV or Hepatitis.
> The presence of cannabis is not exclusionary unless the investigator  
> believes its use will interfere with patient compliance.
> Therapy was no more than 6 months in duration.
> Cervical intra-epithelial neoplasm or FIGO stage I carcinoma of the  
> cervix.
> No uncontrolled or significant cardiac disease.
> Currently in behavior therapy for obsessive compulsive disorder.
> Agree to abstinence or use of an effective barrier method (e.g.,  
> condom) of birth control.
> Appearance of new lesions on bone scan.
> Prior recombinant erythropoietin and/or G-CSF for AZT-related bone  
> marrow suppression.
> No metastatic disease by physical exam and chest x-ray or CT scan of  
> the chest.
> Evidence of regional lymph node metastases (N1-N3).
> Are between ages 18 and 55.
> Responsive or stable disease after prior induction chemotherapy  
> comprising cisplatin or carboplatin AND etoposide or irinotecan.
> Progressive lymphocytosis with an increase of more than 50% over a 2- 
> month period or anticipated doubling time of less than 6 months.
> No prior hemodialysis.
> Diffusion capacity greater than 50% predicted (corrected for  
> hemoglobin) if symptomatic.
> Previously treated with allogeneic stem cell or bone marrow  
> transplantation for primary disease.
> Karnofsky greater than 70%.
> No prior radiotherapy to study lesion, unless evidence of disease  
> progression.
> One of the following stages:.
> Platelet count at least 100,000/mm^3 for good marrow reserve  
> (150,000/mm^3 for poor marrow reserve).
> 4 to 21.
> At least 4 weeks since prior interferon.
> Previously treated brain metastases in continued response to  
> radiotherapy and/or surgery for at least 2 months allowed.
> No HIV or HTLV-1 associated lymphomas.
> Allowed as prophylaxis for Pneumocystis carinii pneumonia (PCP):.
> No other concurrent primary malignancy except carcinoma in situ or  
> nonmelanoma skin cancer.
> Presence of any AIDS-defining neoplasms (excluding Kaposi's sarcoma)  
> such as central nervous system (CNS) lymphoma.
> Positive urine pregnancy test.
> More than 2 weeks since prior surgery, other than biopsy or  
> placement of venous access device.
> Recovered from any prior surgery.
> More than 12 months since prior coronary/peripheral artery bypass  
> graft surgery.
> No prior thoracic irradiation.
> Histologically or cytologically confirmed solid tumor or hematologic  
> malignancy.
> No pre-existing convulsive disorder.
> Unwilling or unable to be fully evaluated for all follow-up visits.
> At least 30 days since prior systemic corticosteroids.
> Have a history of a neurologic disease unrelated to HIV infection.
> Synchronous primary endometrial cancer or history of primary  
> endometrial cancer.
> Patient must have pneumonia as documented by relevant signs and  
> symptoms and a positive chest X-ray.
>> 3 prior regimens.
> Persistent lymphoma by physical examination, radiographic studies,  
> bone marrow evaluations, flow cytometry, or polymerase chain reaction.
> Estrogen and progesterone receptor status known.
> Underlying clinical condition that precludes study completion or  
> places the patient at significant risk.
> Use of illegal drugs or legal drugs for recreational purposes or  
> excessive use of alcohol.
> Extramedullary disease outside liver or spleen.
> Dapsone is permitted but discouraged.
> At least 3 weeks since last major surgery (a lesser period is  
> acceptable if deemed in the best interest of the patient).
> More than 2 weeks since prior minor surgery.
> No prior chemotherapy or radiosensitizers for cancers of the head  
> and neck.
> Diagnosis of stage IV melanoma.
> Prior radiotherapy to study lesions allowed if there is evidence of  
> disease progression.
> No evidence of disease after prior standard treatment with curative  
> intent.
> At least 4 weeks since prior HRT.
> Concurrent oral or IV bisphosphonates for bony metastases are allowed.
> Women must not be pregnant or lactating.
> No medical condition that would interfere with oral administration  
> of erlotinib.
> SGOT no greater than 3 times upper limit of normal (ULN) (no greater  
> than 5 times ULN if liver metastases present).
> Has taken Aricept, Reminyl, or Exelon in the last 5 weeks.
> WBC at least 3,000/mm3.
> Pain for 3 months or longer.
> No other prior malignancy within the past 5 years except adequately  
> treated basal cell or squamous cell skin cancer or carcinoma in situ  
> of the cervix.
> Antimycobacterial drugs other than rifabutin.
> Larynx.
> Participation in other investigational studies within 30 days of the  
> renal transplant.
> For patients on corticosteroids:.
> No known hepatitis B virus.
> Surgery: No prior treatment other than transurethral prostatectomy;  
> No prior orchiectomy.
> Are 16 to 35 years of age.
> Ewing's sarcoma.
> Treatment with bone active agents such as fluoride or  
> bisphosphonates within the previous 2 years.
> Anticoagulant therapy.
> Toxicity Criteria for sensory neuropathy.
> No concurrent hormonal agents, except corticosteroids.
> Age less than 18 years.
> Prior development of a moderate or sever rash or any desquamation  
> while taking thalidomide.
> Children must be able to retain liquids at the time of enrollment.
> Suspected septicemia caused by coagulase-negative staphylococci.
> Failed or ineligible for standard therapy with iodine I 131 and/or  
> surgery.
> Distant metastases with measurable disease in breast or lymph nodes.
> No ductal cancer in situ or multicentric invasive ductal cancer.
> Chest wall tumors with ipsilateral pleural effusions or ipsilateral  
> pleural-based secondary tumor nodules allowed.
> Rheumatoid Arthritis for greater than 1 year from the time of  
> initial diagnosis of RA.
> Stage III (any T3b-T4, N2 or N3, M0).
> Patients must meet criteria for either platinum-resistant or  
> platinum-sensitive ovarian or peritoneal cancer.
> History of localized disease with prior definitive radiotherapy or  
> surgery.
> Previous systemic infection including influenza during this pregnancy.
> No life threatening infection.
> Prior steroid therapy for less than 2 weeks allowed.
> Willing to fast and complete clinical and laboratory evaluations.
> Expected survival of three months or longer.
> At least 4 weeks since prior immunotherapy other than interferon,  
> donor lymphocyte infusion, or pentavalent vaccine Concurrent  
> interferon allowed.
> History or evidence of drug or alcohol abuse.
> No other known condition that would preclude study participation.
> May include neurofibromatosis type I or II.
> Ability and will to participate in study for 4 years.
> Evidence of cytomegalovirus retinitis or colitis.
> History of acute or chronic pancreatitis, gout, or uric acid  
> nephropathy.
> Isoniazid for treatment of tuberculosis, with permission of the  
> protocol chair, when given in conjunction with pyridoxine.
> No concurrent corticosteroid therapy.
> No concurrent radiotherapy except to symptomatic or potentially  
> disabling bone lesion accompanied by other measurable disease.
> Must be a candidate for potential future pulmonary resection.
> Complete or partial remission following 1 induction course with  
> adverse cytogenetic abnormalities at diagnosis.
> Multifocal intraperitoneal tumors.
> Steroids in excess of physiologic replacement doses.
> BCG vaccines.
> Immunoglobulin administration or use of experimental agent within  
> the past 2 months.
> No concurrent tobacco use (e.g., cigarette, cigar, pipe, or chewing  
> tobacco).
> Cirrhosis.
> Normal urinalysis.
> No American Society of Anesthesiologists IV/V disease classification.
> Adequately treated in situ carcinoma of the cervix uteri.
> At least 1 year since prior corticosteroids, estrogens, progestins,  
> or any other steroid hormone.
> At least 1 month since prior beta-carotene compounds.
> No active opportunistic infection.
> Antiviral chemotherapy.
> Chemotherapy administered as a radio-sensitizer does not count as 1  
> regimen.
> Malabsorption.
> Bilirubin no greater than 2 times upper limit of normal* (ULN)  
> (unless due to Gilbert's syndrome).
> Cannot take medications by mouth or absorb drugs.
> Cranial spinal: 1800 cGy.
> No chronic hepatitis B.
> Prior investigational agents incorporated into prior systemic  
> chemotherapy allowed.
> No prophylactic hematopoietic growth factors (e.g., filgrastim (G- 
> CSF)).
> Consent of parent or guardian required. Note:.
> Chemotherapy: At least 4 weeks since prior methotrexate or  
> cyclophosphamide.
> Fertile patients must use effective contraception during and for at  
> least 4 weeks after study participation.
> Tolerating zidovudine (AZT) at time of study entry.
> Soft tissue primitive neuroectodermal tumor (PNET).
> SPV-30.
> No current history of alcohol or drug abuse.
> No concurrent anticoagulants other than those required to maintain  
> the patency of indwelling IV catheters.
> No other active cancer except previously treated carcinoma in situ,  
> non -melanoma skin cancer, or stage I prostate cancer.
> Have consent of parent or guardian if less than 18 years old.
> History of coronary artery disease and/or congestive heart failure  
> allowed if medical management of condition has been stable within  
> the past 6 months.
> Primary refractory AML for which no standard therapy exists.
> High-risk disease, defined as stage III or IV extragonadal germ cell  
> tumors.
> No known hypersensitivity to retinoids or retinoic acid derivatives  
> or to interferon or any component of the injection for this study.
> Have serious heart problems. Patients with high blood pressure  
> controlled by blood pressure medication but no heart disease may be  
> eligible for this study.
> Traumatic brain injury with loss of consciousness of > 24 hours and/ 
> or skull fracture.
> Mediastinal (thymic) large cell.
> Direct bilirubin no greater than 1.5 times ULN.
> No medical contraindication to study therapy.
> No severe diabetes.
> Other: At least 15 kg body weight No severely compromised clinical  
> or nutritional state.
> No marked edema by MRI with significant shift that is not  
> anticipated to be corrected by resection.
> Treatment with biologic response modifiers (e.g., interferon,  
> interleukin) within 14 days prior to study entry. Prior Treatment:  
> Excluded:.
> Anti-HIV drugs other than the study drugs. Concurrent Treatment:  
> Excluded:.
> At least 14 days since other prior major surgery.
> More than 3 months since prior chemopreventive drugs (e.g.,  
> retinoids).
> Intestinal cryptosporidiosis.
> Transplant where a trial reduction of immunosuppressive drug  
> treatment is not feasible.
> No more than 1 prior chemotherapy regimen (phase II).
> Bone marrow specimen showing clumps of tumor cells accompanied by  
> elevated urinary catecholamines.
> Can identify a collateral informant who has frequent contact with  
> the subject.
> History of an AIDS defining illness by the Centers for Disease  
> Control (CDC) definition within 8 weeks prior to study entry.
> Planned revascularization.
> No prior congestive heart failure unless ejection fraction at least  
> 40%.
> No prior surgery for head or neck cancer.
> Bilirubin no greater than 2.0 mg/dL.
> No concurrent immunotherapy during and for 2 weeks after last  
> vaccination.
> Enrollment in HSC protocol #97-0695 "Rehabilitation Intensification  
> Post Hip Fracture".
> Suspicion of need for colectomy.
> No prisoners or parolees HIV negative.
> At least 28 days since prior imatinib mesylate.
> Systemic corticosteroids for > 21 consecutive days.
> Histologic proof of lymphoid malignancy with an expected complete  
> response rate of less than 20 percent OR have failed at least one  
> prior therapy.
> Have had an unexplained fever of at least 38.5 C for 7 days in a row  
> within 30 days prior to screening.
> No other active malignancy except basal cell skin cancer or  
> carcinoma in situ of the cervix.
> Diagnosis of acquired immune deficiency syndrome.
> Ongoing and/or maintenance therapy for opportunistic infection.
> Diagnosis of an unstable medical illness within the last 12 months.
> Currently residing in the community (own home,family member's home,  
> or small group home) and agreeing to 13 weeks of followup in the  
> study.
> Surgery: Patients are excluded if they have had major surgery either  
> during or within four weeks prior to study entry.
> No clinically significant arrhythmia by ECG.
> Zidovudine (AZT) within 7 days prior to administration of study  
> drug. Excluded for at least 4 weeks prior to drug administration:.
> Carcinoid asthma.
> Progesterone receptor status known.
> patients may take ganciclovir for treatment of CMV infections.).
> Recipients of grafts from an HLA-identical sibling.
> Age over 30 years.
> Previous surgeries for SDB, such as adenoidectomy and/or  
> tonsillectomy or other airway-related surgeries.
> More than 5% blasts in the bone marrow or peripheral blood unrelated  
> to recovery of normal hematopoiesis from prior chemotherapy.
> No uncompensated congestive heart failure.
> Severe dysfunction (CrCl less than 30 mL/min).
> Stage III/IV ovarian cancer.
> Must have received at least one prior chemotherapy regimen for  
> metastatic breast cancer.
> No prior trastuzumab.
> Cumulative history of oral glucocorticoid use for at least 6 months  
> over the last year prior to the Screening Visit (the 6 months do not  
> have to be consecutive).
> No active urinary tract infection.
> Study partner to accompany subject to all visits.
> Concurrent therapeutic anticoagulants (e.g., warfarin or heparin)  
> allowed provided there is no prior evidence of underlying  
> abnormality with PT, INR, or PTT.
> No disease invading the airways, aorta, pericardium, or lung.
> Greater than 3.5 g/dL for G peaks or greater than 2.0 g for A peaks.
> No history of any bleeding disorders.
> At least 6 months since prior oral retinoids (3 months for topical  
> retinoids to the face).
> Availability of at least 1 x 10^8 purged autologous mononuclear bone  
> marrow cells per kg of body weight.
> At least 6 months since prior high-dose chemotherapy regimen with  
> stem cell support.
> Patients receiving LHRH analogues must have testosterone level less  
> than 50 ng/dL.
> Pain in the knee of at least 3 or more on a 0 to 10 scale (0 none,  
> 10 extreme pain) within 2 weeks prior to study entry.
> Refractory anemia with excess blasts (RAEB) with IPSS score at least  
> 1.5.
> Aerosol ribavirin for short-term treatment of acute respiratory  
> syncytial virus (RSV).
> Biologic therapy: No prior trastuzumab.
> No uterine sarcomas (leiomyosarcoma), mixed mullerian tumors, and/or  
> adenosarcomas.
> Spinal muscular atrophy.
> Have had a reaction to an anticoagulant (such as warfarin or heparin).
> Reached an ACTG 240 defined endpoint, or are permanently off ACTG  
> 240 study treatment.
> Are breast-feeding and are unwilling to stop breast-feeding.
> At least 3 weeks since prior major surgery.
> At least 1 week since prior radiotherapy to less than 15% of bone  
> marrow.
> Adequate bone marrow, liver and renal functions.
> At least 3 weeks since prior surgery requiring general anesthesia.
> Grade 4 (for hematologic) or Grade 3 (for all other) toxicity.
> Elevated liver enzymes in the year preceeding enrollment.
> Adequate hematologic function.
> Unexplained diarrhea defined as three or more liquid stools per day,  
> persisting more than 7 days within 2 years prior to entry.
> Any disorders for which the study drugs are contraindicated  
> (didanosine (ddI)) is contraindicated in renal impairment, heart  
> disease, receiving renal dialysis.
> Must have evidence of metastatic disease, including either of the  
> following:.
> Transfusion dependent patients. Patients with any of the following  
> prior conditions are excluded:.
> Discordant histologies between nodal tissue and bone marrow on  
> presentation are eligible.
> Isolated CNS relapse not eligible.
> No concurrent hormonal therapy, including aromatase inhibitors, pure  
> antiestrogens, or progestational agents, for breast cancer.
> Localized, non-disseminated.
> Adults of reproductive potential and their partners must agree to  
> use effective contraceptive measures.
> Post-hydration creatinine less than 1.47 mg/dL.
> Prior anthracycline allowed if total dose no greater than 300 mg/m2.
> Patients must be disease free at time of enrollment based on the  
> following surgical criteria:.
> Significant anemia or thrombocytopenia or leukopenia.
> Token Test of the Multilingual Aphasia Examination score < 36.
> Have a CD4 count of at least 50 cells/mm3.
> Known HIV positive status or who have an AIDS-related illness.
> Hx of breast/estrogen-dependent cancer.
> More than 1 month since prior biologic therapy or immunotherapy.
> Prophylactic therapy for Pneumocystis carinii pneumonia (PCP) that  
> may cause leukopenia.
> Weight of 40 kg or greater.
> Presence of opsoclonus, myoclonus, and/or ataxia associated with  
> neuroblastoma considered eligible.
> No prior immunologic therapy directed at the cellular immune system.
> No other malignancy within the past 5 years except treated basal  
> cell or squamous cell skin cancer or carcinoma in situ of the cervix.
> A diagnosis of AIDS by CDC criteria.
> Marginal zone B-cell lymphoma.
> Negative urine toxicology screen (except for methadone or methadone  
> metabolites) within 14 days prior to study entry.
> Prior brain metastases are allowed provided the following are true:.
> Bilirubin less than 2.5 times normal.
> Progressive disease by physical exam, imaging studies, and/or rising  
> prostate-specific antigen (PSA) levels defined by at least 1 of the  
> following criteria*:.
> Drugs known to significantly interact with saquinavir and/or  
> nelfinavir. Patients must be protease inhibitor therapy naive.
> Creatinine clearance or radioisotope glomerular filtration rate  
> (GFR) at least 70 mL/min OR an equivalent normal GFR OR.
> Rituximab, Campath or other unconjucated therapeutic antibody within  
> 4 weeks before the first dose of study drug.
> At least 4 weeks since prior steroids or megestrol.
> Stage I, IIA, or IIB (T1-3, N0-1, M0).
> No known hypersensitivity to phenylethane compounds.
> Locally advanced, unresectable disease.
> Fertile patients must use effective contraception during and for at  
> least 30 days after study participation.
> HIV infection diagnosed by HIV seropositivity and confirmed by  
> Western blot.
> Leukotriene inhibitors (i.e., zafirlukast and zileuton).
> At least 4 weeks since prior immunotherapy or biologic therapy.
> Progression of disease within past 4 weeks by radiological evidence.
> Creatinine no greater than 1.5 mg/dL (urinary diversion allowed).
> No known uncontrolled CNS metastases.
> No prior estramustine or suramin.
> Study therapy must begin within 5 weeks of diagnosis.
> Biopsy-confirmed aphthous ulceration of the mouth or esophagus  
> lasting at least 2 weeks.
> Tension.
> Start preventive treatment for Pneumocystis carinii pneumonia (PCP)  
> within 30 days prior to study entry, if CD4 cell count is below 200  
> cells/microL.
> Tumors tested by FISH must be positive by the specific FISH assay  
> for genetic amplification of HER2.
> Congenital long QT syndrome;.
> No poor nutritional status unlikely to be restored to fair status  
> within 3 weeks.
> Zubrod 0-1.
> Metaplastic carcinomas allowed.
> Histologically confirmed hepatocellular cancer (HCC).
> T2, N0, M0 if primary lesion at least 3 cm.
> Prophylaxis for Mycobacterium avium intracellulare.
> No concurrent phenytoin, carbamazepine, rifampin, barbiturates, or  
> Hypericum perforatum (St. John's Wort).
> Have had a major organ transplant and still have the graft.
> No other concurrent antitumor chemotherapy.
> Patients with low grade lymphoma or CLL will only be eligible if  
> they failed two chemotherapy regimens and have stage IV disease.
> No active or recent uncontrolled bleeding.
> Active therapy with investigational drugs other than treatment for  
> HIV disease, except with approval of the sponsor.
> Acute or chronic meningitis based on any etiology other than  
> cryptococcosis.
> No acute or chronic infections (e.g., malaria).
> Protease inhibitors. NOTE:.
> Babies will not be eligible for this study if they:.
> HIV antibody positive by ELISA or Western blot assays.
> Concurrent intermittent vaginal estrogens allowed if other local  
> measures for intractable vaginal atrophy are insufficient.
> HIV positive as determined by ELISA, Western Blot, or other  
> federally approved HIV test within the past 21 days.
> Any HIV-1 protease inhibitor therapy prior to study entry (e.g.,  
> saquinavir, ritonavir, indinavir, nelfinavir, 141W94).
> No CNS or gonadal involvement.
> Major medical or neurological disease.
> Excessive alcohol consumption or evidence of drug use.
> Recovered from prior cancer therapy.
> Sulfadimidine.
> Cytologically positive effusion.
> Spinal cord injury at or above the T10 spine.
> AST or ALT <2.5 times the upper limit of normal (ULN) within 30 days  
> of study entry.
> Participants of both genders and all races are eligible.
> Must have received 1 prior combination chemotherapy regimen OR at  
> least 1 but no more than 2 prior single-agent regimens.
> History of anaphylaxis or other serious adverse reactions to vaccines.
> No prior therapy for high-grade glioma.
> ischemic or nonischemic cardiomyopathy.
> Patients with no prior chemotherapy for prostate cancer are excluded  
> from the phase II part of the study.
> Have received certain other drugs within 28 days before the study  
> drug will be taken, or think that they will be needed during the  
> study.
> Karnofsky 50-100% (adults).
> No unstable or severe concurrent medical condition that would  
> preclude study participation.
> Progressive disease after gemcitabine-based chemotherapy for  
> metastatic disease.
> No severe uncontrolled ventricular arrhythmias.
> No prior or concurrent cryotherapy.
> Capable of using the product and diaphragm properly.
> Ongoing AZT or ddI therapy of 6 months or longer duration.
> Localized metastases allowed provided the following are true:.
> B-cell lymphoproliferative disorders.
> No concurrent adrenal steroids (inhalant, topical, or optical  
> steroids allowed).
> No chronic cirrhosis.
> Concurrent short-term dexamethasone for chemotherapy-induced emesis  
> is allowed.
> Resistant or recurrent disease after combination chemotherapy with  
> at least one standard regimen.
> Cardiac ejection fraction within the institutional range of normal  
> as measured by echocardiogram.
> Have been immunized against smallpox.
> Pleural effusion.
> Patients must weight at least 40 kg (88 lbs.).
> Histologically and clinically confirmed pleural mesothelioma.
> Gleason score and PSA known.
> Have severe low blood count (anemia).
> SGOT no greater than 1.5 times normal.
> Adult dose of nevirapine, amprenavir, abacavir, lopinavir/ritonavir,  
> or off-label dosing of indinavir/ritonavir for at least 1 week  
> before PK sampling.
> No contraindications to MRI or CT scan (e.g., intracranial vascular  
> clips).
> Treatment with any medications that may cause lupus-like symptoms  
> within 4 weeks of baseline visit (e.g. procainamide, hydralazine).
> Basaloid carcinoma.
> Immunosuppressive or cytotoxic therapy.
> Stage IIIA (T1 or T2, N2) or IIIB disease not amenable to resection  
> or surgery.
> Are able to understand the study and pass a test showing they  
> understand it, and give written informed consent.
> No grade 2 or greater atrioventricular block.
> No prior radiotherapy to more than 15% of bone marrow.
> No secondary lymphoma after prior chemotherapy or radiotherapy for  
> other malignancies.
> Evaluate recurrent abdominal pain;.
> Infectious mononucleosis caused by cytomegalovirus (CMV) or Epstein- 
> Barr virus (EBV).
> No co-existent endocrine conditions.
> No prior or planned radical prostate surgery.
> Hematological function normal.
> Fertile patients must use effective contraception during and for 2  
> months following study.
> No hypersensitivity to any of the study drugs or their ingredients.
> Willing to limit sun exposure on day of PUVA therapy.
> Progressed while on or after treatment on platinum-based regimen.
> No severe hepatic dysfunction.
> Histologically confirmed myeloid metaplasia with myelofibrosis (MMM).
> Progressive disease after at least 1 standard chemotherapy or  
> chemoimmunotherapy regimen (e.g., dacarbazine or cisplatin  
> monotherapy).
> Alkaline phosphatase less than 4 times ULN.
> No history of cancer of the endometrium, vagina, or cervix.
> Progressed or recurred after 1, and only 1, prior cisplatin- or  
> carboplatin-containing systemic regimen for metastatic disease.
> Meets criteria for bipolar disorder, schizophrenia, bulimia/ 
> anorexia, dementia, major depression.
> No inability to comply with study and follow-up procedures.
> Children < 44 months old.
> Benzodiazepines within 14 days prior to study entry.
> Predicted postoperative FEV_1 greater than 1 by spirometry.
> Any other experimental therapy within 3 months of study entry.
> ALS.
> HIV infection. -Antecedent malignancy, whose prognosis is poor (<90%  
> probability of surviving for 5 yrs.).
> Absolute CD4 count of 200 cells/mm3 or greater.
> Have completed at least 60 weeks of treatment on ACTG 328.
> Identical for 1 HLA haplotype and mismatched at the HLA-A, -B, -C,  
> or DRB1 loci of the unshared haplotype.
> Disease progression while receiving an irinotecan-containing regimen  
> for metastatic colorectal cancer OR.
> T4 tumor based on malignant pleural effusion.
> Histologically confirmed previously untreated ovarian epithelial  
> carcinoma, peritoneal carcinoma, or fallopian tube carcinoma.
> At least 24 hours since prior transfusion.
> AST less than 2 times ULN.
> No prior oxaliplatin or irinotecan.
> Refractory to hormonal therapy.
> No prior endocrine therapy for breast cancer.
> Prior sentinel node biopsy or axillary node dissection allowed  
> provided nodes are pathologically negative.
> Acute cerebral trauma.
> Endocrine therapy: No prior hormonal therapy for prostate cancer.
> The subject is a known or suspected drug abuser.
> Cytokine inhibitors.
> No concurrent enrollment in investigational anticancer drug trials  
> that exclude the use of other investigational agents.
> Serum antibody to HTLV-III/LAV with or without viremia.
> On other immune-based therapy (e.g., interleukin-2, alpha  
> interferon, immunoglobulin, thalidomide) within 30 days prior to  
> study entry.
> Clinically significant gastrointestinal symptoms including  
> persistent nausea or abdominal pain.
> Have kidney disease or insufficiency.
> Bone marrow must not show evidence of other conditions associated  
> with myelofibrosis, including the following:.
> No concurrent antiretroviral therapy (HAART) for HIV positive  
> patients.
> Right ventricular enlargement.
> No prior radiotherapy to more than 25% of the total skeleton.
> No abnormal slit-lamp examination using a vital dye (e.g.,  
> fluorescein or Bengal-Rose).
> Non-Hodgkin's lymphoma or multiple myeloma; Autologous stem cells.
> WBC greater than 4,000/mm^3.
> Histologically proven pure germinoma.
> Patients who are iatrogenically immune-suppressed following organ  
> transplantation.
> Patients with unresolved bowel obstruction.
> Renal cancer.
> More than 4 weeks since prior soy products.
> End stage renal disease or receiving hemodialysis treatment.
> More than 14 days since prior investigational agents.
> Are taking certain medications such as ribavirin, hydroxyurea, and  
> ganciclovir.
> No prior lonafarnib.
> Registered to protocol MSKCC-9040 OR.
> Fertile patients must use effective double-barrier contraception  
> during and for 4 weeks after study.
> Can be followed at a participating Pediatric AIDS Clinical Trials  
> Unit (PACTU) for the entire study.
> Must have received 1 prior cytotoxic therapy regimen.
> Have a history of malignancy, except squamous or basal skin cancer.
> If significant clinical hearing loss already present, must accept  
> risk of further hearing loss.
> Increased blast cells (at least 5%) in peripheral blood or bone  
> marrow OR.
> No concurrent ganciclovir or foscarnet for previous CMV reactivation/ 
> infection.
> Histologically confirmed adenocarcinoma of the prostate previously  
> treated with androgen suppression.
> Suitable for nephrectomy.
> CALGB 0-1.
> Urine drug screen positive for a drug of abuse.
> Ability to communicate in English.
> Haemophilus B Conjugate vaccine.
> Age 18 to 50 with ALL in CR2 or greater and ineligible for  
> conventional allogeneic transplantation based on general medical  
> condition.
> Diagnosis of metastatic breast cancer.
> No aspirin (100 mg/day) within 1 week prior to surgery.
> No CNS lymphoma, AIDS-related lymphoma, or chronic lymphocytic  
> leukemia.
> Must have an initial diagnostic specimen that is CD20+.
> At least six months of prior cumulative ZDV therapy.
> No other malignancies within the past 5 years except curatively  
> treated malignancies with low risk of recurrence.
> Current acupressure, or Qi Gong, or acupuncture.
> Subcutaneous panniculitis-like PTCL.
> Current uncontrolled hypertension with systolic blood pressure in  
> excess of 200 mm Hg or diastolic blood pressure in excess of 115 mm  
> Hg.
> Have a diagnosis of other respiratory viruses (influenza, RSV, etc.).
> No standard therapy available that is potentially curative or  
> definitely capable of extending life expectancy.
> At least 6 Raynaud's attacks per week.
> Available tissue for central review.
> Willing and able to comply with the study procedures and visit  
> schedules.
> No concurrent administration of the following drugs:.
> Presence of fatigue with usual fatigue severity at least 3 on the  
> 0-10 numerical scale of the Brief Fatigue Inventory within the past  
> 14 days.
> Meets at least 1 other diagnostic criteria for NF1.
> Must be a resident of the Washington DC area.
> No concurrent prophylactic colony-stimulating factors for  
> myelosuppression.
> No prior HIV medications.
> Have an HIV-1 RNA of at least 5,000 copies/ml.
> Recent chest x-ray (within 24 hours) showing at least unilateral  
> infiltrations.
> Suboptimally debulked stage III or suboptimally or optimally  
> debulked stage IV.
> Isoniazid, if no alternative therapy is available.
> Life expectancy: No imminent demise.
> History of drug-induced neutropenia.
> No concurrent radiotherapy to greater than 10% of total liver, lung,  
> or bone marrow.
> Other anticytomegalovirus (CMV) therapy, particularly systemic  
> ganciclovir, foscarnet, or CMV hyperimmune globulin.
> Lomotil, Imodium, or deodorized opium tincture in a standardized  
> regimen for diarrhea.
> More than 7 days since prior fine needle aspirations or core biopsies.
> Have a drug allergy or other allergy which might cause a problem  
> during the study.
> No positive supraclavicular or scalene lymph nodes with disease  
> extending up into the cervical region OR.
> No concurrent chronic systemic steroids.
> No severe renal dysfunction defined as serum creatinine >1.6 mg/dL.
> Refractory to initial therapy OR recurrent following 1 induction  
> therapy regimen with or without consolidation therapy and/or bone  
> marrow transplantation.
> FEV_1 at least 1 L or 35% of predicted.
> Rhabdomyosarcoma (e.g., alveolar, embryonal, or pleomorphic).
> More than 4 months since prior definitive therapy (surgery or  
> radiotherapy) for brain metastases and must not have evidence of  
> disease on brain CT scan or MRI.
> If the patient does not know his/her vaccine history, it should be  
> presumed that he/she was vaccinated.
> Patients with symptomatic CNS metastases or leptomeningeal  
> involvement.
> No contralateral hilar disease or an exudative, bloody, or  
> cytologically malignant effusion.
> Previous participation in this trial.
> No concurrent intrathecal therapy during the first course of  
> decitabine.
> Any antiretroviral drug except zidovudine (AZT).
> Thrombocytopenia. Patients with the following prior conditions are  
> excluded:.
> Obtained no benefit from prior standard or salvage therapy.
> Significant negative symptoms with few positive symptoms (e.g.  
> hallucinations, delusions) and no evidence of major depression.
> Impaired renal function (serum creatinine > 2.0) and hepatic  
> function (bilirubin more than 2.0 x and transaminase more than 4.0 x  
> of the upper normal limit).
> No significant atelectasis (i.e., atelectasis of an entire lung).
> Adequate psychological support available.
> Not a candidate for stem cell transplantation or refuses one.
> No significant cardiac abnormalities by echocardiogram.
> PSA progression.
> Treatment with opiates within the last six months.
> Subjects must be considered reliable.
> Active malignancy other than Kaposi's sarcoma.
> Acceptable neurological and neuropsychological impairment scores.
> No active pancreatic disease.
> No residual tumor within 10 mm of optic chiasm.
> History of alcohol or drug abuse within the past 6 months.
> are planning to become pregnant.
> HAART regimen of two NRTIs and at least one PI (not nelfinavir).
> Have a gastrointestinal disorder that makes it difficult for  
> patients to absorb food or to take medications by mouth.
> Lycopene.
> No prior radiotherapy for rectal cancer.
> No lymphoma therapy for 3 weeks prior to Study Day 1.
> No more than one prior systemic chemotherapy regimen.
> No other concurrent standard or investigational chemotherapy.
> Have problems with their pregnancy and/or are expecting more than 1  
> baby.
> No prior or concurrent alcohol abuse or drug dependence.
> Primary refractory or relapsed (within the past year) disease.
> Patients who relapsed after autologous or allogeneic bone marrow or  
> peripheral blood stem cell transplantation are not eligible.
> Stable weight (+/- 2 kg) by 28 days prior to study entry.
> No medical or psychiatric condition that would preclude compliance.
> Be able to have a central venous like access maintained throughout  
> the study.
> Positive supraclavicular or scalene lymph nodes must not have  
> disease extending up into the cervical region.
> At least 6 weeks since prior chemotherapy and recovered.
> No severe pulmonary disease/illness.
> Any finding of tuberculosis, elevated ALT or AST, low hemoglobin  
> levels, low WBC and platelet count, high levels of serum creatinine.
> Immunoglobulins or vaccines within the past 3 months.
> Has taken an investigational drug or the medication Felbatol within  
> the previous 30 days.
> Absence of acute opportunistic infection at time of entry.
> Concurrent bisphosphonates (e.g., pamidronate) allowed if initiated  
> before study begins.
> Other curatively treated cancer and disease free for at least 10  
> years.
> Female patients who are not pregnant or lactating.
> Hepatic: No chronic or acute hepatic disorder.
> Stratum 3 (stages III or IV):.
> No history of allergic or other adverse reaction to gabapentin.
> No concurrent cytotoxic chemotherapy.
> Intractable diarrhea (>= 6 loose stools/day for >= 7 consecutive  
> days).
> Have taken at least 2 of the 3 licensed anti-HIV drug classes for at  
> least 3 months.
> Hospitalization within the past 14 days.
> No acute ischemia or active conduction system abnormalities by EKG.
> Resident of Zomba or Blantyre Districts, Malawi.
> Current diagnosis of community-acquired pneumonia.
> HLA genotypically identical donor available (under 75 years of age).
> Cerebral Kaposi's sarcoma.
> WBC greater than 1500/mm3.
> No prior peripheral neuropathy.
> At least 30 days since participation in another clinical study.
> No pre-existing grade 2 or greater motor or sensory peripheral  
> neuropathy except abnormalities due to cancer.
> No prior sirolimus.
> No uncontrolled medical illness.
> No other prior intracerebral chemotherapy.
> Are sensitive to acyclovir, Valtrex, famciclovir, or ganciclovir.
> Involvement in alcohol treatment other than provided by the study or  
> AA.
> Hematopoietic: No clinically significant hematologic disease No  
> hemodynamic instability.
> Have had a serious illness requiring systemic treatment and/or  
> hospitalization within 14 days prior to study entry.
> One tube of peripheral blood and one representative paraffin block  
> of tumor tissue must be available.
> No other concurrent participation in a protocol with pharmacological  
> intervention.
> No other major medical or psychiatric illness that would preclude  
> study compliance.
> Prior therapy with oxaliplatin.
> Not in first CR with Down syndrome.
> No history of second malignancy except adequately treated basal cell  
> skin cancer or carcinoma in situ of the cervix.
> No known peripheral vascular disease.
> No more than 1 cm linear dimension of contact between gadolinium- 
> enhancing tumor and a cerebral ventricle.
> No concurrent corticosteroids unless on stable dose of less than 20  
> mg/day of prednisone or equivalent and administered for reasons  
> unrelated to ovarian cancer.
> Willing and able to undergo serial bronchoscopic examinations.
> No leptomeningeal or brain metastases.
> Other myelosuppressive therapies which may be handled in the same  
> manner as AZT.
> No concurrent birth control pills or other hormonal therapy.
> Patients in the methotrexate arm must have started methotrexate  
> within 6 months of enrollment in the registry.
> No hip prosthesis.
> Failed standard or salvage therapy.
> Are allergic to any part of the chickenpox vaccine, including  
> neomycin.
> Active opportunistic infection requiring hospitalization or exclude  
> medication.
> Measurable disease outside of previously irradiated field unless  
> evidence of progression.
> No other concurrent serious, systemic disorder that would preclude  
> study.
> Other anti-retrovirals after consultation with the Syntex study  
> monitor.
> Acute opportunistic infection or other significant concurrent  
> illness that would preclude participation for the required 36 days.
> Concurrent enrollment on a HSCT protocol with the Experimental  
> Transplantation ; Immunology Branch (ETIB) at the NCI Center for  
> Clinical Research.
> Autism based on DSM-IV criteria.
> No primary germ cell tumor, small cell carcinoma, or lymphoma.
> Rising prostate-specific antigen AND radiographic evidence of  
> extraprostatic prostate cancer by bone scan, CT scan, prostascint  
> scan, or MRI.
> Prior cumulative doses of radiotherapy must not exceed the following:.
> Have used investigational research agents within 30 days prior to  
> enrollment.
> Known CNS metastases treated within 2 months of Day 1 or any  
> uncontrolled CNS metastases.
> Ineligible for a higher priority GOG protocol (if one exists).
> Prior adjuvant or neoadjuvant hormonal therapy of less than 8 months  
> duration allowed.
> Patients must have a Zubrod PS<2 (Appendix 6), Cr<2.0, direct  
> bilirubin <2, and transaminases SGPT <3x normal.
> Medical or psychiatric condition or occupational responsibilities  
> which could interfere with the study.
> 4 erupted maxillary incisors.
> Persistent, relapsed, or progressing malignancy.
> no treatment with systemic drugs for 1 month prior to the start of  
> the study.
> Ineligible for potentially curative surgical resection.
> Any disease or disorder listed in Patient Exclusion Co-existing  
> Conditions.
> Meets the criteria for alcohol dependence with comorbid bipolar  
> disorder.
> AST and/or ALT no greater than 4 times ULN.
> Rheumatoid arthritis or other autoimmune disease (serum ANA > 1:160).
> Presence of dementia, psychosis or other disorder of cognition that  
> impairs ability to participate in minimal contact intervention.
> Diagnosis of AIDS Dementia Complex (stage II or higher).




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