A divide and conquer approach to multiple alignment.

We present a report on work in progress on a divide and conquer approach to multiple alignment. The algorithm makes use of the costs calculated from applying the standard dynamic programming scheme to all pairs of sequences. The resulting cost matrices for pairwise alignment give rise to secondary matrices containing the additional costs imposed by fixing the path through the dynamic programming graph at a particular vertex. Such a constraint corresponds to a division of the problem obtained by slicing both sequences between two particular positions, and aligning the two sequences on the left and the two sequences on the right, charging for gaps introduced at the slicing point. To obtain an estimate for the additional cost imposed by forcing the multiple alignment through a particular vertex in the whole hypercube, we will take a (weighted) sum of secondary costs over all pairwise projections of the division of the problem, as defined by this vertex, that is, by slicing all sequences at the points suggested by the vertex. We then use that partition of every single sequence under consideration into two 'halfs' which imposes a minimal (weighted) sum of pairwise additional costs, making sure that one of the sequences is divided somewhere close to its midpoint. Hence, each iteration can cut the problem size in half. As the enumeration of all possible partitions may restrict this approach to small-size problems, we eliminate futile partitions, and organize their enumeration in a way that starts with the most promising ones.(ABSTRACT TRUNCATED AT 250 WORDS)

Response of immunocompromised children with solid tumors to a conjugate vaccine for Haemophilus influenzae type b.

Serum antibody response to a conjugated Haemophilus influenzae type b polyribosylribitol phosphate-diphtheria toxoid vaccine was assessed in nonvaccinated children aged 1 1/2 to 5 years receiving chemotherapy for solid tumors. Responses occurred in 21 (42%) of 50 children after first vaccination, and in 10 (45%) of 22 revaccinated children.

Decreased counts of blood neutrophils, monocytes, and platelets in human immunodeficiency virus-infected children and young adults treated with diethyldithiocarbamate.

Nineteen young human immunodeficiency virus-infected patients were randomized to receive 400 mg of oral diethyldithiocarbamate (DTC) per m2 or placebo weekly for 12 weeks. Changes in blood CD4+ lymphocytes were not significantly different between groups. However, neutrophil, monocyte, and platelet counts consistently decreased during DTC treatment, suggesting DTC-mediated myelosuppression.

Safety and pharmacokinetics of 566C80, a hydroxynaphthoquinone with anti-Pneumocystis carinii activity: a phase I study in human immunodeficiency virus (HIV)-infected men.

A hydroxynaphthoquinone compound (566C80) has been shown to be effective in the prevention and treatment of murine Pneumocystis carinii pneumonitis. In a phase I study, five cohorts of four human immunodeficiency virus-infected men received 100, 250, 750, 1500, and 3000 mg of the compound orally once daily for 12 days. A sixth cohort received 750 mg three times daily for 5 days, then twice daily for 16 days. Evaluation included clinical, hematologic, and biochemical studies and the pharmacokinetics of 566C80. The only drug-related adverse effect was a maculopapular rash in one patient that resolved without discontinuation of the drug. With the largest dosage tested (3000 mg) the following pharmacokinetic measures were achieved: maximum plasma concentration, 39 micrograms/ml; time to maximum plasma concentration, 8.0 h; area under plasma concentration-time curve at steady state, 1088 h.micrograms/ml; plasma half-life, 51 h; and total plasma clearance, 4.09 l/h. Compound 566C80 offers promise as a new drug class for P. carinii pneumonia.

Infrared, thermistor, and glass-mercury thermometry for measurement of body temperature in children with cancer.

Body temperature is often the sole determinant of whether or not the neutropenic cancer patient is admitted to the hospital for empiric antibiotic therapy. Recently developed infrared tympanic thermometers offer rapid readings, but their accuracy has not been established. We studied two infrared thermometers (FirstTemp and Thermoscan) and a thermistor (IVAC) in children with cancer. Mean infrared measurements did not differ significantly between right and left ear canals, and the mean IVAC temperature did not differ significantly from the left to the right axilla (P greater than 0.05, paired t test). IVAC predictive mode mean temperature was 0.2 degrees C lower than monitor mode mean temperature in the axilla (P less than 0.0001), but 0.1 degree C higher than monitor mode orally (P less than 0.0001). Aiming the infrared instrument at the tympanic membrane using an ear tug resulted in a 0.2 degree C higher mean temperature than casual placement in the ear canal (P less than 0.0001). After compensation for the mean difference in reference oral glass-mercury versus test instrument temperatures, the FirstTemp, Thermoscan, and oral and axillary predictive mode IVAC measurements yielded sensitivities for the detection of fever of 84%, 84%, 82%, and 86%; specificities of 100%, 99%, 100%, and 100%; positive predictive values of 100%, 93%, 100%, and 100%; and negative predictive values of 95%, 98%, 98%, and 98%, respectively. We conclude that each of these instruments detects fever with comparable reliability. Infrared instruments are especially attractive alternatives due to their time efficiency.

Reduced therapy for Wilms' tumor: analysis of treatment results from a single institution.

From 1968 to 1986, 192 patients from 0 to 17 years of age were enrolled in three consecutive protocol-controlled studies of Wilms' tumor at St Jude Children's Research Hospital. Tumors were completely excised at the time of diagnosis whenever possible, and patients were subsequently treated with chemotherapy and radiotherapy according to the initial extent of disease. All patients received dactinomycin and vincristine, with doxorubicin added to the regimens in studies 2 and 3. Chemotherapy was extended to 18 months in study 2 (n = 53), but was limited to 12 months for most patients in study 3 (n = 107). In the third study, radiation was eliminated altogether for patients with stage I or II tumors and was reduced to 12 Gy for those with more advanced disease. Intensification of chemotherapy in study 2 improved the 5-year relapse-free survival rate over that in study 1 (82% v 52%), but the accompanying increase in toxicity was considered unacceptable. Comparison of 2-year relapse-free survival rates in studies 2 and 3 indicated that the reduction of therapy in the latter trial did not jeopardize disease control: 88% v 86% for patients with stage II or III disease, favorable histology; 75% v 57% for the same stages, unfavorable histology; and 57% v 61% for stage IV patients. At least 80% of all patients enrolled in study 3 will be long-term survivors. We conclude that rescheduling of effective antitumor drugs and eliminating or reducing radiotherapy are feasible alternatives in the treatment of Wilms' tumor with favorable histologic features.