A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

BACKGROUND: large scale and reliable proteins' functional annotation is a major challenge in modern biology. Phylogenetic analyses have been shown to be important for such tasks. However, up to now, phylogenetic annotation did not take into account expression data (i.e. ESTs, Microarrays, SAGE, ...). Therefore, integrating such data, like ESTs in phylogenetic annotation could be a major advance in post genomic analyses. We developed an approach enabling the combination of expression data and phylogenetic analysis. To illustrate our method, we used an example protein family, the peptidyl arginine deiminases (PADs), probably implied in Rheumatoid Arthritis. RESULTS: the analysis was performed as follows: we built a phylogeny of PAD proteins from the NCBI's NR protein database. We completed the phylogenetic reconstruction of PADs using an enlarged sequence database containing translations of ESTs contigs. We then extracted all corresponding expression data contained in EST database This analysis allowed us 1/To extend the spectrum of homologs-containing species and to improve the reconstruction of genes' evolutionary history. 2/To deduce an accurate gene expression pattern for each member of this protein family. 3/To show a correlation between paralogous sequences' evolution rate and pattern of tissular expression. CONCLUSION: coupling phylogenetic reconstruction and expression data is a promising way of analysis that could be applied to all multigenic families to investigate the relationship between molecular and transcriptional evolution and to improve functional annotation.

Control of SIV rebound through structured treatment interruptions during early infection.

In a randomized controlled trial with acute simian immunodeficiency virus (SIV)-infected macaques, both highly active antiretroviral therapy (HAART) and HAART with fixed-schedule structured treatment interruption (STI-HAART; alternating 3 weeks on and 3 weeks off therapy) suppressed viral load. In the STI-HAART group, T cell virus-specific immune response (VIR) and control of viral rebound increased concurrently during subsequent interruptions. In contrast, VIR did not increase and SIV rebounded after permanent treatment withdrawal in all animals on continuous HAART. Fixed-schedule STI-HAART appears to be an effective alternative to continuous HAART for the early treatment of retroviral infection.

Prenatal sonographic diagnosis of posterior urethral valves: identification of valves and thickening of the posterior urethral wall.

This report describes 2 heretofore unreported sonographic findings that may aid in the antenatal diagnosis of posterior urethral valves. Each of 2 fetuses showed a prominent or thickened posterior urethra and one or more bright echogenic lines representing valve tissue within a dilated and/or thickened posterior urethra. These findings helped solidify the antenatally suspected diagnosis of posterior urethral valves. The diagnosis was confirmed clinically and surgically during neonatal life. These 2 imaging findings may help in providing a more definitive antenatal diagnosis of posterior urethral valves and allow more expeditious therapy.

Ultrasonographic diagnosis of ectopic pregnancy: importance of transabdominal imaging.

Endovaginal sonography has greatly improved the diagnostic evaluation of suspected ectopic pregnancy. Some authors suggest imaging solely by endovaginal technique for diagnosis. We perform both a transabdominal scan for a global view of the pelvic and abdominal contents and an endovaginal sonographic examination for a higher resolution and focused view of the gynecologic structures. We report three patients with negative endovaginal examinations who had obvious ectopic pregnancies on our subsequent transabdominal examination. These cases remind us of the valuable information that can be obtained with the transabdominal approach and the complementary role it plays with endovaginal sonography.

Endodermal sinus tumor of the ovary: imaging evaluation.

OBJECTIVE: Endodermal sinus tumor of the ovary is a rare complex malignant tumor that occurs in young women. We performed this study to determine the imaging characteristics of this tumor. CONCLUSION: Endodermal sinus tumor of the ovary presents as a large complex abdominal mass that can be predominantly cystic and should be considered in the differential diagnosis of complex abdominal masses in girls and young women. In addition, upon encountering a mass with these imaging characteristics in the proper clinical setting, serum alpha-fetoprotein levels should be measured to help make a presurgical diagnosis and to obtain a baseline value.

Posterior urethral valve: transperineal US for imaging and diagnosis in male infants.

PURPOSE: To compare routine pelvic and transperineal scanning in the ultrasonographic (US) diagnosis of posterior urethral valve (PUV). MATERIALS AND METHODS: Longitudinal and transverse transperineal views were obtained in addition to routine renal and transvesicle views in the prospective US evaluation of 10 male infants (aged 2 days to 6 weeks) clinically suspected of having PUV. High-frequency (5.0- and 7.5-MHz) transducers were used. RESULTS: Five of the boys proved to have PUV. Each had urethral dilation clearly imaged at transperineal US. Only two of these boys had urethral dilatation imaged with the transvesicle approach. In three of the boys, a linear area of echogenicity, consistent with a valve, was imaged, but only with the transperineal approach. The other five boys had no urethral dilatation noted at transperineal or transvesicle US and proved to not have PUV. CONCLUSION: Transperineal imaging can aid in the diagnosis of PUV at US. Transperineal US may enable imaging of the valve itself.

Focal and diffuse increased echogenicity in the renal parenchyma in patients with sickle hemoglobinopathies--an observation.

Eleven patients with sickle hemoglobinopathies undergoing sonographic examinations for reasons unrelated to renal parenchymal disease were incidentally noted to have increased echogenicity in the central portion of the renal parenchyma. This appearance was observed to be a continuum, with some cases showing focally hyperechoic medullary pyramids at one extreme and other cases showing a diffusely echogenic central parenchymal region relative to a thin band of hypoechoic cortical or peripheral parenchyma at the other extreme. The finding of hyperechoic medullae of the kidneys has been reported in patients having conditions associated with hyperuricemia, medullary nephrocalcinosis, or hypokalemia. This sign has not been commonly reported as a finding in patients with sickle syndrome. The thin hypoechoic rim of cortical parenchyma relative to a more echogenic central parenchyma has not been commented on previously.

Immunobiology of primary intracranial tumors. Part 4: levamisole as an immune stimulant in patients and in the ASV glioma model.

Levamisole was evaluated as an immune stimulant in a randomized controlled study of patients with anaplastic gliomas, who had undergone surgical resection and who were also treated with radiotherapy and BCNU chemotherapy. Of 102 patients placed into the study, 85 were determined to comprise the adequately treated group (ATG): a full course of radiotherapy and two cycles of BCNU chemotherapy. Within the ATG, those patients who received levamisole did not demonstrate significantly different serial delayed hypersensitivity reactions, peripheral blood lymphocyte and T-cell counts, or serum IgM levels, compared to those patients not receiving levamisole. There was no significant difference in survival times of the two groups. Studies utilizing the avian sarcoma virus-induced glioma in rats also showed no improvement in survival with levamisole stimulation as the only immune agent, but the combination of active immunization and adjuvant stimulation with bacillus Calmette-Guerin plus levamisole was found to be therapeutically effective in this model and will be used in future pilot studies of active immunization in patients.

Effect of helium/nitrogen/oxygen mixtures on HPNS convulsion threshold in euthermic rats.

This study compares the effects of various so-called trimix mixtures (10, 20, and 40% N2 in He-O2) on the convulsion threshold pressure (Pc) and EEG activity in 60 adult male Wistar rats with chronically implanted electrodes with those in 20 rats in He-O2 only. Restrained animals were individually compressed with trimix mixtures at 80 or 160 atm per hour to a simulated depth of 138 ATA; colonic temperature was maintained at normal levels. Pc was defined as the initial occurrence of overt sustained generalized tonic-clonic seizures, accompanied by typical "spike and wave" patterns in all EEG leads. As in man, in rats trimix increased the depth of the onset of HPNS tremors and myoclonic jerks in all six groups of rats. However, the Pc of the trimix groups was no different from the Pc of the helium-oxygen group (113 ATA), and at 40% N2, rats showed EEG seizures but no overt convulsions. These results are discussed in relation to those of other studies showing the extension of Pc in mice and monkeys attained by adding narcotics to heliox; the paper also considers the relevance of method of compression, addition of nitrogen, core temperature, and species differences, as well as the need for EEG measurements and direct observation of overt convulsions as indicators of an effective antagonism of HPNS.

Synergism between BCNU and irradiation in the treatment of anaplastic gliomas. An in vivo study using the avian sarcoma virus-induced glioma model.

The therapeutic effects of irradiation, BCNU, or combined irradiation and BCNU were studied in the avian sarrcoma virus (ASV)-induced glioma model in rats. Whole-head orthovoltage radiation therapy was given in six equal fractions over 2 weeks, and BCNU was administered intraperitoneally as a single dose of 10 mg/kg. Two series of experiments were performed in order to duplicate the results. In Series I, the median survival times of the experimental groups, in days after randomization were as follows: control group (no treatment), 69; group receiving 200 rads, 84 (p less than 0.05); group receiving BCNU, 80.5 (p less than 0.1); and group receiving 2000 rads + BCNU, 112 (p less than 0.001). In Series 2, the median survival times were: control group, 73.5; group receiving 2300 rads, 85 (p less than 0.01); group receiving BCNU, 92.5 (p less than 0.025); and group receiving 2300 rads + BCNU, 123.5 (p less than 0.001). In both series, combined therapy was significantly better than either radiation or BCNU alone. This is the first time that a synergistic effect of BCNU and irradiation has been reported in an in vivo brain-tumor model and supports the clinical use of this combination in the treatment of malignant gliomas.

Meat-buying practices of Caucasians, Mexican-Americans, and Negroes.

Meat purchases were observed at supermarket checkout counters, socioeconomic data were obtained by questioning shoppers, and card questionnaires were given to 600 shoppers. Two supermarket chains in each of the three ethnic areas of Lubbock, Texas, were used on two days. Ethnic group was significantly related to the choice of half of the twelve meat cuts bought by the greastest number of shoppers and accounted for more significant effects on meat-buying variables than did chain, area, and day. Returned card questionnaires were 77 per cent accurate concerning meat-buying data.

Radiographic chest abnormalities in adult hemophilia.

The chest radiographs of 33 adult hemophiliacs were reviewed for possible pulmonary features of this disease. Only 7 patients showed no abnormalities; 12 patients exhibited scarring, fibrosis, and pleural thickening of the lung, interpreted as the sequelae of intrapulmonary hemorrhage or hemothorax. The remaining 14 patients demonstrated abnormalities of the pulmonary vessels, and 4 of them had evidence of hyperinflation. Possible etiologic factors are discussed.