PubMed Health⌕ Search

Biomedical subjects

J S Shah

Publications and source records attributed to J S Shah.

At least 19 recordsLinked to original sources
PubMed2001

Anesthesia for thoracoscopy.

Thoracoscopy has become a widely used method of achieving minimally invasive thoracic surgery. The anesthesiologist providing perioperative care for VATS is challenged to evaluate the patient carefully; to design a safe anesthetic regimen, taking into account preexisting disorders; to ameliorate physiologic alterations associated with one-lung ventilation and CO2 insufflation; and to provide safe, effective perioperative anesthesia and postoperative pain control.

Anesthesia↗
PubMed1996

Detection of rRNA from four respiratory pathogens using an automated Q beta replicase assay.

Ribosomal RNA targets from Mycobacterium avium complex (23S), Mycoplasma pneumoniae (16S), Pneumocystis carinii (18S) and Legionella pneumophila (16S) were detected in four separate assays on a model automated Q-beta amplification instrument. Sandwich hybridization, reversible target capture, detector probe amplification and fluorescent signal detection occurred in closed, disposable packs at 38 degrees C. Packs were injected with 0.5 ml samples in 3.06 M guanidine thiocyanate. Ten samples per run were read after 7 h, requiring only 4 min loading time. Synthetic RNA transcripts and purified, natural RNAs from up to four different strains per assay were diluted to 10(6) or fewer molecules per sample (approximately 100 cells for prokaryotes, 10 cells for Pneumocystis). All analytes were detected at 10(6) targets. The limits of detection were found at 10(5) to 10(4). Discrimination against competitor RNA was tested using up to 10(9) molecules (1000 X excess) of appropriate test strains. Samples containing either zero targets or 10(7) competitors produced negative results in 95 to 100% of the samples, depending on the assay. Closely related Legionella and Mycoplasma species cross-reacted at high challenge levels of 10(9) molecules as a result of sequence similarities in the target regions. These results demonstrate the utility and versatility of an automated, high sensitivity, closed system for amplified analysis of direct-from-sample testing of respiratory pathogens.

Bacteria↗
PubMed1996

Diversity of host species and strains of Pneumocystis carinii is based on rRNA sequences.

We have amplified by PCR Pneumocystis carinii cytoplasmic small-subunit rRNA (variously referred to as 16S-like or 18S-like rRNA) genes from DNA extracted from bronchoalveolar lavage and induced sputum specimens from patients positive for P. carinii and from infected ferret lung tissue. The amplification products were cloned into pUC18, and individual clones were sequenced. Comparison of the determined sequences with each other and with published rat and partial human P.carinii small-subunit rRNA gene sequences reveals that, although all P. carinii small-subunit rRNAs are closely related (approximately 96% identity), small-subunit rRNA genes isolated from different host species (human, rat, and ferret) exhibit distinctive patterns of sequence variation. Two types of sequences were isolated from the infected ferret lung tissue, one as a predominant species and the other as a minor species. There was 96% identity between the two types. In situ hybridization of the infected ferret lung tissue with oligonucleotide probes specific for each type revealed that there were two distinct strains of P. carinii present in the ferret lung tissue. Unlike the ferret P. carinii isolates, the small-subunit rRNA gene sequences from different human P. carinii isolates have greater than 99% identity and are distinct from all rat and ferret sequences so far inspected or reported in the literature. Southern blot hybridization analysis of PCR amplification products from several additional bronchoalveolar lavage or induced sputum specimens from P. carinii-infected patients, using a 32P-labeled oligonucleotide probe specific for human P. carinii, also suggests that all of the human P. carinii isolates are identical. These findings indicate that human P. carinii isolates may represent a distinct species of P. carinii distinguishable from rat and ferret P. carinii on the basis of characterization of small-subunit rRNA gene sequences.

Animals↗
PubMed1995

Detection of Mycobacterium tuberculosis directly from spiked human sputum by Q-beta replicase-amplified assay.

We report on a rapid, sensitive, Q-Beta replicase-amplified nucleic acid hybridization assay for the detection of Mycobacterium tuberculosis directly from spiked human sputum. Specimens were processed by either an N-acetyl-L-cysteine-NaOH or a 2% NaOH digestion-decontamination method and then washed to neutralize the pH of the cell pellet. The washed sputum pellets were heated at 100 degrees C to inactivate the M. tuberculosis organisms. The heat-inactivated samples were mechanically lysed at 5,000 rpm for 6 min in the GENE-TRAK Sample Processing Instrument in the presence of zirconium oxide beads and a buffer containing guanidine thiocyanate. The released nucleic acid was subjected to the GENE-TRAK Q-Beta replicase-amplified, dual-capture assay. The assay sensitivity was 10(3) purified rRNA targets or 1 CFU of M. tuberculosis spiked into M. tuberculosis-negative human sputum. There was a low level of noise because of the limitations of performing a signal amplification assay in an open system. High levels of other mycobacterial rRNA (approximately 10(7) organisms), including rRNAs of Mycobacterium avium and Mycobacterium gordonae, did not interfere with the sensitivity of the assay.

Bacteriological Techniques↗
PubMed1995

Q-beta replicase-amplified assay for detection of Mycobacterium tuberculosis directly from clinical specimens.

We report the results of a study conducted to evaluate the performance of manual Q-Beta replicase-amplified Mycobacterium tuberculosis complex assay compared with that of culture for detecting M. tuberculosis directly from digested sputum pellets. A total of 261 specimens submitted to three tuberculosis testing laboratories were analyzed. Culture and acid-fast bacillus smear results were provided by the tuberculosis testing laboratories. Of these 261 specimens, 34 (13% prevalence rate) were positive for M. tuberculosis by culture. The samples were digested and decontaminated by the testing laboratories by using their standard digestion and decontamination procedures. An aliquot of the digested and decontaminated pellet was sent to GENE-TRAK. The digested and decontaminated pellet was neutralized by washing it with 0.067 M phosphate buffer (pH 6.8), and the bacteria present in the washed pellet were heat inactivated at 100 degrees C for 15 min. The samples were combined with sample processing buffer containing GuSCN and were treated for 6 min in the GENE-TRAK Sample Processing Instrument to release the nucleic acids. The release rRNA was analyzed in a manual Q-Beta replicase assay format which incorporates elements of sandwich hybridization, reversible target capture, and Q-beta replicase signal amplification technologies. In comparison with culture, the overall assay sensitivity and specificity were 97.1 and 96.5%, respectively. The positive predictive value was 80.5%, and the negative predictive value was 99.5%. After analysis of discrepant results, the assay sensitivity and specificity were 97.3 and 97.8, respectively, and the prevalence rate was 14%. The positive predictive value and the negative predictive value were 87.8 and 99.5%, respectively. The Q-Beta replicase assay is rapid sensitive, semiquantitative, and specific for the direct detection of M. tuberculosis from clinical specimens.

Bacteriological Techniques↗
PubMed1994

Novel, ultrasensitive, Q-beta replicase-amplified hybridization assay for detection of Chlamydia trachomatis.

A sensitive, nonisotopic hybridization assay termed "dual capture" is described. The assay rapidly and specifically detects very low levels of target nucleic acids and organisms. The assay is based on the principles of sandwich hybridization, reversible target capture, and Q-Beta replicase amplification. The assay can be completed in less than 4 h, and in the described model format, it detects Chlamydia trachomatis rRNA or rDNA. Up to 96 samples can be analyzed simultaneously. The assay employs two types of probes: a test-specific capture probe, which mediates the cycling of the target probe complex on and off derivatized magnetic beads, and a replicatable RNA detector molecule containing a sequence complementary to and adjacent to the capture probe site on the target. Following reversible target capture, detection of the signal is accomplished by replication of the detector molecule by Q-Beta replicase in the presence of propidium iodide. A specific assay signal can be detected from as few as 1,000 molecules above the background. In a limited study of 94 urogenital samples the assay detected five of the six culture-positive samples and did not detect the C. trachomatis target in 85 of the 88 culture-negative samples.

Base Sequence↗
PubMed1992

The role of magnesium on the structure of biological apatites.

X-ray diffraction, infrared absorption spectroscopy, and chemical investigation have been carried out on deproteinated samples of turkey leg tendon at different degrees of calcification. The inorganic phase consists of poorly crystalline B carbonated apatite. On increasing calcification, the apatite crystal size, as well as its thermal stability, increase while the relative magnesium content is reduced. On the other hand, synchrotron X-ray diffraction data clearly indicate that apatite lattice parameters do not change as the crystals get larger. At the last stage of calcification the crystal size, chemical composition, and thermal conversion of the apatite crystallites approximate those of bone samples, which have been examined for comparison. The results provide a quantitative relationship between relative magnesium content and extent of apatite conversion into B-tricalcium phosphate by heat treatment. Furthermore, they suggest that the smaller crystallites laid down inside the gap region of the collagen fibrils are richer in magnesium than the longer ones that fill the space between collagen fibrils.

Animals↗
PubMed1992

Cheilitis glandularis.

Cheilitis glandularis is reported in two farmers with characteristic clinical and histopathological features. Both patients were treated with vermilionectomy. The prognosis was good.

Adult↗
PubMed1991

High-pressure scanning electron microscopy of insulating materials: a new approach.

A new SEM technique for imaging uncoated non-conducting specimens at high beam voltages is described which employs a high-pressure environment and an electric field to achieve charge neutralization. During imaging, the specimen surface is kept at a stable low voltage, near earth potential, by directing a flow of positive gas ions at the specimen surface under the action of an electric bias field at a pressure of about 200 Pa. In this way charge neutrality is continuously maintained to obtain micrographs free of charging artefacts. Images are formed by specimen current detection containing both secondary electron and backscattered electron signal information. Micrographs of geological, ceramic, and semiconductor materials obtained with this method are presented. The technique is also useful for the SEM examination of histological sections of biological specimens without any further preparation. A simple theory for the charge neutralization process is described. It is based on the interaction of the primary and emissive signal components with the surrounding gas medium and the resulting neutralizing currents. Further micrographs are presented to illustrate the pressure dependence of the charge neutralization process in two glass specimens which show clearly identifiable charging artefacts in conventional microscopy.

Aluminum Oxide↗
PubMed1987

EXAFS study of structural disorder in carbonate-containing hydroxyapatites.

A structural characterization of pure hydroxyapatite and partially carbonated hydroxyapatites has been performed using EXAFS spectroscopy, X-ray diffraction, and infrared spectroscopy. Our findings show that marked structural changes within the hydroxyapatite unit cell accompany the substitution of the phosphate anion. Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy has shown that the incorporation of carbonate into the phosphate site alters the structural geometry beyond the nearest neighbor oxygen coordination to calcium in a manner consistent with an increase in structural disorder. The nearest neighbor coordination to calcium is not detectably affected by the presence of carbonate.

Durapatite↗
PubMed1987

The 5' flanking sequence of a Trypanosoma brucei variable surface glycoprotein gene.

The mechanism controlling transcription at several telomeric expression sites for variable surface glycoprotein (VSG) genes in Trypanosoma brucei is unknown. Most VSG genes in expression sites have a region 5' of the gene lacking restriction enzyme sites. This 'barren region' is involved in recombination events which replace the VSG gene with a copy of a different, non-telomeric, VSG gene leading to a switch in VSG expression. Alterations in the barren region have been considered as possible modulators of expression of the adjacent VSG gene in other switching events where no gene replacement occurs. The expressed copy of the ILTat 1.3 VSG gene remains in its expression site, on a 160 kilobase (kb) chromosome, in trypanosomes not expressing the ILTat 1.3 VSG. Here we report the complete sequence of the barren region adjacent to this gene, determined both from trypanosomes expressing the gene and from those that are not. The sequence is identical whether or not the ILTat 1.3 VSG gene is expressed. This confirms that alterations in the barren region are not involved in modulation of expression of the gene, as suggested by restriction enzyme mapping. Sequence data from the 5' flanking region of a second telomeric gene copy on an 80 kb minichromosome, and from the ILTat 1.3 expression site after replacement of the ILTat 1.3 gene by another gene from a minichromosome, provide evidence that telomeric VSG genes on minichromosomes are also flanked by long repeat arrays, and that these arrays are involved in inter-telomeric gene replacements as well as replacements by non-telomeric genes.

Animals↗
PubMed1987

Characterization of an Onchocerca-specific DNA clone from Onchocerca volvulus.

A genomic library of a savanna isolate of Onchocerca volvulus was screened to detect recombinant plasmids containing highly repeated DNA sequences of this parasite. Four recombinant plasmids were identified which hybridized specifically to Onchocerca DNA, but not to DNA from humans, black flies, Brugia malayi, B. pahangi, or Wuchereria bancrofti. The recombinant plasmids had a low level of homology to Dirofilaria immitis. All recombinant plasmids contain related DNA sequences based on Southern hybridization analysis. Sequences related to these recombinant plasmids are present in different geographic isolates of O. volvulus and O. ochengi, an animal parasite. Two of the recombinant plasmids contain sequences also found in O. lienalis. One recombinant plasmid, puOvs3, has been characterized in detail, including DNA sequence determination. Radiolabeled puOvs3 is able to detect 100 pg of genomic DNA isolated from O. volvulus worms from both savanna and forest regions. It can differentiate O. volvulus from O. ochengi by Southern blot analysis.

Animals↗
PubMed1986

Characterization of a ribosomal DNA clone of Brugia malayi.

The structure of ribosomal DNA (rDNA) clone pBmr7 from microfilariae of the human parasite Brugia malayi has been examined in detail by Southern blot analysis and S-1 mapping techniques. The results demonstrate that this clone contains regions homologous to 28S, 18S and 5.8S rDNAs. A noncoding or 'spacer' region lies between the 3' end of 28S rDNA and the 5' end of 18S rDNA. An AccI-Sau3AI fragment of approximately 900 bp from this spacer region cross-hybridizes to genomic DNA fragments of different sizes from Brugia pahangi and Dirofilaria immitis. The differences observed in hybridization suggest that this rDNA fragment can be used to differentiate between various filariid species.

Animals↗
PubMed1985

The development of tissue around various prosthetic implants used as replacements for ligaments and tendons.

Currently, no ideal prosthesis is available for the repair or replacement of tendons and ligaments. Although filamentous carbon is a useful fibrogenic material, it does not fulfill the ideal requirements of a soft-tissue prosthesis. A number of other synthetic fibers were examined for biocompatibility and fibrogenic properties in both cell culture and in vivo implantation. It was found that the less extensible materials could adversely affect the normal morphology of the induced collagen. None of the materials examined exhibited mechanical properties similar to those of collagen; therefore, a composite prosthesis was designed to incorporate three criteria: mechanical characteristics similar to those of the normal tissue, fibrogenic capability to induce replacement collagen, and replacement collagen developing with normal morphologic characteristics. A prototype prosthesis for the Achilles tendon in rabbits, evaluated by mechanical and histologic methods, shows that these criteria can be fulfilled and thus form the basis for future prosthetic tendon and ligament research.

Animals↗
PubMed1984

Morphology of human palmaris longus tendon.

A systematic morphological investigation of human palmaris longus tendons by polarisation microscopy and low angle x-ray diffraction is reported. It is shown that contrary to some previously reported observations, and in common with other tension bearing soft collagenous tissues, the fibres in this tendon are crimped. A new method of preparation of the tissue enabling one to see directly the crimped organisation in scanning electron microscopy was used to reinforce the findings by other methods.

Adult↗
PubMed1983

Relationship between multiple copies of a T. brucei variable surface glycoprotein gene whose expression is not controlled by duplication.

Unlike many other T. brucei variable surface glycoprotein (VSG) genes, the IITat 1.3 gene is not duplicated when it is expressed. Analysis of the multiple copies of this gene present in all IITaR 1 trypanosome clones by restriction enzyme mapping and sequencing shows that the expressed copy may have arisen by duplication and transposition to a telomeric site, as is observed for those VSG genes whose expression is linked to duplication. The existence of a mechanism selecting between a number of complete telomeric VSG gene copies for expression is implied by these results. Comparisons of the nontelomeric copies of the IITat 1.3 gene are consistent with involvement of gene duplication and mutational drift in the evolution of new VSG genes.

Animals↗