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P Agarwal

Publications and source records attributed to P Agarwal.

At least 37 records · Page 2Linked to original sources
PubMed2001

Identification and initial characterization of 5000 expressed sequenced tags (ESTs) each from adult human normal and osteoarthritic cartilage cDNA libraries.

OBJECTIVE: To prepare, sequence and analyse adult human cartilage cDNA libraries to study the gene expression pattern between normal and osteoarthritic cartilage. METHODS: Poly A(+)RNA from adult human normal and osteoarthritic articular cartilage was isolated and used to prepare cDNA libraries. Approximately 5000 ESTs from each library were sequenced and analysed using bioinformatic tools. The expression of select genes was confirmed by Northern blot and in situ hybridization analysis. RESULTS: Multiple gene families including several classical cartilage matrix protein encoding genes were identified. Approximately 28-40% of the genes sequenced from these libraries were novel, while half of the genes encoded known proteins and 4-6% of the genes encoded novel homologs of known proteins. Several known genes, whose expression has not been reported previously in cartilage, were also identified. We have confirmed the cartilage expression of three known (CTGF, CTGF-L and clusterin) and two novel homologs of known genes (PCPE-2 and Gal-Nac transferase) by Northern blot and in situ hybridization analysis. CONCLUSION: This is the first report of the preparation and sequencing of cDNA libraries from adult human normal and osteoarthritic articular cartilage. Further analysis of genes identified from these libraries may provide molecular targets for diagnosis and/or treatment of osteoarthritis (OA).

Adult↗
PubMed2000

Superconductivity on the border of itinerant-electron ferromagnetism in UGe2

The absence of simple examples of superconductivity adjoining itinerant-electron ferromagnetism in the phase diagram has for many years cast doubt on the validity of conventional models of magnetically mediated superconductivity. On closer examination, however, very few systems have been studied in the extreme conditions of purity, proximity to the ferromagnetic state and very low temperatures required to test the theory definitively. Here we report the observation of superconductivity on the border of ferromagnetism in a pure system, UGe2, which is known to be qualitatively similar to the classic d-electron ferromagnets. The superconductivity that we observe below 1 K, in a limited pressure range on the border of ferromagnetism, seems to arise from the same electrons that produce band magnetism. In this case, superconductivity is most naturally understood in terms of magnetic as opposed to lattice interactions, and by a spin-triplet rather than the spin-singlet pairing normally associated with nearly antiferromagnetic metals.

Journal Article↗
PubMed2000

Ureaplasma urealyticum and its association with chronic lung disease in Asian neonates.

OBJECTIVE: The aim of the present prospective cohort study was to evaluate the relationship between lower respiratory tract colonization with Ureaplasma urealyticum and development of chronic lung disease (CLD) in a high-risk neonatal population. METHODS: Prospective cohort study of preterm infants with a birthweight < 1,500 g needing mechanical ventilation within 24 h of birth in a tertiary care neonatal unit. Endotracheal aspirates from these infants were cultured within 24 h for U. urealyticum and the rate of colonization was determined. The primary outcome measure was the incidence of CLD at 28 days of life. RESULTS: Of the 41 infants studied, 10 (24%) infants were colonized with U. urealyticum. The colonization rate was higher in babies < 1,000 g compared with babies weighing 1,000-1,500 g (P = 0.04). There was no significant difference between the colonized and non-colonized groups with regard to the antenatal use of steroids, maternal prolonged rupture of membranes, gestational age, birthweight, sex, respiratory distress syndrome, use of surfactant, patent ductus arteriosus and gastrooesophageal reflux. Of the 37 survivors, 20 (54%) developed CLD; eight infants (88.5%) in the colonized group developed CLD compared with 12 infants (42.8%) in the non-colonized group (P = 0.01). CONCLUSIONS: Neonates colonized with U. urealyticum were twice as likely to have CLD than non-colonized babies (relative risk 2.01; 95% confidence interval 1.27-3.37). These data suggest a significant association between colonization with U. urealyticum and CLD in infants weighing < 1,500 g.

Chronic Disease↗
PubMed2000

Comparison study for identifying promoter allelic polymorphism in interleukin 10 and tumor necrosis factor alpha genes.

Cytokines such as tumor necrosis factor (TNF)-alpha and Interleukin (IL)-10 play significant roles in autoimmunity and transplantation tolerance. Allelic polymorphisms that occur in the regulatory regions of these cytokine genes are closely associated with acute and chronic transplant rejection. The presence of a G-to-A polymorphism at position -308 in the promoter region of the TNF-alpha gene can increase transcription six- to sevenfold. Likewise, the G-A polymorphism at position -1082 of the IL-10 promoter results in lower levels of IL-10 protein. Accordingly, a genotype that dictates the production of high levels of TNF-alpha with low IL-10 capabilities is most likely to generate an inflammatory environment that is less receptive to the transplant. The potential for determining a patient's haplotype before transplantation may be an effective way of monitoring the post-transplant status of such patients. A variety of methodologies that address the detection of mutations have been used both in research and clinical diagnostic tests. This study analyzes the genetic variations in cytokines using two methodologies: the traditional allele-specific oligonucleotide (ASO) polymerase chain reaction (PCR) and the newer and more flexible Invader technology. The sensitivity and specificity of the Invader assay for simultaneous investigation of multiple targets makes it a useful tool in such analyses.

Alleles↗
PubMed2000

An assessment of gene prediction accuracy in large DNA sequences.

One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of both methods and accuracy evaluation measures, most of the sequence sets in which the programs are tested are short genomic sequences, and there is concern that these accuracy measures may not extrapolate well to larger, more challenging data sets. Given the absence of experimentally verified large genomic data sets, we constructed a semiartificial test set comprising a number of short single-gene genomic sequences with randomly generated intergenic regions. This test set, which should still present an easier problem than real human genomic sequence, mimics the approximately 200kb long BACs being sequenced. In our experiments with these longer genomic sequences, the accuracy of GENSCAN, one of the most accurate ab initio gene prediction programs, dropped significantly, although its sensitivity remained high. Conversely, the accuracy of similarity-based programs, such as GENEWISE, PROCRUSTES, and BLASTX was not affected significantly by the presence of random intergenic sequence, but depended on the strength of the similarity to the protein homolog. As expected, the accuracy dropped if the models were built using more distant homologs, and we were able to quantitatively estimate this decline. However, the specificities of these techniques are still rather good even when the similarity is weak, which is a desirable characteristic for driving expensive follow-up experiments. Our experiments suggest that though gene prediction will improve with every new protein that is discovered and through improvements in the current set of tools, we still have a long way to go before we can decipher the precise exonic structure of every gene in the human genome using purely computational methodology.

Base Composition↗
PubMed2000

Menstrual disorders in genital tuberculosis.

Study included 120 cases of genital tuberculosis proved by histopathology. Analysis of their menstrual history showed that the common menstrual disorder was oligohypomenorrhoea found in 54.0% cases, menorrhagia in 19.0% cases, and postmenopausal bleeding in 1.6% cases. History of amenorrhoea was present in 14.3% cases. There were 8 cases of secondary amenorrhoea and one case was of primary amenorrhoea. The pelvic examination showed cervical involvement in 43.1% of cases. Tubo-ovarian mass was present in 19.8% cases. Genital tract tuberculosis is a disease of varied symptomatology. A high degree of suspicion and efficient investigation are important for diagnosis.

Adult↗
PubMed1999

Dominant genetic alterations in immortalization: role for 20q gain.

Gain of 20q has been observed in many cancer types, including bladder cancers. However, the biological significance of low-copy-number 20q gain in human cancer pathogenesis has not yet been defined. We reported that immortalization of human uroepithelial cells (HUC) transformed with human papillomavirus 16 (HPV 16) E7 is associated with single-copy 20q gain (P = 2 x 10(-7)). We also observed 20q13.2 amplification in some cell lines, but only after 20 passages. Thus, we hypothesized that low-copy gain of 20q gene(s) contributes in a dominant way to bypassing HUC senescence. To test this hypothesis, we fused precrisis E7-transformed HUCs (pcE7s) with three independent immortal E7-HUCs that acquired a single-copy 20q gain at immortalization. In one of these lines, a single-copy gain of 20q and a 10p12.1-pter loss were the only cytogenetic alterations. Immortal cell hybrids were obtained with all three crosses. Southern analysis for unique HPV16 insertion sites, as well as fluorescence in situ hybridization (FISH) with whole chromosome 20 painting probes (WCP20) for marker chromosomes in the immortal clones, confirmed the hybrid and independent nature of representative immortal clones. In contrast, when we used the same protocol, no immortal somatic cell hybrids were obtained when HPV16 E6 immortal HUC (E6-HUC) that showed 3p and 9p losses, but no 20q gain, were fused with precrisis E6-transformed HUC (pcE6s). This latter observation is consistent with many results demonstrating that recessive changes are required for cell immortalization. Therefore, the new results reported herein for the first time demonstrate that dominant changes can contribute to bypassing senescence, and that such genes may be located on 20q. Genes Chromosomes Cancer 26:304-311, 1999.

Cell Transformation, Neoplastic↗
PubMed1999

Perinatal drug abuse in KK Women's and Children's Hospital.

No local figures are available in Singapore on the incidence of perinatal drug abuse and its effect on the foetus and the neonate. The objectives of this study were to determine the incidence of perinatal drug abuse and neonatal abstinence syndrome; to identify a maternal profile at high risk for substance abuse and to document the presenting features and treatment of infants with neonatal abstinence syndrome. Out of 14,690 births during the period January 1994 to December 1996, 38 (0.25%) had evidence of perinatal drug abuse. The study revealed that a high-risk maternal profile for drug abuse comprised of single mothers (52%); history of smoking (52%); no antenatal care (37%) and belonging to the Malay ethnic group (82%); and younger maternal age. Self-reporting was uncommon, occurring only in 8% and in 40% of cases, there was no known history of maternal drug addiction. The drug abused in all cases was heroin. Human immunodeficiency virus (HIV) screening was done only in a minority (21%) of the mothers and it was negative in all. Eighteen (47%) infants had evidence of neonatal abstinence syndrome with neurological manifestations being the commonest. Urine toxicology screening was positive in 26% of cases and had only 70% sensitivity and 41% positive predictive value. On follow up, default rate was high with 42% babies not attending follow up at the outpatient clinic. In conclusion, there is a need to maintain a high index of suspicion of substance abuse in those with high-risk maternal profile and their neonates should be closely watched for features of neonatal abstinence syndrome. Alternative methods of toxicology screening apart from urine need to be evaluated in order to improve the drug detection rate.

Adolescent↗
PubMed1998

A clinical and videostroboscopic evaluation of laryngeal tuberculosis.

A series of 31 cases of tuberculous laryngitis is reviewed to assess the diagnostic features of the disease. The condition generally presents in males of late middle age who have pulmonary tuberculosis. It presents in a manner similar to laryngeal carcinoma except that painful dysphagia is a prominent symptom. Histological examination of biopsy material is usually the diagnostic procedure. Stroboscopy was able to document a number of abnormalities which included abnormalities of laryngeal configuration, vibratory asymmetry, reduction of amplitude and mucosal wave. Symptoms responded well to antituberculous chemotherapy.

Adult↗
PubMed1998

Low fat intake and coronary artery disease in a population with higher prevalence of coronary artery disease: the Indian paradox.

OBJECTIVE: To determine the association between saturated fat intake and prevalence of coronary artery disease (CAD) and coronary risk factors. DESIGN AND SETTING: Total community cross sectional survey of 20 urban streets out of 196 streets, in the city of Moradabad in north India. SUBJECTS AND METHODS: Adult population between 25 to 64 years inclusive comprised of 1806 subjects (904 men, 902 women) were divided into three groups according to level of saturated fat intake as assessed by 7-day dietary intake records (very low < 7%, low 7 to 10%, high > 10% energy (en) per day). RESULTS: We examined the relationship between CAD risk and levels of % en from fat intake. Low (7 to 10% en/day) and high (> 10% en/day) saturated fat were positively and significantly associated with higher prevalence of CAD. The prevalence of coronary risk factors (hypertension, hypercholesterolemia, obesity and sedentary lifestyle) were significantly higher among subjects with low and high saturated fat intake compared to subjects with very low (< 7%) saturated fat intake. Logistic regression analysis with adjustment for age showed that hypercholesterolemia (OR: men 0.89, women 0.68), hypertension (men 0.92, women 0.56), physical activity (men 0.80, women 0.36), obesity (men 0.82, women 0.88) and smoking (0.70 men) were significant risk factors of CAD. Low and high saturated fat intake were associated with more prestigious occupations, higher and middle income status and better educational levels compared to very low saturated fat intake. CONCLUSIONS: The prevalence of CAD and coronary risk factors was higher in urban Indians with low and high saturated fat intake than those with lower saturated fat intake. These findings suggest that the saturated fat intake should be < 7% en/day for prevention of CAD in Indians.

Adult↗
PubMed1998

Comparative accuracy of methods for protein sequence similarity search.

MOTIVATION: Searching a protein sequence database for homologs is a powerful tool for discovering the structure and function of a sequence. Two new methods for searching sequence databases have recently been described: Probabilistic Smith-Waterman (PSW), which is based on Hidden Markov models for a single sequence using a standard scoring matrix, and a new version of BLAST (WU-BLAST2), which uses Sum statistics for gapped alignments. RESULTS: This paper compares and contrasts the effectiveness of these methods with three older methods (Smith-Waterman: SSEARCH, FASTA and BLASTP). The analysis indicates that the new methods are useful, and often offer improved accuracy. These tools are compared using a curated (by Bill Pearson) version of the annotated portion of PIR 39. Three different statistical criteria are utilized: equivalence number, minimum errors and the receiver operating characteristic. For complete-length protein query sequences from large families, PSW's accuracy is superior to that of the other methods, but its accuracy is poor when used with partial-length query sequences. False negatives are twice as common as false positives irrespective of the search methods if a family-specific threshold score that minimizes the total number of errors (i.e. the most favorable threshold score possible) is used. Thus, sensitivity, not selectivity, is the major problem. Among the analyzed methods using default parameters, the best accuracy was obtained from SSEARCH and PSW for complete-length proteins, and the two BLAST programs, plus SSEARCH, for partial-length proteins.

Databases, Factual↗
PubMed1998

Exercise ECG testing using different protocols in asymptomatic healthy young subjects.

Thirty four healthy young male subjects performed symptom limited exercise on Bruce protocol on treadmill machine. Hyperventilation induced labile repolarisation ST-T abnormalities were observed in 2 whereas exercise induced ST changes (upsloping ST depression in 4 and horizontal ST depression in 1) were observed in 5 additional candidates. Changes were unaccompanied by symptoms or signs and quickly reverted back to normal within 30 sec. of cessation of exercise and hence were 'probable false positives'. Sixty-eight age and sex matched volunteers (including former 34) when exercised on Master's stepper, failed to reveal any change probably due to the lack of continuous ECG monitoring device.

Adult↗