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Murugavel KG, Naranatt PP, Shankar EM, Mathews S, Raghuram K, Rajasambandam P, Jayanthi V, Surendran R, Murali A, Srinivas U, Palaniswamy KR, Srikumari D, Thyagarajan SP. Prevalence of aflatoxin B1 in liver biopsies of proven hepatocellular carcinoma in India determined by an in-house immunoperoxidase test. J Med Microbiol 2008; 56:1455-1459. [PMID: 17965344 DOI: 10.1099/jmm.0.47151-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related death in the world. The incidence of HCC in India is reportedly low and varies from 0.2 to 1.9 %. Aflatoxins, secondary metabolites produced by Aspergillus flavus and Aspergillus parasiticus, are potent human carcinogens implicated in HCC. The prevalence of aflatoxin B1 (AFB1) as co-carcinogen was analysed using an in-house immunoperoxidase test in 31 liver biopsies and 7 liver-resection specimens from histopathologically proven HCC, and in 15 liver biopsies from cirrhosis patients (control group). Serum was tested for hepatitis B and C serological markers using commercial assays, and for AFB1 using an in-house ELISA with a sensitivity of approximately 1 ng ml(-1) for AFB1. In spite of positive AFB1 immunostaining in HCC cases, all serum specimens, from both HCC and the control groups, were AFB1-negative. There were 18 (58.1 %) HCC cases that revealed AFB1 in liver biopsies; 68.8 % (n=11) of non-B non-C hepatitis cases with HCC and 46.1 % (n=6) of the hepatitis B surface-antigen-positive subjects were positive for AFB1. Out of the two hepatitis B/hepatitis C virus co-infected cases, one was positive for AFB1. Of seven tumour-resection samples, six were positive for AFB1. Only one case revealed AFB1 in the non-tumour area of the resected material. Thus AFB1 staining was significantly associated with tumour tissue (P=0.03). Aflatoxins proved to have a significant association with HCC in this peninsular part of the subcontinent. The impact seems to be a cumulative process, as revealed by the AFB1 deposits in HCC liver tissue, even though the serum levels were undetectable.
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Hafiji J, Majmudar V, Mathews S, Green A, Rytina E, Burrows N. A case of bromoderma and bromism. Br J Dermatol 2007; 158:427-9. [DOI: 10.1111/j.1365-2133.2007.08330.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kovacs MJ, Reece DE, Marcellus D, Meyer RM, Mathews S, Dong RP, Eisenhauer E. A phase II study of ZD6474 (Zactima, a selective inhibitor of VEGFR and EGFR tyrosine kinase in patients with relapsed multiple myeloma--NCIC CTG IND.145. Invest New Drugs 2007; 24:529-35. [PMID: 16791411 DOI: 10.1007/s10637-006-9022-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multiple myeloma is a disease in which angiogenesis is postulated to be a target for therapy. Based on this hypothesis, we conducted a phase II trial of ZD6474 (Zactima; a VEGFR inhibitor) 100 mg p.o. daily in patients with relapsed multiple myeloma. The primary efficacy endpoint was objective response as assessed by reduction in M protein. There were 18 patients with a mean age of 64 years. One patient was ineligible and one was not evaluable. Overall, ZD6474 was well tolerated and pharmacokinetic testing demonstrated that adequate drug levels were achieved. The most common drug-related adverse events were nausea, vomiting, fatigue, rash, pruritus, headache, diarrhea, dizziness, and sensory neuropathy, all of which were Grade I-II in severity. There were no drug-related serious adverse events. Laboratory adverse events were infrequent: one patient had Grade III anemia, and there were no Grade III changes in biochemistry. No significant QTc interval changes were seen. There were no responses in M protein levels. In conclusion, ZD6474 was well tolerated at a dose of 100 mg per day and achieved plasma levels predicted to inhibit VEGF signaling. However, this was not reflected in clinical benefit since none of the patients had a reduction in M protein.
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Saarela JM, Rai HS, Doyle JA, Endress PK, Mathews S, Marchant AD, Briggs BG, Graham SW. Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 2007; 446:312-5. [PMID: 17361182 DOI: 10.1038/nature05612] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Accepted: 01/18/2007] [Indexed: 11/09/2022]
Abstract
Although the relationship of angiosperms to other seed plants remains controversial, great progress has been made in identifying the earliest extant splits in flowering-plant phylogeny, with the discovery that the New Caledonian shrub Amborella trichopoda, the water lilies (Nymphaeales), and the woody Austrobaileyales constitute a basal grade of lines that diverged before the main radiation in the clade. By focusing attention on these ancient lines, this finding has re-written our understanding of angiosperm structural and reproductive biology, physiology, ecology and taxonomy. The discovery of a new basal lineage would lead to further re-evaluation of the initial angiosperm radiation, but would also be unexpected, as nearly all of the approximately 460 flowering-plant families have been surveyed in molecular studies. Here we show that Hydatellaceae, a small family of dwarf aquatics that were formerly interpreted as monocots, are instead a highly modified and previously unrecognized ancient lineage of angiosperms. Molecular phylogenetic analyses of multiple plastid genes and associated noncoding regions from the two genera of Hydatellaceae identify this overlooked family as the sister group of Nymphaeales. This surprising result is further corroborated by evidence from the nuclear gene phytochrome C (PHYC), and by numerous morphological characters. This indicates that water lilies are part of a larger lineage that evolved more extreme and diverse modifications for life in an aquatic habitat than previously recognized.
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Jackson WFM, Theologis TN, Gibbons CLMH, Mathews S, Kambouroglou G. Early management of pathological fractures in children. Injury 2007; 38:194-200. [PMID: 17054958 DOI: 10.1016/j.injury.2006.07.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 07/19/2006] [Accepted: 07/26/2006] [Indexed: 02/02/2023]
Abstract
The management of pathological fractures in children remains controversial. The indications for surgical treatment are unclear and the need for histological diagnosis before or after definitive treatment is not clearly defined. We reviewed retrospectively the records of all patients under the age of 16 years who presented over the past 7 years with a fracture as the first manifestation of bone pathology. There were 23 patients (16 boys and 7 girls) of an average age of 12 years and 2 months (range 4.1-15.8 years). There were nine cases of fracture through a simple bone cyst, five cases of fibrous dysplasia, two giant cell tumours, three aneurysmal bone cysts, one chondroblastoma, and three cases of Ewings sarcoma. After review of our cases we propose a simple algorithm for the safe early management and assessment of paediatric pathological fractures. We recommend that primary fixation of pathological fractures should be avoided until histological diagnosis is obtained. Most lesions should eventually be biopsied. However, if radiographic appearances are reassuringly benign, biopsy can be delayed until conservative fracture management is completed. Definitive treatment of benign lesions with protective intra medullary nailing or curettage and grafting can follow frozen section under the same anaesthetic.
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Dore RK, Mathews S, Schechtman J, Surbeck W, Mandel D, Patel A, Zhou L, Peloso P. The immunogenicity, safety, and efficacy of etanercept liquid administered once weekly in patients with rheumatoid arthritis. Clin Exp Rheumatol 2007; 25:40-6. [PMID: 17417989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
OBJECTIVE To evaluate the immunogenicity, safety, and efficacy of 50 mg/mL liquid etanercept. METHODS In a multicenter, open-label study, adults with active rheumatoid arthritis (RA) received 50 mg/mL liquid etanercept subcutaneously once weekly for 24 weeks. Immunogenicity was assessed at baseline and weeks 24 and 28, safety at all study visits, and efficacy at baseline and weeks 12 and 24. RESULTS Of 222 treated patients, 88% completed the study; 81% were women; 84% were white; mean age was 53 years; mean RA duration was 10 years. Antibodies to etanercept, all non-neutralizing, were detected in 12 of 214 patients; 7 of the 12 were borderline positive (antibody titers <1:50). The presence of non-neutralizing anti-etanercept antibodies did not appear to affect clinical safety or efficacy. Few patients reported serious adverse events (6.3%), serious infections (2.3%), or withdrew because of adverse events (4.5%). Most adverse events were mild or moderate. The most common event, injection site reaction, occurred in 29.3% patients. At week 24, 63% of patients achieved an ACR20 response, 36% an ACR50 response, and 14% an ACR70 response. Similar responses were apparent by week 12. Week 24 mean improvement in the Health Assessment Questionnaire disability index scores was 0.6 points; improvement in the Short Form-36 Physical Component Score was 10.0 points. CONCLUSION The 50 mg/mL liquid etanercept formulation administered once weekly was well tolerated. The incidence of anti-etanercept antibodies, the nature and frequency of adverse events, and improvements in signs and symptoms of RA and patient physical function were similar to those in previous etanercept studies.
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Towsey M, Hogan JM, Mathews S, Timms P. The in silico prediction of promoters in bacterial genomes. GENOME INFORMATICS. INTERNATIONAL CONFERENCE ON GENOME INFORMATICS 2007; 19:178-189. [PMID: 18546515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In silico approaches to the identification of bacterial promoters are hampered by poor conservation of their characteristic binding sites. This suggests that the usual position weight matrix models of bacterial promoters are incomplete. A number of methods have been used to overcome this inadequacy, one of which is to incorporate structural properties of DNA. In this paper we describe an extension of the promoter description to include SIDD (stress induced duplex destabilization), DNA curvature and stacking energy. Although we report the best result to date for a realistic promoter prediction task, surprisingly, DNA structural properties did not contribute significantly to this result. We also demonstrate for the first time, that sigma-54 promoters have a stronger association with SIDD than do other promoter types.
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Mathews S. Phytochrome-mediated development in land plants: red light sensing evolves to meet the challenges of changing light environments. Mol Ecol 2006; 15:3483-503. [PMID: 17032252 DOI: 10.1111/j.1365-294x.2006.03051.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Phytochromes are photoreceptors that provide plants with circadian, seasonal, and positional information critical for the control of germination, seedling development, shade avoidance, reproduction, dormancy, and sleep movements. Phytochromes are unique among photoreceptors in their capacity to interconvert between a red-absorbing form (absorption maximum of approximately 660 nm) and a far-red absorbing form (absorption maximum of approximately 730 nm), which occur in a dynamic equilibrium within plant cells, corresponding to the proportions of red and far-red energy in ambient light. Because pigments in stems and leaves absorb wavelengths below about 700 nm, this provides plants with an elegant system for detecting their position relative to other plants, with which the plants compete for light. Certain aspects of phytochrome-mediated development outside of flowering plants are strikingly similar to those that have been characterized in Arabidopsis thaliana and other angiosperms. However, early diverging land plants have fewer distinct phytochrome gene lineages, suggesting that both diversification and subfunctionalization have been important in the evolution of the phytochrome gene family. There is evidence that subfunctionalization proceeded by the partitioning among paralogues of photosensory specificity, physiological response modes, and light-regulated gene expression and protein stability. Parallel events of duplication and functional divergence may have coincided with the evolution of canopy shade and the increasing complexity of the light environment. Within angiosperms, patterns of functional divergence are clade-specific and the roles of phytochromes in A. thaliana change across environments, attesting to the evolutionary flexibility and contemporaneous plasticity of phytochrome signalling in the control of development.
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Bennett JR, Mathews S. Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A. AMERICAN JOURNAL OF BOTANY 2006; 93:1039-51. [PMID: 21642169 DOI: 10.3732/ajb.93.7.1039] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Partial sequences of the nuclear gene encoding the photoreceptor phytochrome A (PHYA) are used to reconstruct relationships within Orobanchaceae, the largest of the parasitic angiosperm families. The monophyly of Orobanchaceae, including nonphotosynthetic holoparasites, hemiparasites, and nonparasitic Lindenbergia is strongly supported. Phytochrome A data resolve six well-supported lineages that contain all of the sampled genera except Brandisia, which is sister to the major radiation of hemiparasites. In contrast to previous plastid and ITS trees, relationships among these major clades also are generally well supported. Thus, the robust phylogenetic hypothesis inferred from the PHYA data provides a much better context in which to evaluate the evolution of parasitism within the group. Ninety-eight species of Orobanchaceae, representing 43 genera, are included and Brandisia, Bungea, Cymbaria, Esterhazya, Nesogenes, Phtheirospermum, Radamaea, Siphonostegia, and Xylocalyx are confirmed as members of Orobanchaceae. The earliest diverging lineage of hemiparasites is identified for the first time; it contains Bungea, Cymbaria, Monochasma, Siphonostegia, and the monotypic Schwalbea, which is federally endangered. This basal clade is marked by the presence of two novel introns. A second, apparently independent gain of one of these introns marks a clade of largely European taxa. There is significant rate heterogeneity among PHYA sequences, and the presence of multiple PHYA in some taxa is consistent with observed ploidy levels.
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Mathew PV, Mathews S, Bhat KG. Solar disinfection of drinking water. THE JOURNAL OF COMMUNICABLE DISEASES 2005; 37:321-4. [PMID: 17278665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
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Theuri J, Phelps-Durr T, Mathews S, Birchler J. A comparative study of retrotransposons in the centromeric regions of A and B chromosomes of maize. Cytogenet Genome Res 2005; 110:203-8. [PMID: 16093673 DOI: 10.1159/000084953] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Accepted: 02/14/2004] [Indexed: 11/19/2022] Open
Abstract
Bacterial Artificial Chromosomes (BACs) derived from the B chromosome, based on homology with the B specific sequence, were subcloned and sequenced. Analysis of DNA sequence data indicated the presence of 23 common retroelements, as well as novel sequences of B chromosome origin. Generally, where the same retrotransposon type was observed in both A and B chromosomes, there were more copies per unit of sequence in the B centromeric region (the major site of B repeat) than in the A centromere, except for Huck-1. Based on previous estimates of the age of the major burst of transposition into the maize genome, the oldest retrotransposons (Ji-6 and Tekay, approximately 5.0 and 5.2 million years ago, respectively) were found in the B centromere region only, while the next two oldest (Huck-1 and Opie-1) were found in both the A and B sequences. Phylogenetic analysis of Opie retroelements from both A and B centromeres indicated that some of the B Opie centromeric sequences share a more recent common ancestor with A Opie retroelements than they do with other B Opie centromeric sequences. These results imply that the supernumerary maize B chromosome has coexisted with the A chromosomes during that period of transposition. They also support the hypothesis that the B chromosome had its origins from A chromosome elements, or that alternative origins, such as being donated to the maize genome in a wide species cross, preceded six million years ago, because the spectrum of retrotransposons in the two chromosomes is quite similar.
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Abstract
Photoreceptors are critical molecules that function at the interface between organism and environment. Plants use specific light signals to determine their place in time and space, allowing them to synchronize their growth, metabolism, and development to the environments in which they occur. Thus, innovation in light sensing mechanisms is expected to coincide with adaptation and diversification. Three studies involving the well-characterized phytochrome photoreceptor system in plants indicate that much work is yet needed to test this expectation. In early diverging flowering plants, episodic positive selection influenced the evolution of phytochrome A, but little of the functional data needed to link molecular adaptation with a change in gene function are available. In the model plant Arabidopsis thaliana, known functional differences between a recently duplicated gene pair remain difficult to characterize at the sequence level. In parasitic plants, patterns of development that in autotrophs are under the control of light signals are highly modified, suggesting that phytochromes and other photoreceptors function differently in nonphotosynthetic plants. Analyses of phytochrome A coding sequences indicate that they are evolving under relaxed constraints in nonphotosynthetic Orobanchaceae, consistent with the expectation of functional change. Further work is needed to determine which of the processes mediated by phyA may have been altered, a line of investigation that may improve our understanding of divergence points in downstream signaling pathways.
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Mathews S. Analytical Methods for Studying the Evolution of Paralogs Using Duplicate Gene Datasets. Methods Enzymol 2005; 395:724-45. [PMID: 15865992 DOI: 10.1016/s0076-6879(05)95037-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Gene duplication is widely viewed as an important source of raw material for functional innovation in proteins because at least some duplicate copies will evolve new or slightly modified functions. The study of the molecular processes by which functional innovation occurs interests both evolutionary biologists and protein chemists, and the development of methods to investigate these processes has led to a productive meeting of disciplines and an availability of complementary approaches for exploring datasets. This has resulted in insights into past events, prediction of current function, and prediction of future change. The methods fall broadly into two categories: those that rely on detection of shifts in selective constraints and those that rely on detection of correlations between molecular changes and functional shifts. Strengths and limitations of the methods are evaluated here in the context of the question being addressed, the input required, and the specific metric that is evaluated in each test.
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Goss G, Hirte H, Miller WH, Lorimer IAJ, Stewart D, Batist G, Parolin DAE, Hanna P, Stafford S, Friedmann J, Walsh W, Mathews S, Douglas L, Seymour LK. A phase I study of oral ZD 1839 given daily in patients with solid tumors: IND.122, a study of the Investigational New Drug Program of the National Cancer Institute of Canada Clinical Trials Group. Invest New Drugs 2005; 23:147-55. [PMID: 15744591 DOI: 10.1007/s10637-005-5860-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
PURPOSE To define the maximum tolerated dose (MTD), the dose limiting toxicity (DLT), the biological active (BA) dose and the pharmacokinetics (PK) of the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor ZD1839 (Iressa) when administered continuously as a once daily dose in patients with advanced, incurable solid tumours. PATIENTS AND METHODS Twenty-eight patients were enrolled in cohorts of three from three National Cancer Institute of Canada Clinical Trials Group (NCIC CTG) centers. ZD1839 was given at doses from 150 to 800 mg daily orally and patients underwent a pretreatment and a 28 day post treatment tumor biopsy, while PK sampling was performed on days 8, 15, 22, 29, and a toxicity assessment every 28 days. RESULTS All twenty-eight patients were evaluable for non-hematological and hematological toxicity. Twenty-seven were evaluable for response. The MTD was not reached but DLT included reversible rash and diarrhea. One patient with urachal cancer had a transient 55% decrease in tumor size and two other patients (breast and non-small cell lung cancer) had minor responses; three additional patients had pharmacodynamic evidence of target effect. PK demonstrated steady state within the first 2 weeks of dosing and dose dependent exposure. CONCLUSION It appears that ZD 1839 at a dose of 800 m/day was tolerable, although some patients required dose modification for diarrhea. Doses above 250 m/day demonstrate biologic activity and could be consider for future study in a variety of EGFR positive tumor types.
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Burleigh JG, Mathews S. Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. AMERICAN JOURNAL OF BOTANY 2004; 91:1599-613. [PMID: 21652311 DOI: 10.3732/ajb.91.10.1599] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Effects of taxonomic sampling and conflicting signal on the inference of seed plant trees supported in previous molecular analyses were explored using 13 single-locus data sets. Changing the number of taxa in single-locus analyses had limited effects on log likelihood differences between the gnepine (Gnetales plus Pinaceae) and gnetifer (Gnetales plus conifers) trees. Distinguishing among these trees also was little affected by the use of different substitution parameters. The 13-locus combined data set was partitioned into nine classes based on substitution rates. Sites evolving at intermediate rates had the best likelihood and parsimony scores on gnepine trees, and those evolving at the fastest rates had the best parsimony scores on Gnetales-sister trees (Gnetales plus other seed plants). When the fastest evolving sites were excluded from parsimony analyses, well-supported gnepine trees were inferred from the combined data and from each genomic partition. When all sites were included, Gnetales-sister trees were inferred from the combined data, whereas a different tree was inferred from each genomic partition. Maximum likelihood trees from the combined data and from each genomic partition were well-supported gnepine trees. A preliminary stratigraphic test highlights the poor fit of Gnetales-sister trees to the fossil data.
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Sunny L, Yeole BB, Kurkure AP, Hakama M, Shiri R, Mathews S, Shastri NG, Advani SH. Cumulative risk and trends in prostate cancer incidence in Mumbai, India. Asian Pac J Cancer Prev 2004; 5:401-5. [PMID: 15546245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Information relating to cancer incidence trends in a community forms the scientific basis for the planning and organization of prevention, diagnosis and treatment of cancer. We here estimated the cumulative risk and trends in incidence of prostate cancer in Mumbai, India, using data collected by the Bombay Population-based Cancer Registry from the year 1986 to 2000. METHODS During the 15 year period, a total of 2864 prostate cancer cases (4.7% of all male cancers and 2.4% of all cancers) were registered by the Bombay Population-based Cancer Registry. For evaluation of the trend, we applied a linear regression model based on the logarithm of the observed incidence rates. The annual percentage changes were also computed for the evaluation. Cumulative incidence rates percentages were calculated by adding up the age specific incidence rates at single ages and then expressed as a percentage. RESULTS Analysis of the trends in age-adjusted incidence rates of prostate cancer during the period 1986 to 2000 showed no statistically significant increase or decrease and the rates proved stable across the various age groups (00-49, 50-69 and 70+) also. The probability estimates indicated that one out of every 59 men will contract a prostate cancer at some time in his whole life and 99% of the chance is after he reaches the age of 50. CONCLUSION The stability in age adjusted-incidence rates indicates that there are no changes in the etiological factors for prostate cancer in Mumbai, India. These findings may be of general interest because changes in diagnostic practices are confounded in the time trends of prostate cancer change in many western countries preventing inferences on the changes in risk.
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Wilson DP, Mathews S, Wan C, Pettitt AN, McElwain DLS. Use of a quantitative gene expression assay based on micro-array techniques and a mathematical model for the investigation of chlamydial generation time. Bull Math Biol 2004; 66:523-37. [PMID: 15006447 DOI: 10.1016/j.bulm.2003.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2003] [Accepted: 09/02/2003] [Indexed: 11/20/2022]
Abstract
Chlamydia is an important pathogen which possesses a unique developmental cycle. We used real-time PCR technology to measure gene transcript levels in Chlamydia trachomatis strain L2. By measuring 16S rRNA transcript levels, and developing a mathematical model of the chlamydial developmental cycle fitting the data, we predict an average generation time of approximately 2.6 h. Additionally, potentially this modelling also provides the foundation for the application of emerging micro-array technology in which identification of the gene signals that trigger a chlamydial body to start replicating or transform to its infectious form can be made possible.
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Sunny L, Yeole BB, Hakama M, Shiri R, Sastry PSRK, Mathews S, Advani SH. Oral cancers in Mumbai, India: a fifteen years perspective with respect to incidence trend and cumulative risk. Asian Pac J Cancer Prev 2004; 5:294-300. [PMID: 15373710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
OBJECTIVE We estimated the time trends in the incidence and the risk of developing an oral cancer in Mumbai, Indian population using the data collected by the Bombay Population Based Cancer Registry during the 15 year period from 1986 to 2000. METHODS A total of 9,670 oral cancers (8.2% of all neoplasms) were registered, of which 6577 were in males and 3093 in females (10.7% and 5.4% of the respective totals for the two genders). For evaluation of the trend, we applied a linear regression model based on the logarithm of the observed incidence rates. The annual percentage changes were also computed for the incidence rates to evaluate the time trend. RESULTS In males, a statistically significant decreasing trend in the overall age-adjusted incidence rates were observed during the period 1986 to 2000, with an yearly decrease of 1.70%. This decrease was significant for men above the age of 40, but for young adult men below the age of 40, there was no significant decrease, the level being stable. In females, the overall decreasing trend in the age-adjusted incidence rates of oral cancers was not significant, but in the age group 40-59, a significant decline was observed. The probability estimates indicated that one out of every 57 men and one out of every 95 women will contract any oral cancer at some time in their whole life and 97% of the chance is after he or she completes the age of 40. CONCLUSION The observed decreasing trend in oral cancers in Indian men may be attributed to a decrease in the usage of pan and tobacco. The high prevalence of the usage of smokeless tobacco among young adult men and women may explain the stable trend in oral cancer incidence in this group. These findings help to strengthen the association between tobacco use and oral cancer risk.
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Provan J, Biss PM, McMeel D, Mathews S. Universal primers for the amplification of chloroplast microsatellites in grasses (Poaceae). ACTA ACUST UNITED AC 2004. [DOI: 10.1111/j.1471-8286.2004.00636.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sunny L, Yeole BB, Hakama M, Shiri R, Mathews S, Falah Hassani K, Advani SH. Decreasing trend in the incidence of stomach cancer in Mumbai, India, during 1988 to 1999. Asian Pac J Cancer Prev 2004; 5:169-74. [PMID: 15244520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
The time trend in incidence of stomach cancer in males and females in Mumbai, India during 1988 to 1999 was estimated using data collected by the Bombay Population-based Cancer Registry. During the 12-year period, a total of 3657 stomach cancer cases (3.9% of all cancers) were registered by the Bombay Population-based Cancer Registry of which 2467 (5.1% of all male cancers) were in males and 1184 (2.6% of all female cancers) in females. For evaluation of the trend, we applied a linear regression model based on the logarithm of the observed incidence rates. The annual percentage changes were also computed for the incidence rates for evaluating the time trend. A statistically significant decreasing trend in the overall age-adjusted incidence rates of stomach cancer was observed during the period 1988 to 1999, with an yearly decrease of 4.44% in males and 2.56% in females. This decrease was most striking in males in the age groups 40-59 and 60+, and in females only in the age group 40-59. The probability estimates indicated that one out of every 92 men and one out of every 187 women will contract a stomach cancer at some time in their whole life and 95% of the chance is after his or her 40th birthday. The decreasing trend in the age-adjusted incidence rates of stomach cancer in both the sexes indicates that there is a critical change in the etiology of this cancer. The findings may provide clues relating to various life-style and environmental changes impacting on stomach cancer incidence.
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Mathews S, Burleigh JG, Donoghue MJ. Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms. Mol Biol Evol 2003; 20:1087-97. [PMID: 12777523 DOI: 10.1093/molbev/msg123] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Flowering plant diversity now far exceeds the combined diversity of all other plant groups. Recently identified extant remnants of the earliest-diverging lines suggest that the first angiosperms may have lived in shady, disturbed, and moist understory habitats, and that the aquatic habit also arose early. This would have required the capacity to begin life in dimly lit environments. If so, evolution in light-sensing mechanisms may have been crucial to their success. The photoreceptor phytochrome A is unique among angiosperm phytochromes in its capacity to serve a transient role under conditions where an extremely high sensitivity is required. We present evidence of altered functional constraints between phytochrome A (PHYA) and its paralog, PHYC. Tests for selection suggest that an elevation in nonsynonymous rates resulted from an episode of selection along the branch leading to all angiosperm PHYA sequences. Most nucleotide sites (95%) are selectively constrained, and the ratio of nonsynonymous to synonymous substitutions on branches within the PHYA clade does not differ from the ratio on the branches in the PHYC clade. Thus, positive selection at a handful of sites, rather than relaxation of selective constraints, apparently has played a major role in the evolution of the photosensory domain of phytochrome A. The episode of selection occurred very early in the history of flowering plants, suggesting that innovation in phyA may have given the first angiosperms some adaptive advantage.
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Davis CC, Bell CD, Fritsch PW, Mathews S. Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): implications for tertiary tropical floras and Afroasian biogeography. Evolution 2002; 56:2395-405. [PMID: 12583580 DOI: 10.1111/j.0014-3820.2002.tb00165.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major tenet of African Tertiary biogeography posits that lowland rainforest dominated much of Africa in the late Cretaceous and was replaced by xeric vegetation as a response to continental uplift and consequent widespread aridification beginning in the late Paleogene. The aridification of Africa is thought to have been a major factor in the extinction of many African humid-tropical lineages, and in the present-day disparity of species diversity between Africa and other tropical regions. This primarily geologically based model can be tested with independent phylogenetic evidence from widespread African plant groups containing both humid- and xeric-adapted species. We estimated the phylogeny and lineage divergence times within one such angiosperm group, the acridocarpoid clade (Malpighiaceae), with combined ITS, ndhF, and trnL-F data from 15 species that encompass the range of morphological and geographic variation within the group. Dispersal-vicariance analysis and divergence-time estimates suggest that the basal acridocarpoid divergence occurred between African and Southeast Asian lineages approximately 50 million years ago (mya), perhaps after a southward ancestral retreat from high-latitude tropical forests in response to intermittent Eocene cooling. Dispersion of Aeridocarpus from Africa to Madagascar is inferred between approximately 50 and 35 mya, when lowland humid tropical forest was nearly continuous between these landmasses. A single dispersal event within Acridocarpus is inferred from western Africa to eastern Africa between approximately 23 and 17 mya, coincident with the widespread replacement of humid forests by savannas in eastern Africa. Although the spread of xeric environments resulted in the extinction of many African plant groups, our data suggest that for others it provided an opportunity for further diversification.
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Mathews S. Author reply. Ophthalmology 2002. [DOI: 10.1016/s0161-6420(02)01205-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Davis CC, Bell CD, Mathews S, Donoghue MJ. Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae. Proc Natl Acad Sci U S A 2002; 99:6833-7. [PMID: 11983870 PMCID: PMC124489 DOI: 10.1073/pnas.102175899] [Citation(s) in RCA: 252] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2001] [Accepted: 03/25/2002] [Indexed: 11/18/2022] Open
Abstract
Explanations for biogeographic disjunctions involving South America and Africa typically invoke vicariance of western Gondwanan biotas or long distance dispersal. These hypotheses are problematical because many groups originated and diversified well after the last known connection between Africa and South America (approximately 105 million years ago), and it is unlikely that "sweepstakes" dispersal accounts for many of these disjunctions. Phylogenetic analyses of the angiosperm clade Malpighiaceae, combined with fossil evidence and molecular divergence-time estimates, suggest an alternative hypothesis to account for such distributions. We propose that Malpighiaceae originated in northern South America, and that members of several clades repeatedly migrated into North America and subsequently moved via North Atlantic land connections into the Old World during episodes starting in the Eocene, when climates supported tropical forests. This Laurasian migration route may explain many other extant lineages that exhibit western Gondwanan distributions.
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