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Abstract
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
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25 |
17696 |
2
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Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001; 68:978-89. [PMID: 11254454 PMCID: PMC1275651 DOI: 10.1086/319501] [Citation(s) in RCA: 5768] [Impact Index Per Article: 240.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2000] [Accepted: 02/09/2001] [Indexed: 11/04/2022] Open
Abstract
Current routine genotyping methods typically do not provide haplotype information, which is essential for many analyses of fine-scale molecular-genetics data. Haplotypes can be obtained, at considerable cost, experimentally or (partially) through genotyping of additional family members. Alternatively, a statistical method can be used to infer phase and to reconstruct haplotypes. We present a new statistical method, applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms; often, error rates are reduced by > 50%, relative to its nearest competitor. Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources.
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research-article |
24 |
5768 |
3
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Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. Association mapping in structured populations. Am J Hum Genet 2000; 67:170-81. [PMID: 10827107 PMCID: PMC1287075 DOI: 10.1086/302959] [Citation(s) in RCA: 1163] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2000] [Accepted: 05/04/2000] [Indexed: 11/03/2022] Open
Abstract
The use, in association studies, of the forthcoming dense genomewide collection of single-nucleotide polymorphisms (SNPs) has been heralded as a potential breakthrough in the study of the genetic basis of common complex disorders. A serious problem with association mapping is that population structure can lead to spurious associations between a candidate marker and a phenotype. One common solution has been to abandon case-control studies in favor of family-based tests of association, such as the transmission/disequilibrium test (TDT), but this comes at a considerable cost in the need to collect DNA from close relatives of affected individuals. In this article we describe a novel, statistically valid, method for case-control association studies in structured populations. Our method uses a set of unlinked genetic markers to infer details of population structure, and to estimate the ancestry of sampled individuals, before using this information to test for associations within subpopulations. It provides power comparable with the TDT in many settings and may substantially outperform it if there are conflicting associations in different subpopulations.
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research-article |
25 |
1163 |
4
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Moran CP, Lang N, LeGrice SF, Lee G, Stephens M, Sonenshein AL, Pero J, Losick R. Nucleotide sequences that signal the initiation of transcription and translation in Bacillus subtilis. MOLECULAR & GENERAL GENETICS : MGG 1982; 186:339-46. [PMID: 6181373 DOI: 10.1007/bf00729452] [Citation(s) in RCA: 657] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We have determined the nucleotide sequence of two Bacillus subtilis promoters (veg and tms) that are utilized by the principal form of B. subtilis RNA polymerase found in vegetative cells (sigma 55-RNA polymerase) and have compared our sequences to those of several previously reported Bacillus promoters. Hexanucleotide sequences centered approximately 35 (the "--35" region) and 10 (the "--10" region) base pairs upstream from the veg and tms transcription starting points (and separated by 17 base pairs) corresponded closely to the consensus hexanucleotides (TTGACA and TATAAT) attributed to Escherichia coli promoters. Conformity to the preferred --35 and --10 sequences may not be sufficient to promote efficient utilization by B. subtilis RNA polymerase, however, since three promoters (veg, tms and E. coli tac) that conform to these sequences and that are utilized efficiently by E. coli RNA polymerase were used with highly varied efficiencies by B. subtilis RNA polymerase. We have also analyzed mRNA sequences in DNA located downstream from eight B. subtilis chromosomal and phage promoters for nucleotide sequences that might signal the initiation of translation. In accordance with the rules of McLaughlin, Murray and Rabinowitz (1981), we observe mRNA nucleotide sequences with extensive complementarity to the 3' terminal region of B. subtilis 16S rRNA, followed by an initiation codon and an open reading frame.
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43 |
657 |
5
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Jokovic A, Locker D, Stephens M, Kenny D, Tompson B, Guyatt G. Validity and reliability of a questionnaire for measuring child oral-health-related quality of life. J Dent Res 2002; 81:459-63. [PMID: 12161456 DOI: 10.1177/154405910208100705] [Citation(s) in RCA: 532] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Oral-health-related quality of life measures that exist are designed for adults. This study aimed to develop and evaluate the CPQ(11-14), a self-report measure of the impact of oral and oro-facial conditions on 11- to 14-year-old children. An item pool was generated with the use of a literature review and interviews with health professionals, parents, and child patients. The 36 items rated the most frequent and bothersome by 83 children were selected for the CPQ(11-14). Validity testing involved a new sample of 123 children. Test-retest reliability was assessed in a subgroup of these children (n = 65). Mean CPQ(11-14) scores were highest for oro-facial (31.4), lower for orthodontic (24.3), and lowest for pedodontic (23.3) patients. There were significant associations between the CPQ(11-14) score and global ratings of oral health (p < 0.05) and overall well-being (p < 0.01). The Cronbach's alpha and intraclass correlation coefficient for the CPQ(11-14) were 0.91 and 0.90, respectively. These results suggest that the CPQ(11-14) is valid and reliable.
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23 |
532 |
6
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O'Brien PE, Brown WA, Smith A, McMurrick PJ, Stephens M. Prospective study of a laparoscopically placed, adjustable gastric band in the treatment of morbid obesity. Br J Surg 1999; 86:113-8. [PMID: 10027373 DOI: 10.1046/j.1365-2168.1999.00964.x] [Citation(s) in RCA: 194] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Surgical control of morbid obesity should benefit from a minimally invasive approach and the ability to adjust the degree of gastric restriction. METHODS The Lap-Band adjustable gastric banding system was evaluated prospectively in a consecutive series of 302 patients, and data on perioperative outcome and weight loss pattern at up to 4 years of follow-up are presented. Some 302 patients (89 per cent women; mean age 39 years, mean weight 124 kg) were entered into the study. Laparoscopic placement was used in 277 patients. Previous gastric stapling surgery was the principal reason for an elective open approach. RESULTS The incidence of significant early complications was 4 per cent and included two perforations of the stomach after open placement. The mean length of stay after laparoscopic placement was 3.9 days and only one complication (infected reservoir site) occurred in these patients. The principal late complication of prolapse of the stomach through the band occurred in 27 patients (9 per cent). Significant modification of technique and patient care has enabled reduction of this complication in the latter part of the series. Mean(s.d.) excess weight loss was 51.0(17) per cent at 12 months (n = 120), 58.3(20) per cent at 24 months (n = 43), 61.6(2) per cent at 36 months (n = 25) and 682(21) per cent at 48 months (n = 12). CONCLUSION The Lap-Band is an effective method for achieving good weight loss in the morbidly obese at up to 4 years of follow-up. Laparoscopic placement has been associated with a short length of stay and a low frequency of complications. The ability to adjust the setting of the device to achieve different degrees of gastric restriction has enabled progressive weight loss throughout the period of study.
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26 |
194 |
7
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Bengzon AR, Rasmussen T, Gloor P, Dussault J, Stephens M. Prognostic factors in the surgical treatment of temporal lobe epileptics. Neurology 1968; 18:717-31. [PMID: 5692332 DOI: 10.1212/wnl.18.8.717] [Citation(s) in RCA: 185] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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57 |
185 |
8
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Nagachinta T, Stephens M, Reitz B, Polk BF. Risk factors for surgical-wound infection following cardiac surgery. J Infect Dis 1987; 156:967-73. [PMID: 3680996 DOI: 10.1093/infdis/156.6.967] [Citation(s) in RCA: 176] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In a prospective study of 1,009 adult patients undergoing elective cardiac surgery at The Johns Hopkins Hospital, we determined the association between a variety of preoperative and operative parameters and the risk of postoperative sternal- or mediastinal-wound infection. Of the parameters reflecting nutritional state, only one, reduced level of albumin in serum, was significantly associated with sternal- or mediastinal-wound infection by univariate analysis. The final multiple logistic regression analysis indicated that four variables were significant (P less than .05) independent predictors of sternal- or mediastinal-wound infection: obesity (relative odds = 3.8; 95% confidence limits = 1.9-7.5), diabetes mellitus (relative odds = 2.6; 95% confidence limits = 1.4-4.8), length of hospital stay before surgery greater than five days (relative odds = 2.0; 95% confidence limits = 1.2-3.5), and current cigarette smoking (relative odds = 1.8; 95% confidence limits = 1.1-3.1). Of these variables, perhaps only smoking will lend itself routinely to attempts at intervention.
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38 |
176 |
9
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Locker D, Matear D, Stephens M, Lawrence H, Payne B. Comparison of the GOHAI and OHIP-14 as measures of the oral health-related quality of life of the elderly. Community Dent Oral Epidemiol 2001; 29:373-81. [PMID: 11553110 DOI: 10.1034/j.1600-0528.2001.290507.x] [Citation(s) in RCA: 170] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVES This paper compares the performance of the GOHAI and the OHIP-14 as measures of the oral health-related quality of life of the compromised elderly. METHODS Data were obtained from a cross-sectional survey of 225 participants, most of whom lived in a large geriatric care centre. RESULTS The mean age of subjects was 83 years and the majority had one or more chronic medical conditions and physical disabilities. Their main oral problems were high rates of tooth loss and xerostomia. Additive and simple count methods were used to derive GOHAI and OHIP-14 scores. Using the additive method, 8.4% had a GOHAI score of zero and 30.3% an OHIP-14 score of zero. Using the simple count method the percentage with a score of zero was 15.1% and 45.8%. Both measures discriminated between dentate subjects with and without one or more dentures, with and without a chewing problem and with and without dry mouth. Both also showed significant associations with self-rated oral health and satisfaction with oral health status. Associations tended to be stronger between GOHAI scores and these variables. The measures were equally good at predicting overall psychological well-being and life satisfaction. Although the GOHAI identified more oral functional and psychosocial impacts than the OHIP-14, neither was markedly superior to the other when used as discriminatory measures. However, the high prevalence of subjects with zero scores may compromise the ability of the OHIP-14 to detect within-subject change.
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Comparative Study |
24 |
170 |
10
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Williams NM, Preece A, Morris DW, Spurlock G, Bray NJ, Stephens M, Norton N, Williams H, Clement M, Dwyer S, Curran C, Wilkinson J, Moskvina V, Waddington JL, Gill M, Corvin AP, Zammit S, Kirov G, Owen MJ, O'Donovan MC. Identification in 2 Independent Samples of a Novel Schizophrenia RiskHaplotype of the Dystrobrevin Binding Protein Gene (DTNBP1). ACTA ACUST UNITED AC 2004; 61:336-44. [PMID: 15066891 DOI: 10.1001/archpsyc.61.4.336] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CONTEXT Recent research suggests that variation in the gene encoding dystrobrevin binding protein (DTNBP1) confers susceptibility to schizophrenia. Thus far, no specific risk haplotype has been identified in more than 1 study. OBJECTIVES To confirm DTNBP1 as a schizophrenia susceptibility gene, to identify and replicate specific risk and protective haplotypes, and to explore relationships between DTNBP1 and the phenotype. DESIGN Genetic association study based on mutation detection and case-control analysis. SETTING All subjects were unrelated and ascertained from general (secondary care) psychiatric inpatient and outpatient services. PARTICIPANTS The Cardiff, Wales, sample included 708 white subjects from the United Kingdom and Ireland (221 females) who met DSM-IV criteria for schizophrenia and were individually matched for age, sex, and ethnicity to 711 blood donor controls (233 females). Mean +/- SD age at first psychiatric contact for cases was 23.6 +/- 7.7 years; mean age at ascertainment was 41.8 +/- 13.5 years. The Dublin, Ireland, sample included 219 white subjects from the Republic of Ireland who met DSM-III-R criteria for schizophrenia or schizoaffective disorder and 231 controls. The mean age of the Irish cases was 46.0 +/- 8.5 years; mean age at first psychiatric contact was 25.2 +/- 12.4 years. MAIN OUTCOME MEASURE Evidence for association between the DTNBP1 locus and schizophrenia. RESULTS In the Cardiff sample, there was no evidence for association with previously implicated haplotypes but strong evidence for association with multiple novel haplotypes. Maximum evidence was found for a novel 3-marker haplotype (global P<.001), composed of 1 risk haplotype (P =.01) and 2 protective haplotypes, 1 common (P =.006) and 1 rare (P<.001). Specific risk and protective haplotypes were replicated in the Dublin sample (P =.02,.047, and.006, respectively). The only phenotypic variable associated with any haplotype was between the common protective haplotype and higher educational achievement (P =.02, corrected for multiple tests). CONCLUSIONS DTNBP1 is a susceptibility gene for schizophrenia. Specific risk and protective haplotypes were identified and replicated. Association with educational achievement may suggest protection mediated by IQ, although this needs to be confirmed in an independent data set.
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21 |
153 |
11
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Thomas P, Stephens M, Wilkie G, Amar M, Lunt GG, Whiting P, Gallagher T, Pereira E, Alkondon M, Albuquerque EX. (+)-Anatoxin-a is a potent agonist at neuronal nicotinic acetylcholine receptors. J Neurochem 1993; 60:2308-11. [PMID: 8492133 DOI: 10.1111/j.1471-4159.1993.tb03519.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The effects of the nicotinic agonist (+)-anatoxin-a have been examined in four different preparations, representing at least two classes of neuronal nicotinic receptors. (+)-Anatoxin-a was most potent (EC50 = 48 nM) in stimulating 86Rb+ influx into M10 cells, which express the nicotinic receptor subtype comprising alpha 4 and beta 2 subunits. A presynaptic nicotinic receptor mediating acetylcholine release from hippocampal synaptosomes was similarly sensitive to (+)-anatoxin-a (EC50 = 140 nM). alpha-Bungarotoxin-sensitive neuronal nicotinic receptors, studied using patch-clamp recording techniques, required slightly higher concentrations of this alkaloid for activation: Nicotinic currents in hippocampal neurons were activated by (+)-anatoxin-a with an EC50 of 3.9 microM, whereas alpha 7 homooligomers reconstituted in Xenopus oocytes yielded an EC50 value of 0.58 microM for (+)-anatoxin-a. In these diverse preparations, (+)-anatoxin-a was between three and 50 times more potent than (-)-nicotine and approximately 20 times more potent than acetylcholine, making it the most efficacious nicotinic agonist thus far described.
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32 |
97 |
12
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Curie K, Speller DC, Simpson RA, Stephens M, Cooke DI. A hospital epidemic caused by gentamicin-resistant Klebsiella aerogenes. J Hyg (Lond) 1978; 80:115-23. [PMID: 340580 PMCID: PMC2129979 DOI: 10.1017/s0022172400053432] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the 15 months, February 1976 to April 1977, more than 241 patients became colonized with a strain of Klebsiella aerogenes, capsular serotype K2, resistant to most antibiotics. Urinary tract infection was the most common clinical manifestation but bacteraemia and, occasionally, infections of other sites were encountered. The main reservoir of the epidemic klebsiella was the gut, urine and skin of colonized patients. Gut carriage among staff was very uncommon. The most susceptible patients were elderly males, with debilitating illnesses and urinary tract abnormalities, especially if they were catheterized or receiving antibiotics. Likely vehicles for spread were the hands of staff, and contaminated bedpans and urinals. Control measures were directed at these factors. At the end of April 1977 no new cases had occurred for 3 months in the ward in which the outbreak began, and which had been the main focus of infection, and only 5 patients in the affected hospitals were known to be colonized by the epidemic klebsiella.
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research-article |
47 |
67 |
13
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Turic D, Langley K, Mills S, Stephens M, Lawson D, Govan C, Williams N, Van Den Bree M, Craddock N, Kent L, Owen M, O'Donovan M, Thapar A. Follow-up of genetic linkage findings on chromosome 16p13: evidence of association of N-methyl-D aspartate glutamate receptor 2A gene polymorphism with ADHD. Mol Psychiatry 2004; 9:169-73. [PMID: 14966475 DOI: 10.1038/sj.mp.4001387] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Attention deficit hyperactivity disorder (ADHD) is a childhood onset disorder, for which there is good evidence that genetic factors contribute to the aetiology. Recently reported linkage findings suggested evidence of a susceptibility locus on chromosome 16p13 (maximum LOD score of 4.2, P=5 x 10(-6)). The GRIN2A (glutamate receptor, ionotropic, N-methyl D-aspartate 2A) gene that encodes the N-methyl D-aspartate receptor subunit 2A (NMDA2A) maps to this region of linkage. As this is also a good functional candidate gene for ADHD, we undertook family-based association analysis in a sample of 238 families. We found significant evidence of association with a GRIN2A exon 5 polymorphism (chi(2)=5.7, P=0.01). Our data suggest that genetic variation in GRIN2A may confer increased risk for ADHD and that this, at least in part, might be responsible for the linkage result on 16p reported by Smalley et al. We conclude that replication is required and that further work examining for association of GRIN2A polymorphisms with ADHD is warranted.
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66 |
14
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Speller DC, Raghunath D, Stephens M, Viant AC, Reeves DS, Wilkinson PJ, Broughall JM, Holt HA. Epidemic infection by a gentamicin-resistant Staphylococcus aureus in three hospitals. Lancet 1976; 1:464-6. [PMID: 55729 DOI: 10.1016/s0140-6736(76)91485-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A Staphylococcus aureus strain, resistant to aminoglycosides, including gentamicin and tobramycin, and to penicillin, lincomycin, and other antibiotics, caused an outbreak of hospital infection in a surgical ward which spread to the intensive-therapy unit and to two other hospitals. 21 patients were colonised and 9 of these had overt clinical infection. Administration of antibiotics to which the staphylococcus was resistant was associated with colonisation. The use of gentamicin, tobramycin, and lincomycin in these hospitals has increased as has the occurrence of bacterial resistance to these agents. An antibiotic policy to control their use is essential to preserve their value in life-threatening infections by bacteria resistant to other agents.
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Case Reports |
49 |
62 |
15
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Stephens M, Gibbs AR, Pooley FD, Wagner JC. Asbestos induced diffuse pleural fibrosis: pathology and mineralogy. Thorax 1987; 42:583-8. [PMID: 3660310 PMCID: PMC460856 DOI: 10.1136/thx.42.8.583] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lungs from seven cases of diffuse pleural fibrosis with known asbestos exposure were studied to determine the gross and microscopic pathological features and relate these to the analysed mineral fibre content of the lung. All seven individuals had had substantial exposure, ranging from two to 25 years, and chronic chest problems and at necropsy all cases met the criteria for compensatable disease. Macroscopically, all had extensive visceral pleural fibrosis and extensive areas of adhesions, and four also had discrete parietal pleural plaques. The histological features were similar in all the cases--most strikingly the basket weave pattern of the thickened pleura and a dense subpleural parenchymal interstitial fibrosis with fine honeycombing, extending up to 1 cm into the underlying lung. The similar histological appearances raise the possibility that diffuse pleural fibrosis and pleural plaques have a similar pathogenesis. Amphibole asbestos (crocidolite and amosite) counts were high in six of the seven cases and chrysotile counts in four; four cases had high mullite counts, but the importance of this is not known. It is concluded that diffuse pleural fibrosis is a specific asbestos associated entity, of uncertain pathogenesis, with mineral fibre counts falling between those found with plaques and those in minimal asbestosis.
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research-article |
38 |
59 |
16
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Attanoos RL, Suvarna SK, Rhead E, Stephens M, Locke TJ, Sheppard MN, Pooley FD, Gibbs AR. Malignant vascular tumours of the pleura in "asbestos" workers and endothelial differentiation in malignant mesothelioma. Thorax 2000; 55:860-3. [PMID: 10992539 PMCID: PMC1745618 DOI: 10.1136/thorax.55.10.860] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Three cases of diffuse malignant vascular tumours of the pleura are described which mimicked malignant mesothelioma clinically and pathologically (so called "pseudomesothelioma"). All had occupational histories of exposure to asbestos. The relationship of these tumours to mesothelioma and asbestos exposure is discussed. METHODS To examine the histogenetic relationship between mesothelioma and these three tumours an immunohistochemical analysis of vascular marker (CD31, CD34, and Von Willebrand factor) expression was undertaken in 92 cases of pleural mesothelioma, in addition to these three tumours. Electron microscopic fibre analysis of lung tissue was performed on each of the three cases to assess asbestos fibre content. RESULTS Diffuse pleural epithelioid haemangioendotheliomas may closely resemble malignant mesothelioma clinically and pathologically but, of the 92 pleural mesotheliomas tested, none showed expression of CD31, CD34, and Von Willebrand factor. Although all three cases had claimed exposure to asbestos, ferruginous bodies typical of asbestos were only seen by light microscopy in case 2, and only in this subject was the asbestos fibre content raised in comparison with the range seen in a non-exposed background population. The latent period in the pleural epithelioid haemangioendotheliomas ranged from 18 to 60 years. CONCLUSIONS Endothelial differentiation does not appear to occur in mesothelioma and therefore should be clearly separated from it. No definite association between pleural epithelioid haemangioendothelioma and exposure to asbestos can be made from this small series but further investigation is warranted.
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research-article |
25 |
54 |
17
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Edenberg HJ, Strother WN, McClintick JN, Tian H, Stephens M, Jerome RE, Lumeng L, Li TK, McBride WJ. Gene expression in the hippocampus of inbred alcohol-preferring and -nonpreferring rats. GENES BRAIN AND BEHAVIOR 2005; 4:20-30. [PMID: 15660665 DOI: 10.1111/j.1601-183x.2004.00091.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The hippocampus is sensitive to the effects of ethanol and appears to have a role in the development of alcohol tolerance. The objective of this study was to test the hypothesis that there are innate differences in gene expression in the hippocampus of inbred alcohol-preferring (iP) and -nonpreferring (iNP) rats that may contribute to differences in sensitivity to ethanol and/or in the development of tolerance. Affymetrix microarrays were used to measure gene expression in the hippocampus of alcohol-naive male iP and iNP rats in two experiments (n=4 and 6 per strain in the two experiments). Combining data from the two experiments, there were 137 probesets representing 129 genes that significantly differed (P < or = 0.01); 62 probesets differed at P < or = 0.001. Among the 36% of the genes that were expressed more in the iP than iNP rat at this level of significance, many were involved in cell growth and adhesion, cellular stress reduction and anti-oxidation, protein trafficking, regulation of gene expression, synaptic function and metabolism. Among the 64% of the genes that had lower expression in the hippocampus of iP than iNP rats were genes involved in metabolic pathways, cellular signaling systems, protein trafficking, cell death and neurotransmission. Overall, the data indicate that there are significant innate differences in gene expression in the hippocampus between iP and iNP rats, some of which might contribute to the differences observed in the development of alcohol tolerance between the selectively bred P and NP lines.
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Research Support, U.S. Gov't, P.H.S. |
20 |
50 |
18
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Morvan X, Saby NPA, Arrouays D, Le Bas C, Jones RJA, Verheijen FGA, Bellamy PH, Stephens M, Kibblewhite MG. Soil monitoring in Europe: a review of existing systems and requirements for harmonisation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2008; 391:1-12. [PMID: 18063012 DOI: 10.1016/j.scitotenv.2007.10.046] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Revised: 10/08/2007] [Accepted: 10/15/2007] [Indexed: 05/25/2023]
Abstract
Official frameworks for soil monitoring exist in most member states of the European Union. However, the uniformity of methodologies and the scope of actual monitoring are variable between national systems. This review identifies the differences between existing systems, and describes options for harmonising soil monitoring in the Member States and some neighbouring countries of the European Union. The present geographical coverage is uneven between and within countries. In general, national and regional networks are much denser in northern and eastern regions than in southern Europe. The median coverage in the 50 km x 50 km EMEP cells applied all over the European Union, is 300 km(2) for one monitoring site. Achieving such minimum density for the European Union would require 4100 new sites, mainly located in southern countries (Italy, Spain, Greece), parts of Poland, Germany, the Baltic countries, Norway, Finland and France. Options are discussed for harmonisation of site density, considering various risk area and soil quality indicator requirements.
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Review |
17 |
48 |
19
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Offori TW, Platt CC, Stephens M, Hopkinson GB. Angiosarcoma in congenital hereditary lymphoedema (Milroy's disease)--diagnostic beacons and a review of the literature. Clin Exp Dermatol 1993; 18:174-7. [PMID: 8482001 DOI: 10.1111/j.1365-2230.1993.tb01008.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In cases of congenital lymphoedema the finding of ulceration, violaceous nodules or papules, or apparent traumatic ecchymoses should act as a diagnostic beacon warning of dangers. A case is reported of a high-grade angiosarcoma developing in a patient with congenital hereditary lymphoedema (Milroy's disease). This is the second paper to report this complication, the third case report and the first case in which the diagnosis is substantiated by immunohistochemistry and lectin histochemistry. A review of cases of angiosarcoma complicating congenital hereditary and non-hereditary lymphoedema is also presented.
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Case Reports |
32 |
46 |
20
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Couper JJ, Clarke CF, Byrne GC, Jones TW, Donaghue KC, Nairn J, Boyce D, Russell M, Stephens M, Raymond J, Bates DJ, McCaul K. Progression of borderline increases in albuminuria in adolescents with insulin-dependent diabetes mellitus. Diabet Med 1997; 14:766-71. [PMID: 9300227 DOI: 10.1002/(sici)1096-9136(199709)14:9<766::aid-dia467>3.0.co;2-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We aimed to determine the natural history of borderline increases in albuminuria in adolescents with insulin-dependent (Type 1) diabetes mellitus (IDDM) and factors which are associated with progression to persistent microalbuminura. Fifty-five normotensive adolescents with IDDM and intermittent microalbuminura (overnight albumin excretion ratte of 20-200 micrograms min-1 on one of three consecutive timed collections, n = 29) or borderline albuminura (mean overnight albumin excretion rate of 7.2-20 micrograms min-1 on one of three consecutive timed collections, n = 30) were followed prospectively at 3 monthly intervals. The endpoint was persistent microalbuminuria defined as a minimum of three of four consecutive overnight albumin excretion rates of greater than 20 micrograms min-1. One hundred and forty-two adolescents with IDDM and normoalbuminura were also followed prospectively. Fifteen of the 59 patients (25.4%) with intermittent (9/29) or borderline (6/30) albuminura progressed to persistent microalbuminura (progressors) over 28 (15-50) months [median (range)] in comparison with two of the 142 patients with normoalbuminuria at entry (relative risk = 12.6; p = 0.001). Progressors to persistent microalbuminura were pubertal and had higher systolic (p = 0.02) and diastolic (p = 0.02) blood pressure, and HbA1c (p = 0.004) than non-progressors. All patients remained normotensive. Glomerular filtration rate, apolipoproteins, dietary phosphorus, protein and sodium intakes, and prevalence of smoking did not differ between progressors and non-progressors. Total renin was higher in the diabetic patients without a difference between progressors and non-progressors. In conclusion there is a relatively high rate of progression to persistent microalbuminuria in pubertal adolescents with borderline increases in albuminura and duration greater than 3 years. These patients require attention to minimize associated factors of poor metabolic control and higher blood pressure in the development of incipient nephropathy.
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Comparative Study |
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Gillespie WA, Sellin MA, Gill P, Stephens M, Tuckwell LA, Hilton AL. Urinary tract infection in young women, with special reference to Staphylococcus saprophyticus. J Clin Pathol 1978; 31:348-50. [PMID: 580432 PMCID: PMC1145272 DOI: 10.1136/jcp.31.4.348] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Acute urinary tract infections in young women attending a clinic for sexually transmitted diseases were caused by the same bacteria, in the same proportions, as those that caused infections in women students. Staphylococcus saprophyticus biotype 3 (formerly called Micrococcus subgroup 3) was the commonest organism after coliform bacilli and caused about 30% of the infections. It was uncommon in women over 25 years of age and rarely caused asymptomatic bacteriuria in pregnancy. Most infections, irrespective of the causative organism, started soon after sexual intercourse, but neither the staphylococci nor the other organisms were associated with promiscuity, as judged by numbers of sexual partners or the incidence of sexually transmitted diseases. There was no evidence that the staphylococci were sexually transmitted. The reasons for the virulence of Staph. saprophyticus and its predilection for the urinary tract of young women remain unknown.
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research-article |
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45 |
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Plomin R, Turic DM, Hill L, Turic DE, Stephens M, Williams J, Owen MJ, O'Donovan MC. A functional polymorphism in the succinate-semialdehyde dehydrogenase (aldehyde dehydrogenase 5 family, member A1) gene is associated with cognitive ability. Mol Psychiatry 2004; 9:582-6. [PMID: 14981524 DOI: 10.1038/sj.mp.4001441] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Succinate-semialdehyde dehydrogenase (SSADH) deficiency is a rare cause of learning disability. We have investigated SSADH to assess its contribution to cognitive ability in the general population in both case-control- and family-based analyses. Sequence analysis of SSADH revealed four changes affecting the encoded protein, only one of which had a minor allele whose frequency is even moderately common. We genotyped this functional polymorphism in 197 high-IQ cases, 201 average-IQ controls and 196 parent high-IQ offspring trios. The minor allele was significantly less frequent in high-IQ cases and was significantly less frequently transmitted by parents to high-IQ subjects than chance expectation. A previous study has shown that the minor allele encodes a lower activity enzyme than the major allele. These data suggest that higher SSADH activity is associated with higher intelligence across the general population. The effect is small, with each allele having an effect size translating to about 1.5 IQ points.
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Matear DW, Locker D, Stephens M, Lawrence HP. Associations between xerostomia and health status indicators in the elderly. ACTA ACUST UNITED AC 2016; 126:79-85. [PMID: 16562776 DOI: 10.1177/1466424006063183] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aims: This study investigated the associations between xerostomia (dry mouth) (low, moderate and high) with other categorical variables (e.g. demographic and health status indicators). This paper aims to report on the severity of xerostomia in the elderly population and investigate the relationship with other aspects of perceived health. Method: Data were obtained from a cross-sectional survey of 225 elderly people from a large multilevel geriatric care centre. The centre consists of three levels of care: an apartment building in which residents live more or less independently, a home for the aged, and a chronic care hospital. Participants in the study were recruited when they attended the dental care facility. Data were collected by means of a personal interview conducted either at the dental care facility or the participant’s residence. Results: The mean age was 83 years. Most were females (72%) and almost all (99%) reported one or more chronic medical conditions; 88% had physical disabilities. Xerostomia was recorded on a seven-point scale. Scores were categorised as low, medium or high and the proportions were 49.3%, 30.3% and 20.4% respectively. Bivariate analysis showed no association between dry mouth and sex, age, general health change or life satisfaction. However, when the high xerostomia group was separated out and odds ratios calculated they were 2.3 to 4.9 times more likely to experience a negative impact on health than the low group. Xerostomia did not have a significant impact on chewing capacity, morale or stress, although it contributed to the variability of the oral health-related quality of life measures. It was the only variable with a significant effect (OR 2.55) for the Oral Health Impact Profile-14 and displayed a higher odds ratio (2.76) for the Geriatric Oral Health Assessment Index. Selfreported xerostomia in the elderly population can be categorised into a severity scale. Those suffering most from xerostomia are more likely to experience a negative impact on general health. Conclusion: The key finding in this study is that xerostomia has a significant and negative impact on the quality of life of elderly individuals, though oral function may be less affected.
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Dubos R, Schaedler RW, Stephens M. THE EFFECT OF ANTIBACTERIAL DRUGS ON THE FECAL FLORA OF MICE. ACTA ACUST UNITED AC 2010; 117:231-43. [PMID: 19867223 PMCID: PMC2137605 DOI: 10.1084/jem.117.2.231] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Oral administration of penicillin, terramycin, or chloramphenicol to NCS mice rapidly brought about profound changes in their fecal flora. The lactobacilli disappeared completely, whereas the numbers of enterococci and Gram-negative bacilli reached very high levels. In contrast, no effect on the fecal flora could be detected following administration of isoniazid in any amount. The intensity and duration of the effects on the fecal flora were related to the type of drug and to the amount of it administered. Chloramphenicol produced disturbances which were less profound and of shorter duration than those produced by penicillin or terramycin. The duration of the disturbances in the fecal flora produced by antibacterial drugs was markedly conditioned by the nutritional regimen. The fecal flora returned to its pretreatment state (large numbers of lactobacilli, few enterococci, and few Gram-negative bacilli) within less than 4 weeks after discontinuing the drug when the mice were fed a complex diet of ill defined composition (commercial pellets). Contrariwise, the fecal flora remained markedly different from that of control mice when the animals were fed semisynthetic diets containing as source of protein either 15 per cent casein or 15 per cent wheat gluten (both supplemented with cystine); or 15 per cent wheat gluten supplemented with lysine, threonine, and cystine. The fecal flora of mice treated with penicillin contained large numbers of lactose-fermenting Gram-negative bacilli, not found in the untreated animals. These lactose fermenters persisted for several months after discontinuance of the drug in mice fed either the casein or gluten diets, but they disappeared rapidly from mice fed pellets. Similar results, although less striking, were obtained with Swiss mice from colonies maintained under usual conditions, and therefore having a fecal flora more complex than that of NCS mice.
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Journal Article |
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Stephens M, Kwan AP, Bayliss MT, Archer CW. Human articular surface chondrocytes initiate alkaline phosphatase and type X collagen synthesis in suspension culture. J Cell Sci 1992; 103 ( Pt 4):1111-6. [PMID: 1487493 DOI: 10.1242/jcs.103.4.1111] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The type X collagen is a short chain collagen associated with calcific cartilage and/or the expression of the hypertrophic chondrocyte phenotype. In articular cartilage, type X collagen is restricted to the basal zone of calcified cartilage adjacent to the subchondral bone. However, during pathological change such as in osteoarthritis, the synthesis of type X collagen becomes more widespread but never extends to the articular surface. Using immunocytochemistry and fluorography of newly synthesised collagens, we report that surface articular chondrocytes (which occupy the uppermost 10–15% of the tissue depth) from normal human cartilage initiate de novo synthesis of both type X collagen and alkaline phosphatase when maintained in suspension culture.
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