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Scott W, Hentemann M, Rowley B, Bull C, Bullion A, Johnson J, Redman A, Liu N, Jones R, Sibley E. 444 Novel 2,3-dihydroimidazo[1,2-c]quinazolines PI3K inhibitors: Discovery and SAR. EJC Suppl 2010. [DOI: 10.1016/s1359-6349(10)72151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Chen C, Ali S, Nakuci E, McSweeney D, Brown J, Szwaya J, Bull C, Savage R, Ashwell M, Chan T. 119 ARQ 087: A potent ATP-independent fibroblast growth factor receptor (FGFR) kinase inhibitor showing in vivo anti-tumor activity in FGFR2-driven tumors. EJC Suppl 2010. [DOI: 10.1016/s1359-6349(10)71824-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Bull C, Irving E, Willis I. Further Palaeomagnetic Results from South Victoria Land, Antarctica. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1365-246x.1962.tb00355.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Hartgroves L, Koudstaal W, McLeod C, Moncorgé O, Thompson C, Ellis J, Bull C, Havenga M, Goudsmit J, Barclay W. Rapid generation of a well-matched vaccine seed from a modern influenza A virus primary isolate without recourse to eggs. Vaccine 2010; 28:2973-9. [DOI: 10.1016/j.vaccine.2010.02.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 02/01/2010] [Accepted: 02/10/2010] [Indexed: 12/19/2022]
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O'Callaghan N, Bull C, Fenech M. Abstract A11: Development of minimally invasive techniques for monitoring genome health: A preventative health approach to reducing disease. Cancer Prev Res (Phila) 2010. [DOI: 10.1158/1940-6207.prev-09-a11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
It is becoming increasingly evident that risk for developmental and degenerative disease, including cancers, increases with more DNA damage. Importantly, DNA damage is influenced (and can be modified) by nutritional status. Optimal concentrations of nutrients for reduction of genome damage are also dependent on many factors (genetic background, age, nutrient uptake) that vary from individual to individual.
In the genomic health era of personalised nutrition for disease prevention, there is a need to develop minimally invasive methodologies to measure alterations in disease risk biomarkers in an effort to identify at risk individuals early in disease progression. Using qPCR techniques developed by us, we aimed to evaluate the use of buccal cells and saliva as a minimally-invasive approach to measure markers of genome health in a cross-sectional study.
Buccal cells, saliva and blood samples were collected from 91 volunteers. This cohort comprised 18M and 25F in the young group (aged 18–31 years), and 25M and 23F in the older group (65–75yrs). Telomere length was determined in lymphocytes, buccal cells and saliva (by qPCR). Telomere length was negatively correlated with age; the strength of this correlation varied between gender and tissue type.
We report that buccal cells and saliva can be used to measure DNA damage. Further research is required to evaluate the effectiveness of buccal cells and/or saliva as a minimally-invasive biomarker of oxidative DNA damage, genome health and disease risk status.
The development of dietary patterns, functional foods and supplements that are designed to improve genome-health maintenance in an individual with increased disease risk may lead to a preventative health strategy based on the diagnosis and individualised nutritional prevention of genome damage.
Citation Information: Cancer Prev Res 2010;3(1 Suppl):A11.
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Senti G, Johansen P, Haug S, Bull C, Gottschaller C, Müller P, Pfister T, Maurer P, Bachmann MF, Graf N, Kündig TM. Use of A-type CpG oligodeoxynucleotides as an adjuvant in allergen-specific immunotherapy in humans: a phase I/IIa clinical trial. Clin Exp Allergy 2009; 39:562-70. [DOI: 10.1111/j.1365-2222.2008.03191.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ahern V, Bull C, Harris J, Matthews K, Willis D. Subspecialization of radiation therapists in Australia and New Zealand. ACTA ACUST UNITED AC 2007; 51:104-5. [PMID: 17419852 DOI: 10.1111/j.1440-1673.2007.01676.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gorst-Rasmussen A, Spiegelhalter DJ, Bull C. Monitoring the introduction of a surgical intervention with long-term consequences. Stat Med 2007; 26:512-31. [PMID: 16538698 DOI: 10.1002/sim.2548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Surgical innovations are often introduced for their expected long-term benefits, but the decision to abandon the existing treatment must be based on the available short-term data and rational judgment. We present a framework for monitoring the introduction of a surgical intervention with long-term consequences and failure-time endpoints. The framework is based on Bayesian methods, and formally combines study data, clinical opinion, and external evidence to construct a posterior survival function from which intuitive summary statistics can be extracted to aid decision making. It incorporates learning effects and is adaptable to a wide variety of settings. The methods are illustrated on survival data from a cohort of 325 consecutive neonates treated for simple transposition of the great arteries with either the Senning or the Switch operation during the period 1978-1998.
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Brown KL, Ridout DA, Hoskote A, Verhulst L, Ricci M, Bull C. Delayed diagnosis of congenital heart disease worsens preoperative condition and outcome of surgery in neonates. Heart 2006; 92:1298-302. [PMID: 16449514 PMCID: PMC1861169 DOI: 10.1136/hrt.2005.078097] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES To assess whether the route by which neonatal congenital heart disease (CHD) is first recognised influences outcome after surgery. METHODS Surgical neonates admitted to a tertiary cardiac unit between March 1999 and February 2002 were retrospectively reviewed with analysis of risk factors for outcome. Three routes to initial recognition of CHD were compared: antenatal diagnosis, detection on the postnatal ward, and presentation after discharge to home. Outcome measures were mortality and duration of perioperative ventilation. RESULTS 286 neonates had cardiac surgery with a median duration of ventilation of 101 h and in-hospital mortality of 12%. Recognition of CHD was antenatal in 20%, on the postnatal ward in 55% and after discharge to home in 25%. Multiple regression analyses, including the cardiac diagnosis, associated problems and other risk factors, indicated that severe cardiovascular compromise on admission to the cardiac unit was significantly related to mortality and prolonged ventilation. Considered in isolation, the route to recognition of heart disease did not influence mortality or ventilation time. Route to initial recognition did, however, influence the patient's condition on admission to the cardiac unit. Cardiovascular compromise and end organ dysfunction were least likely when recognition was antenatal and most common when presentation followed discharge to home. CONCLUSION The setting in which neonatal CHD is first recognised has an impact on preoperative condition, which in turn influences postoperative progress and survival after surgery. Optimal screening procedures and access to specialist care will improve outcome for neonates undergoing cardiac surgery.
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Lim KSH, Vinod SK, Bull C, O'Brien P, Kenny L. Prioritization of radiotherapy in Australia and New Zealand. ACTA ACUST UNITED AC 2005; 49:485-8. [PMID: 16351613 DOI: 10.1111/j.1440-1673.2005.01391.x] [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] [Indexed: 11/27/2022]
Abstract
The purpose of this study was to document how radiation oncology departments in Australia and New Zealand manage extended waiting lists by prioritizing patients for radiotherapy and how these centres define the "waiting time". A literature search on strategies for management of waiting lists in radiotherapy, both locally and internationally, was performed. A collaborative survey of all the radiotherapy departments in Australia and New Zealand was then undertaken. Of the 32 centres surveyed around Australia and New Zealand, 25 (77%) responded. There was considerable variation in the definitions used for "waiting times". Eleven of the 25 centres had formally documented protocols. New Zealand has a national policy for prioritization of patients for radiotherapy. Six centres had verbal protocols. Four centres had no significant waiting times and did not require a protocol for prioritization. One centre prioritized according to clinician discretion, two centres used a first-come, first-served basis. One centre replied but their protocol was missing. The variation in the definition of waiting time reduces its usefulness as an indirect measure of resources and as a method of comparing centres. There is also wide variation in the management of waiting lists, particularly in the prioritization schedules used by different centres. The major factor contributing to waiting lists at present is a shortage of radiation oncology staff, particularly radiation therapists. The implementation of standardized protocols for prioritizing patients may be useful in helping to manage scarce resources not withstanding the need to increase the resource base. However, the existence of such protocols should not give legitimacy to undue delays in commencing radiation treatment.
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Knowles R, Griebsch I, Dezateux C, Brown J, Bull C, Wren C. Newborn screening for congenital heart defects: a systematic review and cost-effectiveness analysis. Health Technol Assess 2005; 9:1-152, iii-iv. [PMID: 16297355 DOI: 10.3310/hta9440] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES To provide evidence to inform policy decisions about the most appropriate newborn screening strategy for congenital heart defects, identifying priorities for future research that might reduce important uncertainties in the evidence base for such decisions. DATA SOURCES Electronic databases. Groups of parents and health professionals. REVIEW METHODS A systematic review of the published medical literature concerning outcomes for children with congenital heart defects was carried out. A decision analytic model was developed to assess the cost-effectiveness of alternative screening strategies for congenital heart defects relevant to the UK. A further study was then carried out using a self-administered anonymous questionnaire to explore the perspectives of parents and health professionals towards the quality of life of children with congenital heart defects. The findings from a structured review of the medical literature regarding parental experiences were linked with those from a focus group of parents of children with congenital heart defects. RESULTS Current newborn screening policy comprises a clinical examination at birth and 6 weeks, with specific cardiac investigations for specified high-risk children. Routine data are lacking, but under half of affected babies, not previously identified antenatally or because of symptoms, are identified by current newborn screening. There is evidence that screen-positive infants do not receive timely management. Pulse oximetry and echocardiography, in addition to clinical examination, are alternative newborn screening strategies but their cost-effectiveness has not been adequately evaluated in a UK setting. In a population of 100,000 live-born infants, the model predicts 121 infants with life-threatening congenital heart defects undiagnosed at screening, of whom 82 (68%) and 83 (69%) are detected by pulse oximetry and screening echocardiography, respectively, but only 39 (32%) by clinical examination alone. Of these, 71, 71 and 34, respectively, receive a timely diagnosis. The model predicts 46 (0.5%) false-positive screening diagnoses per 100,000 infants with clinical examination, 1168 (1.3%) with pulse oximetry and 4857 (5.4%) with screening echocardiography. The latter includes infants with clinically non-significant defects. Total programme costs are predicted of pound 300,000 for clinical examination, pound 480,000 for pulse oximetry and pound 3.54 million for screening echocardiography. The additional cost per additional timely diagnosis of life-threatening congenital heart defects ranges from pound 4900 for pulse oximetry to pound 4.5 million for screening echocardiography. Including clinically significant congenital heart defects gives an additional cost per additional diagnosis of pound 1500 for pulse oximetry and pound 36,000 for screening echocardiography. Key determinants for cost-effectiveness are detection rates for pulse oximetry and screening echocardiography. Parents and health professionals place similar values on the quality of life outcomes of children with congenital heart defects and both are more averse to neurological than to cardiac disability. Adverse psychosocial effects for parents are focused around poor management and/or false test results. CONCLUSIONS Early detection through newborn screening potentially can improve the outcome of congenital heart defects; however the current programme performs poorly, and lacks monitoring of quality assurance, performance management and longer term outcomes. Pulse oximetry is a promising alternative newborn screening strategy but further evaluation is needed to obtain more precise estimates of test performance and to inform optimal timing, diagnostic and management strategies. Although screening echocardiography is associated with the highest detection rate, it is the most costly strategy and has a 5% false-positive rate. Improving antenatal detection of congenital heart defects increases the cost per timely postnatal diagnosis afforded by any newborn screening strategy but does not alter the relative effects of the strategies. An improvement of timely management of screen positive infants is essential. Further research is required to refine the detection rate and other aspects of pulse oximetry, to evaluate antenatal screening strategies more directly, and to investigate the psychosocial effects of newborn screening for congenital heart defects.
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Abstract
AIM To understand why doctors differ in their recommendations in situations where there is little certainty about the long term outcomes of the possible treatment options. METHODS A correlational design was used to examine the relation between preference for different treatment options and beliefs about likely outcomes for these options. Eighty doctors, with a mean of nine years in paediatric cardiology/surgery, attending a conference on serious congenital heart disease were studied. Main outcome measures were: ratings of the extent to which each of four treatment options were favoured; and subjective probabilities for three outcomes-death, survival with "good heart function" (New York Heart Association functional class (NYHA) I or II), and survival with "poor heart function" (NYHA III or IV)-for different treatment options over a 20 year time frame. RESULTS Preference for one treatment option over another was most closely associated with the subjective estimate of the additional years with "good heart function" that it offered 10-20 years after surgery (Pearson's r = 0.66, p < 0.001). In influencing a preference, the possibility of early death was subordinate to optimising the late outcome. CONCLUSIONS Doctors' treatment preferences are consistent with selecting the option that maximises the chance of the best outcome (long term survival with good heart function). Doctors' recommendations imply that they place more value on years of life in the child's far future than on life-years in the immediate future.
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Bull C. High pressure studies and structure of electronic perovskites. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302086956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Bull C, Sobanov Y, Röhrdanz B, O'Brien J, Lehrach H, Hofer E. The centromeric part of the human NK gene complex: linkage of LOX-1 and LY49L with the CD94/NKG2 region. Genes Immun 2001; 1:280-7. [PMID: 11196705 DOI: 10.1038/sj.gene.6363678] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The natural killer (NK) gene complex is a genomic region containing lectin-type receptor genes. We have established a contig of PAC and BAC clones comprising about 1 Mb of the centromeric part of the NK gene complex. This region extends from the LOX-1 gene, which encodes a receptor for oxidized LDL and was found within 100 kb telomeric of the STS marker D12S77, contains the CD94 and NKG2 NK receptor genes and reaches beyond D12S852 on the proximal side. In this part we have mapped the human LY49L gene, a homologue of the rodent Ly49 genes, which encode important MHC class I receptors for the regulation of NK cell activity in rodents. The LY49L gene is localized 100 to 200 kb centromeric of the NKG2 gene cluster and 300 to 400 kb telomeric of the STS marker D12S841. Genomic sequencing of the complete gene including promoter and intron sequences confirmed that the structure is similar to the mouse Ly49 genes. Screening of several cDNA libraries did not detect any transcripts of putative additional human LY49 genes. In addition, in the course of these studies several EST sequences were localized in the region, one immediately upstream of the LY49L gene.
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MESH Headings
- Antigens, CD/genetics
- Antigens, Ly
- Base Sequence
- Centromere/genetics
- DNA/analysis
- Expressed Sequence Tags
- Genetic Linkage
- Genome, Human
- Humans
- Killer Cells, Natural/physiology
- Lectins, C-Type
- Membrane Glycoproteins/genetics
- Molecular Sequence Data
- NK Cell Lectin-Like Receptor Subfamily C
- NK Cell Lectin-Like Receptor Subfamily D
- Promoter Regions, Genetic/genetics
- Receptors, Immunologic/genetics
- Receptors, LDL/genetics
- Receptors, NK Cell Lectin-Like
- Receptors, Natural Killer Cell
- Receptors, Oxidized LDL
- Scavenger Receptors, Class E
- Sequence Homology, Nucleic Acid
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White JR, Farukhi Z, Bull C, Christensen J, Gordon T, Paidas C, Nichols DG. Predictors of outcome in severely head-injured children. Crit Care Med 2001; 29:534-40. [PMID: 11373416 DOI: 10.1097/00003246-200103000-00011] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Determine variables in the acute care period associated with survival and pediatric intensive care unit (PICU) length of stay (LOS) for children with severe traumatic brain injury. DESIGN Retrospective cohort. SETTING Level 1 pediatric trauma center. PATIENTS Children (0-17 yrs) admitted 1991 to 1995 with nonpenetrating traumatic brain injury and admission Glasgow Coma Scale score of <or=8. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS The first 72 hrs of hospitalization were analyzed in detail for 136 patients. The primary end point was survival; secondary end points were PICU LOS, cost, and day at which Glasgow Coma Scale score was >or=14. Predictors of outcome were abstracted, including Pediatric Trauma Score, Glasgow Coma Scale score, Pediatric Risk of Mortality, physiologic variables, computed tomography evidence of brain injury, and neuroresuscitative medications. The fatality rate was 24%. Age and gender were similar between groups (p >or= .1). Survival was independently predicted by 6-hr Glasgow Coma Scale score (odds ratio [OR] 4.6; 95% confidence interval [CI] 2.06-11.9; p < .001) and maximum systolic blood pressure (OR 1.05; 95% CI 1.01-1.09; p < .02). Odds of survival increased 19-fold when maximum systolic blood pressure was >or=135 mm Hg (OR 18.8; 95% CI 2.0-178.0; p < .01). By discharge, 67% of patients had an age-appropriate Glasgow Coma Scale score. Median hospital costs were 8,798 dollars for survivors: only mannitol use independently predicted high cost (odds ratio 4.9; 95% CI 1.2-19.1; p < .01). For survivors, median PICU LOS was 2 days, although 25% had LOS >6 days. Six-hour Glasgow Coma Scale score (OR 0.62; 95% CI 0.48-0.80; p < .001) and mannitol (OR 7.9; 95% CI 2.3-27.3; p < .001) were each independently associated with a prolonged LOS among survivors. CONCLUSIONS Patients with higher 6-hr Glasgow Coma Scale scores were more likely to survive. Adjusting for severity of injury, survival was associated with maximum systolic blood pressure >or=135 mm Hg, suggesting that supranormal blood pressures are associated with improved outcome. Mannitol administration was associated with prolonged LOS, yet conferred no survival advantage. We suggest reevaluation of blood pressure targets and mannitol use in children with severe traumatic brain injury.
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Bull C, Yates R, Sarkar D, Deanfield J, de Leval M. Scientific, ethical, and logistical considerations in introducing a new operation: a retrospective cohort study from paediatric cardiac surgery. BMJ (CLINICAL RESEARCH ED.) 2000; 320:1168-73. [PMID: 10784538 PMCID: PMC27358 DOI: 10.1136/bmj.320.7243.1168] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To review the initial impact on mortality of infants with congenital heart disease of a new surgical technique that is now taken for granted. DESIGN Retrospective cohort study. SETTING A tertiary paediatric cardiology centre. SUBJECTS 325 consecutive neonates with simple transposition of the great arteries admitted before, during, and after the preferred management changed from the Senning operation to the arterial switch (1978-98); and 100 consecutive neonates requiring a different neonatal open heart operation that did not change in that period. MAIN OUTCOME MEASURES Mortality before and early after operation reconstructed sequentially as the series evolved and retrospectively once the series was complete; actuarial survival associated with the different treatment strategies. RESULTS For both the transposition and the comparison group, early mortality in 1998 was lower than in 1978. During that period, however, there was a phase temporally related to the adoption of the switch operation in which early mortality for transposition increased. Actuarial survival of recent patients with "intention to treat" with arterial switch is superior to those with intention to treat with the Senning operation, as predicted when the switch operation was first adopted. CONCLUSIONS A period of increased hazard for individual patients may occur when a specialist community, a particular unit, and an individual surgeon are all learning a new technique concurrently. Obtaining informed consent during this time of uncertainty is helped by clarity about the objectives of treatment and availability of relevant local and international data.
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Sarkar D, Bull C, Yates R, Wright D, Cullen S, Gewillig M, Clayton R, Tunstill A, Deanfield J. Comparison of long-term outcomes of atrial repair of simple transposition with implications for a late arterial switch strategy. Circulation 1999; 100:II-176-81. [PMID: 10567300 DOI: 10.1161/01.cir.100.suppl_2.ii-176] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND We report the single-institution, long-term results of 358 patients with simple transposition of the great arteries surviving >30 days after a Mustard (n=226, 1965 to 1980) or Senning (n=132, 1978 to 1992) procedure. METHODS AND RESULTS Outcome measures included late death, reintervention, ECG and ambulatory ECG rhythm, new arrhythmia, and functional status. Average follow-up was 13.4 (range 0.32 to 17.9) years for the Senning group and 11.7 (range 0.04 to 23.9) years for the Mustard group. The Senning group had a better survival rate at 5, 10, and 15 years (95% versus 86%, 94% versus 82%, and 94% versus 77%, respectively). In both groups, the majority of late deaths were sudden, without preceding ventricular dysfunction. Survival and survival free of reintervention were significantly better in the Senning group (relative risk [RR] 0.34, P=0.06 versus RR 0.39, P=0.027). Loss of sinus rhythm was comparable and unrelated to death. After era correction, the incidence of atrial flutter was similar and strongly associated with late death in both groups. Clinical systemic ventricular failure was uncommon, and at last follow-up, 92% of the Senning group and 89% of the Mustard group were in New York Heart Association class I. In a model exploring the implications of elective arterial switch conversion, this would only be beneficial if the hazard late after switch was markedly reduced and/or the hazard after the Senning procedure increased with time. CONCLUSIONS Late outcomes after the Senning procedure are superior to those after the Mustard procedure. Both groups had late sudden deaths that were not associated with clinical systemic ventricular failure. Good functional status after the Senning procedure suggests that a strategy of elective switch conversion cannot be justified for patients with isolated transposition.
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Herwig R, Poustka AJ, Müller C, Bull C, Lehrach H, O'Brien J. Large-scale clustering of cDNA-fingerprinting data. Genome Res 1999; 9:1093-105. [PMID: 10568749 PMCID: PMC310829 DOI: 10.1101/gr.9.11.1093] [Citation(s) in RCA: 147] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Clustering is one of the main mathematical challenges in large-scale gene expression analysis. We describe a clustering procedure based on a sequential k-means algorithm with additional refinements that is able to handle high-throughput data in the order of hundreds of thousands of data items measured on hundreds of variables. The practical motivation for our algorithm is oligonucleotide fingerprinting-a method for simultaneous determination of expression level for every active gene of a specific tissue-although the algorithm can be applied as well to other large-scale projects like EST clustering and qualitative clustering of DNA-chip data. As a pairwise similarity measure between two p-dimensional data points, x and y, we introduce mutual information that can be interpreted as the amount of information about x in y, and vice versa. We show that for our purposes this measure is superior to commonly used metric distances, for example, Euclidean distance. We also introduce a modified version of mutual information as a novel method for validating clustering results when the true clustering is known. The performance of our algorithm with respect to experimental noise is shown by extensive simulation studies. The algorithm is tested on a subset of 2029 cDNA clones coming from 15 different genes from a cDNA library derived from human dendritic cells. Furthermore, the clustering of these 2029 cDNA clones is demonstrated when the entire set of 76,032 cDNA clones is processed.
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Bull C. Current and potential impact of fetal diagnosis on prevalence and spectrum of serious congenital heart disease at term in the UK. British Paediatric Cardiac Association. Lancet 1999; 354:1242-7 ik. [PMID: 10520632 DOI: 10.1016/s0140-6736(99)01167-8] [Citation(s) in RCA: 234] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Assessment of the effect of fetal diagnosis on the prevalence of congenital heart disease at term requires national ascertainment because referral patterns are not rigorously structured. METHODS Between 1993 and 1995, all 17 paediatric cardiac centres in the UK submitted to a database lists of all fetuses diagnosed, and all infants needing surgery or interventional catheterisation or dying in the first year of life because of structural heart disease; details included the postal area of residence. FINDINGS There were 4799 affected pregnancies, 4165 babies born alive, 1124 fetal diagnoses, and 567 terminations of pregnancy because the fetus had structural heart disease. Thus, a fetal diagnosis was made in 23.4% of affected pregnancies (11.7% of all affected livebirths) with geographical variability in diagnostic rates. INTERPRETATION Fetal cardiac screening has an effect on the prevalence and types of congenital heart disease seen at term because many affected pregnancies are terminated. If detection rates of affected fetuses rose nationally to those seen in the 15 postal areas where detection rates were significantly higher than the national average in 1993-95, we would expect about 218 fewer affected individuals to be born annually.
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Carter WO, Bull C, Bortolon E, Yang L, Jesmok GJ, Gundel RH. A murine skeletal muscle ischemia-reperfusion injury model: differential pathology in BALB/c and DBA/2N mice. J Appl Physiol (1985) 1998; 85:1676-83. [PMID: 9804569 DOI: 10.1152/jappl.1998.85.5.1676] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ischemia-reperfusion injuries can occur with diseases such as myocardial infarction and stroke and during surgical procedures such as organ transplantation and correction of aortic aneurysms. We developed a murine model to mimic abdominal aortic aneurysm repair with cross-clamping of the aorta distal to the renal artery. After model development, we compared the normal complement BALB/c mouse with the C5-deficient DBA/2N mouse. To assess quantitative differences, we measured neuromuscular function up to 72 h after ischemia with a subjective clinical scoring system, as well as plasma chemistries, hematology, and histopathology. There were significant increases in clinical scores and creatine phosphokinase, lactate dehydrogenase, and muscle histopathology scores in BALB/c mice compared with those in DBA/2N mice and sham-surgery mice. Muscle histopathology scores of the cranial tibialis and quadriceps correlated well with clinical signs, creatine phosphokinase, and lactate dehydrogenase, and indicated the greatest pathology in these muscle groups. We developed a murine model of skeletal muscle ischemia-reperfusion injury that can utilize the benefits of murine genetic and transgenic models to assess therapeutic principles of this model. Additionally, we have shown a significant reduction in clinical signs, plasma muscle enzyme concentrations, and muscle pathology in the C5-deficient DBA/2N mouse in this model.
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Hahlin M, Jaworski RC, Wain GV, Harnett PR, Neesham D, Bull C. Integrated multimodality therapy for embryonal rhabdomyosarcoma of the lower genital tract in postpubertal females. Gynecol Oncol 1998; 70:141-6. [PMID: 9698493 DOI: 10.1006/gyno.1998.4983] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Embryonal rhabdomyosarcoma of the female lower genital tract is generally regarded as a neoplasm occurring in childhood, but has also been reported in adults. The philosophy of therapy, largely based on data obtained from pediatric patients, has evolved slowly from ultraradical surgery, without adjuvant therapy, to neoadjuvant chemotherapy followed by less radical surgery and postoperative radiation. We report here three cases of lower genital tract rhabdomyosarcoma in postpubertal females. A failure to observe complete responses from any single treatment modality suggests that for embryonal rhabdomyosarcoma in adult and adolescent women a multimodality approach to therapy is essential.
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Stark J, Bull C, Stajevic M, Jothi M, Elliott M, de Leval M. Fate of subpulmonary homograft conduits: determinants of late homograft failure. J Thorac Cardiovasc Surg 1998; 115:506-14; discussion 514-6. [PMID: 9535436 DOI: 10.1016/s0022-5223(98)70312-5] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PATIENTS AND METHODS Between 1971 and 1993, 656 conduits were placed in the subpulmonary position. Patients receiving heterografts or valveless conduits and patients dying within 90 days of insertion were excluded; thus 405 homograft conduits were studied. There were 293 aortic homografts, 94 pulmonary, and 18 of unknown type. The end point of conduit failure was defined by conduit replacement for whatever reason, balloon dilation of the conduit, or death of the patient with the conduit in place. The following factors were analyzed: aortic versus pulmonary homograft, antibiotic preservation versus cryopreservation, ABO and Rh compatibility, type of material used for conduit extension, age at operation, size of the conduit, diagnosis, and reoperations. Conduit number (1 to 405) in the series was included in the multivariable model. RESULTS First conduits and conduits inserted earlier in the series appeared to last longer than second and subsequent conduits and those inserted later in the series (p = 0.001 and 0.003, respectively). Overall survival of conduits at 5, 10, and 15 years was 84% (95% CL, 80% to 88%), 58% (95% CL, 50% to 66%), and 31% (95% CL, 19% to 43%). Corresponding figures for the first conduits were 88% (95% CL, 84% to 92%), 65% (95% CL, 56% to 73%), and 34% (95% CL, 20% to 47%). The longest surviving homograft conduit in our series lasted 22.7 years. Regarded univariately, reoperation (redo worse), order number (recent worse), type of conduit (pulmonary worse than aortic), preservation (cryopreserved worse than antibiotic preserved), and age at operation (older patients worse) were statistically significant. However, in multivariable analysis, including all the above in the model, only reoperation and order number had significant predictive power. When patient survival was considered, patients operated on more recently survived longer despite the fact that their conduits were being replaced earlier. Overall, survival of patients at 5 and 15 years was 95% (95% CL, 93% to 98%) and 85% (95% CL, 77% to 92%), respectively. CONCLUSIONS Pulmonary and aortic homografts, both cryopreserved and preserved in nutrient antibiotic solution, give similar results. All conduits will probably have to be replaced during the lifetime of the patient. In view of the worse performance of replacement conduits, techniques of repair that avoid the use of conduits should be further explored. Despite gradual deterioration of homograft conduits, they remain an important tool in the correction of many complex lesions with excellent 15-year patient survival.
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Sorensen K, Levitt G, Bull C, Chessells J, Sullivan I. Anthracycline dose in childhood acute lymphoblastic leukemia: issues of early survival versus late cardiotoxicity. J Clin Oncol 1997; 15:61-8. [PMID: 8996125 DOI: 10.1200/jco.1997.15.1.61] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Late abnormalities of left ventricular (LV) performance occur in most survivors of childhood acute lymphoblastic leukemia (ALL) treated with moderate anthracycline doses. We studied the prevalence of late cardiotoxicity in patients treated with lower anthracycline doses and related this to survival. PATIENTS AND METHODS Echocardiograms were performed in 50 normal children and 120 relapse-free ALL survivors 6.2 +/- 2.0 years after the end of cumulative daunorubicin doses of 90 mg/m2 (n = 40), 180 mg/m2 (n = 40), or 270 mg/m2 (n = 40) on UKALL X pilot (1982 to 1984) or UKALL X (1985 to 1989) protocols. Age at treatment onset was 4.7 +/- 2.8 years. Cardiac abnormalities were reviewed in light of the UKALL X 5-year disease-free survival rates of 57% (95% confidence interval [CI], 51% to 63%), 61% to 62% (95% CI, 56% to 68%), and 71% (95% CI, 66% to 76%) for the groups that received 90, 180, and 270 mg/m2 of daunorubicin, respectively. RESULTS ALL survivors had reduced LV fractional shortening (FS) compared with normal (32.3% +/- 4.4% v 35.9% +/- 4.2%, P < .005), which was accounted for by increased LV end-systolic stress (49.4 +/- 13.5 v 42.2 +/- 9.1 g/cm2, P < .001), whereas LV contractility independent of loading conditions was normal for the group as a whole. Of 27 patients (23%) with cardiac abnormalities, 25 (21%) had increased end-systolic stress, whereas only two (2%) had reduced contractility. The proportion with cardiac abnormality was similar in the three dose groups. Anthracycline dose, age at treatment, sex, follow-up duration, growth hormone, pubertal status, hemoglobin level, and total WBC count at presentation were not predictive of increased LV end-systolic stress. CONCLUSION There was a reduced incidence and severity of cardiac abnormalities with the lower anthracycline dose protocols (90 to 270 mg/m2) studied compared with previous reports in which subjects had received moderate anthracycline doses (approximately 300 to 550 mg/m2). Cumulative anthracycline dose within the range 90 to 270 mg/m2 did not relate to cardiac abnormalities. This suggests that there may be no safe anthracycline dose to avoid late cardiotoxicity, but reinforces the use of the protocol that affords best survival within the dose range studied.
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Gardiner HM, Dhillon R, Bull C, de Leval MR, Deanfield JE. Prospective study of the incidence and determinants of arrhythmia after total cavopulmonary connection. Circulation 1996; 94:II17-21. [PMID: 8901713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Atrial distension after Fontan operation may predispose to arrhythmia. Modifications aimed at decreasing the extent of right atrial distension (total cavopulmonary connection, TCPC) have been associated with a lower incidence of early arrhythmia, but serial evaluation has not been performed. METHODS AND RESULTS All 119 patients undergoing TCPC between March 1987 and December 1993 were enrolled in a prospective study to evaluate the incidence and determinants of arrhythmia by use of ambulatory ECG (AECG) monitoring. Median age at surgery was 5.9 years (range, 0.5 to 19.7 years), and median follow-up was 4.9 years (2.0 to 8.7 years). AECGs were performed before and after surgery and serially during follow-up. There were 17 early deaths, including 8 among 20 patients who had new arrhythmia documented in the operating in the operating room or intensive care unit. For the 102 patients who survived > 30 days after surgery, the proportion free of new AECG arrhythmia or first arrhythmic symptoms was 93% (CI, 89% to 99%) at 2 years and 78% (CI, 66% to 90%) at 5 years. Actuarial analysis treats occurrence of arrhythmia as permanent; however, most of the arrhythmia during follow-up was transient, so that the proportion of patients without arrhythmia was similar before and during follow-up. To date, there has been only 1 late arrhythmic death. CONCLUSIONS The low prevalence of clinically important arrhythmia during medium-term follow-up supports the TCPC as the preferred option for Fontan surgery.
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