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Biomedical subjects

Ian Bradbury

Publications and source records attributed to Ian Bradbury.

At least 19 recordsLinked to original sources
PubMed2025

Reference genome bias in light of species-specific chromosomal reorganization and translocations.

BACKGROUND: Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements-such as chromosomal inversions-in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling can lead to errors and/or biases in the datasets generated for downstream analyses. RESULTS: Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod (Arctogadus glacialis), polar cod (Boreogadus saida), and Atlantic cod (Gadus morhua) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15-20 × coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts the mapping statistics, including mapping depth and mapping quality, as well as core population genetic estimates, such as heterozygosity levels, nucleotide diversity (π), and cross-species genetic divergence (DXY). Furthermore, using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that some of the verified species-specific inversions are split across multiple genomic regions when mapped against a heterospecific reference. CONCLUSIONS: Inaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.

Animals↗
PubMed2006

Infant-feeding attitudes of expectant mothers in Northern Ireland.

Northern Ireland (NI) has one of the lowest rates of breast-feeding initiation and duration in both the UK and the industrialized world. This study therefore aimed to explore the relationship between infant-feeding attitudes and feeding intention and outcome in expectant mothers within NI. Expectant mothers (n = 200) were recruited from hospital antenatal booking clinics. Each completed a demographic questionnaire and the self-administered Iowa Infant Feeding Attitude Scale (IIFAS). Participants (n = 192) were followed up after birth through the Northern Ireland Maternity System. The IIFAS distinguished between those mothers who intended to breast-feed (higher IIFAS scores) and those who intended to artificially feed (lower IIFAS scores) as well as between those who breast-fed and those who artificially fed on discharge from hospital. The IIFAS was also able to distinguish between mothers in regard to feeding intention and outcome on the basis of education, socio-economic class, income and marital status. This suggests that the IIFAS could prove useful in the targeting and evaluation of intervention to promote breast-feeding.

Adolescent↗
PubMed2006

The relationship between whole-blood serotonin and subjective mood in apparently healthy postmenopausal women.

The aim of this research has been to determine the degree to which biochemical indices of mood reflect subjective mood. Potential relationships between whole-blood (WB) serotonin (5-hydroxytryptamine, 5-HT) levels as determined by the positive and negative affect schedule (PANAS) have been explored in apparently healthy postmenopausal women (n=39). Partial correlations indicated that WB 5-HT was positively associated with positive affect (p=0.03). No association was apparent for negative affect. These findings indicate that WB 5-HT and positive affect are related in postmenopausal women.

Affect↗
PubMed2006

Avoiding model selection bias in small-sample genomic datasets.

MOTIVATION: Genomic datasets generated by high-throughput technologies are typically characterized by a moderate number of samples and a large number of measurements per sample. As a consequence, classification models are commonly compared based on resampling techniques. This investigation discusses the conceptual difficulties involved in comparative classification studies. Conclusions derived from such studies are often optimistically biased, because the apparent differences in performance are usually not controlled in a statistically stringent framework taking into account the adopted sampling strategy. We investigate this problem by means of a comparison of various classifiers in the context of multiclass microarray data. RESULTS: Commonly used accuracy-based performance values, with or without confidence intervals, are inadequate for comparing classifiers for small-sample data. We present a statistical methodology that avoids bias in cross-validated model selection in the context of small-sample scenarios. This methodology is valid for both k-fold cross-validation and repeated random sampling.

Algorithms↗
PubMed2006

Instance-based concept learning from multiclass DNA microarray data.

BACKGROUND: Various statistical and machine learning methods have been successfully applied to the classification of DNA microarray data. Simple instance-based classifiers such as nearest neighbor (NN) approaches perform remarkably well in comparison to more complex models, and are currently experiencing a renaissance in the analysis of data sets from biology and biotechnology. While binary classification of microarray data has been extensively investigated, studies involving multiclass data are rare. The question remains open whether there exists a significant difference in performance between NN approaches and more complex multiclass methods. Comparative studies in this field commonly assess different models based on their classification accuracy only; however, this approach lacks the rigor needed to draw reliable conclusions and is inadequate for testing the null hypothesis of equal performance. Comparing novel classification models to existing approaches requires focusing on the significance of differences in performance. RESULTS: We investigated the performance of instance-based classifiers, including a NN classifier able to assign a degree of class membership to each sample. This model alleviates a major problem of conventional instance-based learners, namely the lack of confidence values for predictions. The model translates the distances to the nearest neighbors into 'confidence scores'; the higher the confidence score, the closer is the considered instance to a pre-defined class. We applied the models to three real gene expression data sets and compared them with state-of-the-art methods for classifying microarray data of multiple classes, assessing performance using a statistical significance test that took into account the data resampling strategy. Simple NN classifiers performed as well as, or significantly better than, their more intricate competitors. CONCLUSION: Given its highly intuitive underlying principles--simplicity, ease-of-use, and robustness--the k-NN classifier complemented by a suitable distance-weighting regime constitutes an excellent alternative to more complex models for multiclass microarray data sets. Instance-based classifiers using weighted distances are not limited to microarray data sets, but are likely to perform competitively in classifications of high-dimensional biological data sets such as those generated by high-throughput mass spectrometry.

Algorithms↗
PubMed2006

Three-stage contingent screening for Down syndrome.

OBJECTIVE: To demonstrate the potential value of three-stage sequential screening for Down syndrome. METHODS: Protocols were considered in which maternal serum pregnancy associated plasma protein-A (PAPP-A) and free beta-human chorionic gonadotropin (hCG) measurements were taken on all women in the first trimester. Those women with very low Down syndrome risks were screened negative at that stage and nuchal translucency (NT) was measured on the remainder and the risk reassessed. Those with very low risk were then screened negative and those with very high risk were offered early diagnostic testing. Those with intermediate risks received second-trimester maternal serum alpha-fetoprotein, free beta-hCG, unconjugated estriol and inhibin-A. Risk was then reassessed and those with high risk were offered diagnosis. Detection rates and false-positive rates were estimated by multivariate Gaussian modelling using Monte-Carlo simulation. RESULTS: The modelling suggests that, with full adherence to a three-stage policy, overall detection rates of nearly 90% and false-positive rates below 2.0% can be achieved. Approximately two-thirds of pregnancies are screened on the basis of first-trimester biochemistry alone, five out of six women complete their screening in the first trimester, and the first-trimester detection rate is over 60%. CONCLUSION: Three-stage contingent sequential screening is potentially highly effective for Down syndrome screening. The acceptability of this protocol and its performance in practice, should be tested in prospective studies.

Algorithms↗
PubMed2006

Electrical stimulation in cerebral palsy: a randomized controlled trial.

A randomized placebo-controlled trial was carried out to investigate the efficacy of neuromuscular electrical stimulation (NMES) and threshold electrical stimulation (TES) in strengthening the quadriceps muscles of both legs in children with cerebral palsy (CP). Sixty children (38 males, 22 females; mean age 11y [SD 3y 6mo]; age range 5-16y) were randomized to one of the following groups: NMES (n=18), TES (n=20), or placebo (n=22). Clinical presentations were diplegia (n=55), quadriplegia (n=1), dystonia (n=1), ataxia (n=1), and non-classifiable CP (n=2). Thirty-four children walked unaided, 17 used posterior walkers, six used crutches, and the remaining three used sticks for mobility. Peak torque of the left and right quadriceps muscles, gross motor function, and impact of disability were assessed at baseline and end of treatment (16wks), and at a 6-week follow-up visit. No statistically significant difference was demonstrated between NMES or TES versus placebo for strength or function. Statistically significant differences were observed between NMES and TES versus placebo for impact of disability at the end of treatment, but only between TES and placebo at the 6-week follow-up. In conclusion, further evidence is required to show whether NMES and/or TES may be useful as an adjunct to therapy in ambulatory children with diplegia who find resistive strengthening programmes difficult.

Adolescent↗
PubMed2006

Joint project of the International Network of Agencies for Health Technology Assessment--Part 2: Managing the diffusion of positron emission tomography with health technology assessment.

OBJECTIVES: Since 1997, members of the International Network of Agencies for Health Technology Assessment (INAHTA) have collaborated on a Joint Project to track the diffusion, evaluation, and clinical policy of positron emission tomography (PET). Part 2 of this updated Joint Project report summarizes HTA-based strategies for directing the clinical use of PET and a discussion on the value of HTA in managing the diffusion of high cost diagnostic technologies, which were presented at an INAHTA-sponsored workshop at the Health Technology Assessment International Annual Meeting in 2004 on strategies for managing high cost diagnostic technologies. METHODS: A summary of the workshop proceedings is presented. CONCLUSIONS: Sharing assessment work, universal agreement in assessment conclusions, stakeholder input, and modeling techniques help manage the uncertainty in the evidence base while targeting clinical use of PET toward the most promising indications. Emphasis on HTA findings, linkage between financing of clinical PET and outcome evaluation, and targeted dissemination of scientific findings empower providers to reduce unnecessary utilization and contain costs within a quality improvement framework. Above all, a trustworthy source of HTA information and a process that is conducive to using scientific evidence as the basis for decision making are essential for managing the diffusion of complex and costly diagnostic technologies in patient care.

Capital Financing↗
PubMed2006

The rate of intestinal absorption of natural food folates is not related to the extent of folate conjugation.

BACKGROUND: Evidence is conflicting as to whether the bioavailability of food folates is influenced by the extent of their conjugation. OBJECTIVE: The objective was to compare the bioavailability of 3 representative food folate sources with various degrees of glutamylation-ie, egg yolk, spinach, and yeast, whose polyglutamyl folate content measured 0%, 50%, and 100%, respectively. DESIGN: In a randomized crossover trial, 13 male subjects, after a prestudy folate saturation procedure, received in random order either placebo or 500 mug total folate, which was provided as concentrated freeze-dried extract removed from the normal food matrix of egg yolk, spinach, or yeast. Blood samples (n = 10) were collected before and up to 10 h after treatments, which were administered at weekly intervals. RESULTS: A significant increase from baseline plasma folate concentrations was observed by 0.5 h after treatment with egg yolk folate or spinach folate and by 1 h after treatment with yeast folate, and the concentrations remained significantly elevated for 3-5 h; no plasma folate response was observed after placebo treatment. The overall responses, calculated as plasma folate area under the curve (AUC) for egg yolk, spinach, and yeast folate, were 122.6 +/- 23.6, 136.2 +/- 21.4, and 102.5 +/- 21.1 nmol . h/L, respectively. No significant differences in AUC were seen between monoglutamyl (egg yolk) folate and either of the polyglutamate-containing folates examined. CONCLUSION: These results suggest that the ratio of monoglutamate to polyglutamate in natural folates is not a factor that limits the extent of intestinal absorption of food folate.

Administration, Oral↗
PubMed2006

Whole blood analysis of phagocytosis, apoptosis, cytokine production, and leukocyte subsets in healthy older men and women: the ZENITH study.

Few studies to date have examined age-related changes in markers of immune status in healthy older individuals. The immune status of 93 healthy individuals aged 55-70 years was assessed by two- and three-color flow cytometry and biochemical analysis. There were significant age effects (p <or=.05) on monocyte phagocytic activity and cluster of differentiation (CD) 3/human leukocyte antigen-D-related (HLA-DR) late-activated T lymphocytes (% expression). There was a significant (p <or= 0.1) Age x Sex interaction in absolute counts (x 10(9)/L) of CD3/CD8 total cytotoxic T lymphocytes (CTL), the CD4 T- helper to CD8 CTL ratio, the CD3/CD4/CD45RA naïve T helper to CD3/CD4/CD45RO memory T helper lymphocyte ratio, and interleukin (IL)-1beta (% expression) by activated monocytes. The study shows that alterations in markers of immune status occur between 55 and 70 years, and provides reference values for the lymphocyte measures in healthy men and postmenopausal women in this age group. The study further highlights the need for sex-specific reference ranges for such markers.

Aged↗
PubMed2005

Associations between whole-blood serotonin and subjective mood in healthy male volunteers.

Little is known regarding the relationship between how mood is experienced and biochemical factors. This research has explored potential relationships between whole-blood serotonin (5-HT) and subjective mood, measured using the Positive and Negative Affect Schedule (PANAS), in healthy males (n=23). Univariate linear regression analysis indicated that 5-HT levels were positively related to positive affect (P=0.002) but not negative affect. Whole-blood 5-HT concentrations therefore appear to predict mood in healthy males. More research using larger samples and including females is needed to explore further associations between biomarkers and subjective measures of mood.

Affect↗
PubMed2005

Effect of folic acid supplementation on mood and serotonin response in healthy males.

Evidence suggests that low folate status may be detrimental to mood and associated with depleted cerebrospinal fluid levels of the neurotransmitter serotonin (5-hydroxytryptamine; 5-HT). A placebo-controlled trial was carried out to determine the effect of folic acid supplementation (100 microg for 6 weeks followed by 200 microg for a further 6 weeks) upon subjective mood (Positive and Negative Affect Schedule) and biochemical markers of mood (5-HT) in healthy males (n 23). Blood samples were obtained at baseline (week 0) and during the intervention at week 6 and week 12. Subjective mood assessments were obtained at week 0 and week 12. The results showed an increase in serum and erythrocyte folate concentrations (P=0.02 and P=0.003, respectively) and a corresponding decrease in plasma homocysteine (P=0.015) in response to the folic acid intervention. Neither subjective mood nor 5-HT levels, however, were significantly altered in response to the change in folate status. Folic acid given at physiological doses did not appear to improve the mood of healthy folate-replete individuals over a 12-week period. Further research is needed to address the effect of folic acid supplementation or of longer duration or increased dose, particularly in the face of sub-optimal folate status.

Adult↗
PubMed2005

Survival trees for analyzing clinical outcome in lung adenocarcinomas based on gene expression profiles: identification of neogenin and diacylglycerol kinase alpha expression as critical factors.

We present survival trees as an exploratory tool for revealing new insights into gene expression profiles in combination with clinical patient data. Survival trees partition the patient data studied into groups with similar survival outcomes and identify characteristic genetic profiles within these groups. We demonstrate the application of survival trees in a study involving the expression profiles of 3,588 genes in 211 lung adenocarcinoma patients. The survival tree identified a group of early-stage cancer patients with relatively low survival rates and another group of advanced-stage patients with remarkably good survival outcome. For both groups, the tree identified characteristic expression profiles of genes that might play a role in cancerogenesis and disease progression, notably the genes for the netrin receptor neogenin and the Ras/Rho kinase modulator diacylglycerol kinase alpha.

Adenocarcinoma↗
PubMed2005

Repeated measures screening for Down's Syndrome.

OBJECTIVE: To demonstrate the potential value of screening for Down's Syndrome using highly correlated repeated measures of serum markers taken in the first and second trimesters of pregnancy. DESIGN: A Monte Carlo simulation study. POPULATION: Detection rates and false positive rates relating to the maternal age distribution of England and Wales for the period 1996 to 1998 were obtained using marker distributions from the SURUSS study. RESULTS: Screening using first trimester nuchal translucency and repeated measures of uE3 and PAPP-A in the first and second trimester has an estimated false positive rate of 0.3% for an 85% detection rate. This should be compared with the integrated test with an estimated false positive rate of 1.2% for the same detection rate. CONCLUSIONS: The performance of repeated measures screening tests, and their acceptability to women, should be assessed in further prospective studies.

Biomarkers↗
PubMed2004

Homocysteine is lower in the third trimester of pregnancy in women with enhanced folate status from continued folic acid supplementation.

BACKGROUND: In many countries, current recommendations are that women take a daily 400-mug folic acid supplement from before conception until the end of the 12th week of gestation for the prevention of neural tube defects. Low folate status is associated with an increased concentration of plasma total homocysteine (tHcy), a risk factor associated with pregnancy complications such as preeclampsia. METHODS: In a longitudinal study, we determined tHcy and corresponding folate status in 101 pregnant women at 12, 20, and 35 weeks of gestation, in 35 nonpregnant controls sampled concurrently, and in a subgroup (n = 21 pregnant women and 19 nonpregnant controls) at 3 days postpartum. RESULTS: Plasma tHcy was significantly lower throughout pregnancy compared with nonpregnant controls, with values lowest in the second trimester before increasing toward nonpregnant values in the third trimester. Importantly, mean tHcy concentrations were lower in pregnant women taking folic acid supplements than in those not, an effect that reached significance in the third trimester (5.45 vs 7.40 micromol/L; P <0.05). During the third trimester, tHcy concentrations were significantly higher in pregnant women with a history of miscarriage than in women with no previous history (8.15 vs 6.38 micromol/L; P <0.01). CONCLUSIONS: This is the first longitudinal study to show that homocysteine concentrations increase in late pregnancy toward nonpregnant values; an increase that can be limited by enhancing folate status through continued folic acid supplementation. These results indicate a potential role for continued folic acid supplementation in reducing pregnancy complications associated with hyperhomocysteinemia.

Adolescent↗