A comparison of inflammatory myopathies at whole-body turbo STIR MRI.
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Female↗
Biomedical subjects
P Cunningham
Publications and source records attributed to P Cunningham.
A comparison of fast MRI of hips with and without parallel imaging using SENSE.
This study was undertaken to qualitatively and quantitatively compare fast MRI of hips with and without parallel imaging using SENSE (sensitivity encoding). 27 patients underwent MRI of the hips with coronal T1 turbo spin echo (TSE) (repetition time (TR) 500 ms, effective echo time (TEeff) 15 ms, Turbo Factor 4), coronal IR-TSE (TR 2000 ms, TEeff 30 ms, inversion time (TI) 160 ms, Turbo Factor 20) and axial T2 TSE (TR 3000 ms, TEeff 80 ms, Turbo Factor 20) weighted images acquired with and without SENSE with a reduction factor of 2. Conventional imaging was performed in 8 min and 36 s. Images acquired with SENSE were acquired in 5 min and 31 s without a discernible reduction in image quality or a significant quantitative reduction in image signal to noise ratio, contrast to noise ratio or edge enhancement.
Adult↗
Antibodies to prion and Acinetobacter peptide sequences in bovine spongiform encephalopathy.
An amino acid sequence homology has been identified between the bovine prion sequence (RPVDQ) and the Acinetobacter calcoaceticus enzyme, uridine-diphosphate-N-acetyl glucosamine-1-carboxy-vinyl-transferase which also contains (RPVDQ). Class-specific IgA, IgG and IgM antibodies against synthetic peptides containing the structurally related sequences present in bovine prion and A. calcoaceticus were measured in 189 bovine spongiform encephalopathy (BSE) positive cattle, 127 BSE negative cattle and 87 healthy control animals using an ELISA technique. Class-specific IgA, IgG and IgM antibodies against the structurally related synthetic peptides were significantly elevated in BSE positive cattle when compared to BSE negative cattle (P < 0.001) and healthy control animals (P < 0.001). These autoantibodies may have a role in the pathogenesis of BSE.
Acinetobacter calcoaceticus↗
Brain death and organ donation: an audit in the Irish National Transplantation and Neurosurgical Centre.
We set out to identify the reasons why potential organ donors (PODs) fail to become actual donors and the causes of under-utilization of organs offered for donation. We audited 354 patients who died in the intensive Care Unit over 18 months. Of 155 PODs, 78 (50%) did not undergo brain stem testing (BST) because of (i) unavoidable death from non-CNS causes before BST (n = 50), (ii) treatment withdrawal without BST (n = 17) and (iii) preconditions for BST were not fulfilled (n = 11). Brain death was confirmed in 75 patients. Relatives refused consent for donation in 25 patients organ donation was not discussed with the family in 6, and medical contraindications to organ donation prevented donation in 5. Thirty seven (24% of all PODs) became organ donors who provided a total of 216 organ. All donated kidneys were utilized but unsuitability and logistic issues prevented utilization of 20% and 13% of all donated organs respectively. The commonest reason for failure to utilise potential organ donors was failure to perform BST. In most cases this was because BSTs were not possible but more aggressive management of and the routine performance of BST in all PODs could increase the number of donors. Not approaching relatives to ask consent for organ donation and a high rate of refusal by relatives also led to loss of organ donors.
Brain Death↗
alpha- and beta-A2Hg3M2S8 (A = K, Rb; M = Ge, Sn): polar quaternary chalcogenides with strong nonlinear optical response.
The closely related phases alpha- and beta-A(2)Hg(3)M(2)S(8) (A = K, Rb; M = Ge, Sn) have been discovered using the alkali polychalcogenide flux method and are described in detail. They present new structure types with a polar noncentrosymmetric crystallographic motif and strong nonlinear second-harmonic generation (SHG) properties. The alpha-allotropic form crystallizes in the orthorhombic space group Aba2 with a = 19.082(2) A, b = 9.551(1) A, c = 8.2871(8) A for the K(2)Hg(3)Ge(2)S(8) analogue, and a = 19.563(2) A, b = 9.853(1) A, c = 8.467(1) A for the K(2)Hg(3)Sn(2)S(8) analogue. The beta-form crystallizes in the monoclinic space group C2 with a = 9.5948(7) A, b = 8.3608(6) A, c = 9.6638(7) A, beta = 94.637 degrees for the K(2)Hg(3)Ge(2)S(8) analogue. The thermal stability and optical and spectroscopic properties of these compounds are reported along with detailed solubility and crystal growth studies of the alpha-Kappa(2)Hg(3)Ge(2)S(8) in K(2)S(8) flux. These materials are wide gap semiconductors with band gaps at approximately 2.40 and approximately 2.64 eV for the Sn and Ge analogues, respectively. Below the band gap the materials exhibit a very wide transmission range to electromagnetic radiation up to approximately 14 microm. alpha-K(2)Hg(3)Ge(2)S(8) shows anisotropic thermal expansion coefficients. SHG measurements, performed with a direct phase-matched method, showed very high nonlinear coefficient d(eff) for beta-K(2)Hg(3)Ge(2)S(8) approaching 20 pm/V. Crystals of K(2)Hg(3)Ge(2)S(8) are robust to air exposure and have a high laser-damage threshold.
Journal Article↗
The problem of bias in training data in regression problems in medical decision support.
This paper describes a bias problem encountered in a machine learning approach to outcome prediction in anticoagulant drug therapy. The outcome to be predicted is a measure of the clotting time for the patient; this measure is continuous and so the prediction task is a regression problem. Artificial neural networks (ANNs) are a powerful mechanism for learning to predict such outcomes from training data. However, experiments have shown that an ANN is biased towards values more commonly occurring in the training data and is thus, less likely to be correct in predicting extreme values. This issue of bias in training data in regression problems is similar to the associated problem with minority classes in classification. However, this bias issue in classification is well documented and is an on-going area of research. In this paper, we consider stratified sampling and boosting as solutions to this bias problem and evaluate them on this outcome prediction problem and on two other datasets. Both approaches produce some improvements with boosting showing the most promise.
Bias↗
Novel deletion of HIV type 1 reverse transcriptase residue 69 conferring selective high-level resistance to nevirapine.
A novel deletion of residue 69 of the HIV-1 reverse transcriptase (RT) gene was detected in combination with mutations V75I/V and F77L/F in a patient with partial virological response to several antiretroviral drug regimens, including stavudine (D4T), didanosine (DDI), lamivudine (3TC), saquinavir (SQV), and nevirapine (NVP). Longitudinal analysis of samples revealed that this deletion emerged upon reinitiation DDI/D4T therapy following a toxicity-induced short discontinuation of all antiretrovirals. Analysis of the resistance phenotype showed a greater than 62-fold increase of the IC50 of NVP, but no significant change in sensitivity to other single nonnucleoside reverse transcriptase inhibitors (NNRTIs). The mutated virus showed only a moderately reduced sensitivity to DDI (6.7-fold) and D4T (4.8 fold). In a subsequent sample 3 months later additional RT mutations were found, including A62V, Y188L, and Q151M, conferring high-level cross-resistance to multiple nucleoside analogs. Our findings provide evidence that the deletion of RT residue 69 selectively confers high-level NVP resistance.
Adult↗
Genetic evidence for Near-Eastern origins of European cattle.
The limited ranges of the wild progenitors of many of the primary European domestic species point to their origins further east in Anatolia or the fertile crescent. The wild ox (Bos primigenius), however, ranged widely and it is unknown whether it was domesticated within Europe as one feature of a local contribution to the farming economy. Here we examine mitochondrial DNA control-region sequence variation from 392 extant animals sampled from Europe, Africa and the Near East, and compare this with data from four extinct British wild oxen. The ancient sequences cluster tightly in a phylogenetic analysis and are clearly distinct from modern cattle. Network analysis of modern Bos taurus identifies four star-like clusters of haplotypes, with intra-cluster diversities that approximate to that expected from the time depth of domestic history. Notably, one of these clusters predominates in Europe and is one of three encountered at substantial frequency in the Near East. In contrast, African diversity is almost exclusively composed of a separate haplogroup, which is encountered only rarely elsewhere. These data provide strong support for a derived Near-Eastern origin for European cattle.
Africa↗
Impact of HIV type 1 protease, reverse transcriptase, cleavage site, and p6 mutations on the virological response to quadruple therapy with saquinavir, ritonavir, and two nucleoside analogs.
Genotype alterations of HIV-1 protease, reverse transcriptase, cleavage sites p7/p1 and p1/p6, as well as p6(gag) and transframe protein p6* were studied in an observational cohort of 42 individuals who received antiretroviral therapy consisting of saquinavir, ritonavir, and two nucleoside analogs. In a multivariate logistic regression analysis, the prior protease inhibitor experience (odds ratio, 6.20; 95% CI, 1.22-31.38) and the presence of primary protease mutations (odds ratio, 9.99; 95% CI, 1.05-94.72) were independently associated with virological failure. Moreover, a trend was observed in that individuals with N-terminal amino acid insertions in the proline-rich motif of the p6(gag) protein were less likely to experience virological failure (OR, 0.17; 95% CI, 0.02-1.35; p = 0.09). In contrast, the presence of secondary protease, reverse transcriptase, or cleavage site mutations was not independently associated with treatment failure. However, mutations at cleavage site p7/p1 (p = 0.01) and C-terminal p6* mutations (p = 0.02) were both associated with primary protease mutations. In conclusion, the presence of primary protease mutations was the most important predictor of the subsequent virological response. Moreover, there is some evidence that insertions in the proline-rich area of the p6(gag) protein may affect the virological response. The relationship between mutations of cleavage sites or C-terminal p6* residues and protease mutations suggests that these alterations may serve a compensatory role, increasing viral fitness.
Adult↗
The psychological effects of Hurricane Andrew on ethnic minority and Caucasian children and adolescents: a case study.
The impact of Hurricane Andrew on 212 African American, Caucasian, and Hispanic elementary and middle school children was examined at 6 months postdisaster. Using self-report instruments, this case study examined the predictive utility of several hypothesized mediators of children's reactions to disaster. Results showed higher levels of intrusive symptomatology for girls and for elementary school children as compared with their middle school counterparts. No differences were found with reference to race. The lack of findings concerning race is addressed, as well as implications for future studies.
Adolescent↗
Antibody responses to Acinetobacter spp. and Pseudomonas aeruginosa in multiple sclerosis: prospects for diagnosis using the myelin-acinetobacter-neurofilament antibody index.
Antibody responses to Acinetobacter (five strains), Pseudomonas aeruginosa, Escherichia coli, myelin basic protein (MBP), and neurofilaments were measured in sera from 26 multiple sclerosis (MS) patients, 20 patients with cerebrovascular accidents (CVA), 10 patients with viral encephalitis, and 25 healthy blood donors. In MS patients, elevated levels of antibodies against all strains of Acinetobacter tested were present, as well as antibodies against P. aeruginosa, MBP, and neurofilaments, but not antibodies to E. coli, compared to the CVA group and controls. The myelin-Acinetobacter-neurofilament antibody index appears to distinguish MS patients from patients with CVAs or healthy controls. The relevance of such antibodies to the neuropathology of MS requires further evaluation.
Acinetobacter↗
Rapid restoration of CD4 T cell subsets in subjects receiving antiretroviral therapy during primary HIV-1 infection.
OBJECTIVE: To compare the effect of highly active antiretroviral therapy on immune reconstitution in subjects with acute and chronic HIV-1 infection. DESIGN: Prospective study including 58 treatment-naive subjects who commenced indinavir or nelfinavir and two nucleosides during primary (PHI; n = 28) or chronic HIV-1 infection (CHI; n = 30). METHODS: Naive (CD45RA+ 62L+), memory (CD45RA-) and activated (CD38+ HLA-DR+) T cell subsets were quantified at 1-2 monthly time intervals using 4-colour flow cytometry. RESULTS: At 1 year, HIV-1 RNA declined in both cohorts to undetectable levels (< 50 copies/ml), while median CD4 lymphocyte count increased from 470 to 758 x 10(6) cells/l in PHI and from 204 to 310 x 10(6) cells/l in CHI, reaching > 500 x 10(6) cells/l in 93% of PHI, but only in 37% of CHI subjects (P < 0.001). Naive CD4 lymphocytes increased from 106 to 176 x 10(6) cells/l in PHI and from 41 to 44 x 10(6) cells/l in CHI (PHI versus CHI at 12 months: P = 0.003), while memory cells rose from 368 to 573 x 10(6) cells/l in PHI and from 148 to 223 x 10(6) cells/l in CHI (P < 0.001). Early increases (< 3 months) of CD4 lymphocytes were larger in subjects with PHI, consisting of naive CD45RA+ CD62L+ as well as memory CD45RA- CD62L+ cells (P = 0.001). CD4 activation declined from 5 to 2% in PHI and from 13 to 6% in CHI (P = 0.001), while CD8 cell activation was reduced from 33 to 15% in PHI and from 42 to 19% in CHI (P = 0.02). CONCLUSION: Immune reconstitution was more complete, occurred earlier and comprised both naive and memory CD4 T lymphocytes in subjects who commenced antiretroviral therapy during primary HIV-1 infection.
Acute Disease↗
Stability problems with artificial neural networks and the ensemble solution.
Artificial neural networks (ANNs) are very popular as classification or regression mechanisms in medical decision support systems despite the fact that they are unstable predictors. This instability means that small changes in the training data used to build the model (i.e. train the ANN) may result in very different models. A central implication of this is that different sets of training data may produce models with very different generalisation accuracies. In this paper, we show in detail how this can happen in a prediction system for use in in-vitro fertilisation. We argue that claims for the generalisation performance of ANNs used in such a scenario should only be based on k-fold cross-validation tests. We also show how the accuracy of such a predictor can be improved by aggregating the output of several predictors.
Algorithms↗
Emergency medicine and "acute" general practice: comparing apples with oranges.
Emergency Departments (EDs) operate at the interface between the inpatient and ambulatory sectors of health care. Because of shared funding between the Commonwealth and States for ambulatory care, there has been intense focus on the ED patient population, and the potential to shift the locus of care for non-inpatients. One of the frequently cited models for the provision of after-hours GP services is the Balmain General Practice Casualty (GPC). This paper analyses the GPC model, looking in detail at casemix, clinical quality, waiting times and cost-effectiveness. It is argued that the services provided and the casemix of the patient population of GPC and EDs are distinctly different. Cost-effectiveness for GPC has not been objectively established. Health service planning should recognise the distinct but complementary roles of general practice and emergency medicine. Evaluation of alternative models of service provision should critically examine the available evidence, and comparisons should be based on a precise analysis of equivalent services.
Cost-Benefit Analysis↗
Tuning diversity in bagged ensembles.
In this paper, we investigate how the level of diversity amongst individual neural networks in a bagged ensemble can significantly influence overall ensemble generalization performance. We propose a new technique that tunes this diversity so that ensemble generalization performance is optimized and evaluate its performance on benchmark regression data-sets.
Algorithms↗
Impact of early HIV-1 RNA and T-lymphocyte dynamics during primary HIV-1 infection on the subsequent course of HIV-1 RNA levels and CD4+ T-lymphocyte counts in the first year of HIV-1 infection. Sydney Primary HIV Infection Study Group.
Plasma HIV-1 RNA and CD4+ T-cell counts after HIV-1 seroconversion are important independent markers that predict the clinical course of HIV-1 infection. The prognostic significance of these parameters during primary HIV-1 infection, however, remains largely unknown. In a cohort of 53 male study subjects (age, 33 +/- 7 years), who consecutively presented with primary HIV-1 infection, we analyzed the relationship between early plasma HIV-1 RNA, CD4+ and CD8+ T-cell counts, beta2-microglobulin, and p24-antigen levels determined in the first 3 months and subsequent plasma HIV-1 RNA levels and CD4+ T-cell counts 6 to 12 months after onset of primary symptoms. Peak, nadir, and median HIV-1 RNA levels in the first 30 days were already significantly associated with HIV-1 RNA levels at 6 to 12 months (p = .02, p < .0001, and p = .01, respectively). Similarly, early nadir and median CD4+ T-lymphocyte counts in the first 30 days showed a significant relationship with CD4+ T-cell counts at 6 to 12 months (p = .009 and p = .0008, respectively). Study subjects with an early decline of CD4+ counts to <500 cells/microl had an eightfold higher risk that CD4+ counts were <500 cells/microl at 1 year. Of all evaluated virologic parameters, only nadir HIV-1 RNA at 76 days predicted CD4+ counts at 6 to 12 months (p = .006). Early HIV-1 RNA levels and CD4+ counts are already associated with the time course of those parameters 6 to 12 months after onset of symptoms. Nadir viral load was the strongest predictor of HIV-1 RNA levels as well as of CD4+ counts at 6 to 12 months. An early decline of CD4+ T lymphocytes may be a useful clinical prognostic marker for rapid disease progression.
Adult↗
Correolide and derivatives are novel immunosuppressants blocking the lymphocyte Kv1.3 potassium channels.
The voltage-gated potassium channel, Kv1.3, is specifically expressed on human lymphocytes, where it controls membrane potential and calcium influx. Blockade of Kv1.3 channels by margatoxin was previously shown to prevent T cell activation and attenuate immune responses in vivo. In the present study, a triterpene natural product, correolide, was found to block Kv1.3 channels in human and miniswine T cells by electrophysiological characterization. T cell activation events, such as anti-CD3-induced calcium elevation, IL-2 production, and proliferation were inhibited by correolide in a dose-dependent manner. More potent analogs were evaluated for pharmacokinetic profiles and subsequently tested in a delayed-type hypersensitivity (DTH) response to tuberculin in the miniswine. Two compounds were dosed orally, iv, or im, and both compounds suppressed DTH responses, demonstrating that small molecule blockers of Kv1.3 channels can act as immunosuppressive agents in vivo. These studies establish correolide and its derivatives as novel immunosuppressants.
Animals↗
Phenotypic analysis of CD8+ T lymphocytes in a cohort of HIV type 1-infected patients treated with saquinavir, ritonavir, and two nucleoside analogs for 1 year, and association with plasma HIV type 1 RNA.
The phenotype of circulating CD8+ T lymphocytes and its association with plasma HIV-1 RNA were analyzed in 34 HIV-1-infected subjects, who were treated with saquinavir, ritonavir, and two nucleoside analogs (HAART) for 1 year. Four-color flow cytometry was applied to measure the expression of cell surface antigens CD38, HLA-DR, CD45RA, CD28, and CD62L on CD8+ T lymphocytes. The results were compared with data on 35 HIV-1-seronegative subjects, 18 untreated asymptomatic HIV-1-seropositive individuals, and 24 HIV-1-infected subjects receiving reverse transcriptase inhibitors (RTIs). Subjects receiving HAART showed a significantly elevated number and percentage of CD38- and HLA-DR-positive and CD28-negative CD8+ T lymphocytes as well as a lower percentage of naive (CD45RA+62L+) CD8+ T lymphocytes compared with HIV-1-uninfected controls. Even subjects with undetectable plasma HIV-1 RNA showed a persistent elevation of activated CD8+ T lymphocytes. However, fewer activated CD8+ T lymphocytes were observed in subjects receiving HAART than in untreated individuals and subjects administered RTIs. In individuals receiving RTIs, CD8+ cell activation was not significantly reduced compared with untreated subjects. Of all evaluated activation markers, the percentage of CD8+ T lymphocytes expressing CD38 and the combination of CD38 and HLA-DR showed the best correlation with plasma HIV-1 RNA. The persistence of CD8+ T lymphocyte activation in subjects receiving HAART strongly suggests ongoing viral activity, even in subjects with undetectable plasma HIV-1 RNA. A complete normalization of immunologic changes of CD8+ T lymphocytes would therefore require a more potent drug regimen or a longer duration of therapy.
ADP-ribosyl Cyclase↗