Evidence-based guidelines and decision support services: a discussion and evaluation in triple assessment of suspected breast cancer

Widespread health service goals to improve consistency and safety in patient care have prompted considerable investment in the development of evidence-based clinical guidelines. Computerised decision support (CDS) systems have been proposed as a means to implement guidelines in practice. This paper discusses the general concept in oncology and presents an evaluation of a CDS system to support triple assessment (TA) in breast cancer care. Balanced-block crossover experiment and questionnaire study. One stop clinic for symptomatic breast patients. Twenty-four practising breast clinicians from United Kingdom National Health Service hospitals. A web-based CDS system. Clinicians made significantly more deviations from guideline recommendations without decision support (60 out of 120 errors without CDS; 16 out of 120 errors with CDS, P<0.001). Ignoring minor deviations, 16 potentially critical errors arose in the no-decision-support arm of the trial compared with just one (P=0.001) when decision support was available. Opinions of participating clinicians towards the CDS tool became more positive after they had used it (P<0.025). The use of decision support capabilities in TA may yield significant measurable benefits for quality and safety of patient care. This is an important option for improving compliance with evidence-based practice guidelines

Fast MCMC sampling for hidden markov models to determine copy number variations

<p>Abstract</p> <p>Background</p> <p>Hidden Markov Models (HMM) are often used for analyzing Comparative Genomic Hybridization (CGH) data to identify chromosomal aberrations or copy number variations by segmenting observation sequences. For efficiency reasons the parameters of a HMM are often estimated with maximum likelihood and a segmentation is obtained with the Viterbi algorithm. This introduces considerable uncertainty in the segmentation, which can be avoided with Bayesian approaches integrating out parameters using Markov Chain Monte Carlo (MCMC) sampling. While the advantages of Bayesian approaches have been clearly demonstrated, the likelihood based approaches are still preferred in practice for their lower running times; datasets coming from high-density arrays and next generation sequencing amplify these problems.</p> <p>Results</p> <p>We propose an approximate sampling technique, inspired by compression of discrete sequences in HMM computations and by <it>kd</it>-trees to leverage spatial relations between data points in typical data sets, to speed up the MCMC sampling.</p> <p>Conclusions</p> <p>We test our approximate sampling method on simulated and biological ArrayCGH datasets and high-density SNP arrays, and demonstrate a speed-up of 10 to 60 respectively 90 while achieving competitive results with the state-of-the art Bayesian approaches.</p> <p><it>Availability: </it>An implementation of our method will be made available as part of the open source GHMM library from <url>http://ghmm.org</url>.</p

Reduced Lentivirus Susceptibility in Sheep with TMEM154 Mutations

Visna/Maedi, or ovine progressive pneumonia (OPP) as it is known in the United States, is an incurable slow-acting disease of sheep caused by persistent lentivirus infection. This disease affects multiple tissues, including those of the respiratory and central nervous systems. Our aim was to identify ovine genetic risk factors for lentivirus infection. Sixty-nine matched pairs of infected cases and uninfected controls were identified among 736 naturally exposed sheep older than five years of age. These pairs were used in a genome-wide association study with 50,614 markers. A single SNP was identified in the ovine transmembrane protein (TMEM154) that exceeded genome-wide significance (unadjusted p-value 3×10−9). Sanger sequencing of the ovine TMEM154 coding region identified six missense and two frameshift deletion mutations in the predicted signal peptide and extracellular domain. Two TMEM154 haplotypes encoding glutamate (E) at position 35 were associated with infection while a third haplotype with lysine (K) at position 35 was not. Haplotypes encoding full-length E35 isoforms were analyzed together as genetic risk factors in a multi-breed, matched case-control design, with 61 pairs of 4-year-old ewes. The odds of infection for ewes with one copy of a full-length TMEM154 E35 allele were 28 times greater than the odds for those without (p-value<0.0001, 95% CI 5–1,100). In a combined analysis of nine cohorts with 2,705 sheep from Nebraska, Idaho, and Iowa, the relative risk of infection was 2.85 times greater for sheep with a full-length TMEM154 E35 allele (p-value<0.0001, 95% CI 2.36–3.43). Although rare, some sheep were homozygous for TMEM154 deletion mutations and remained uninfected despite a lifetime of significant exposure. Together, these findings indicate that TMEM154 may play a central role in ovine lentivirus infection and removing sheep with the most susceptible genotypes may help eradicate OPP and protect flocks from reinfection

Cell cycle-independent phospho-regulation of Fkh2 during hyphal growth regulates Candida albicans pathogenesis.

The opportunistic human fungal pathogen, Candida albicans, undergoes morphological and transcriptional adaptation in the switch from commensalism to pathogenicity. Although previous gene-knockout studies have identified many factors involved in this transformation, it remains unclear how these factors are regulated to coordinate the switch. Investigating morphogenetic control by post-translational phosphorylation has generated important regulatory insights into this process, especially focusing on coordinated control by the cyclin-dependent kinase Cdc28. Here we have identified the Fkh2 transcription factor as a regulatory target of both Cdc28 and the cell wall biosynthesis kinase Cbk1, in a role distinct from its conserved function in cell cycle progression. In stationary phase yeast cells 2D gel electrophoresis shows that there is a diverse pool of Fkh2 phospho-isoforms. For a short window on hyphal induction, far before START in the cell cycle, the phosphorylation profile is transformed before reverting to the yeast profile. This transformation does not occur when stationary phase cells are reinoculated into fresh medium supporting yeast growth. Mass spectrometry and mutational analyses identified residues phosphorylated by Cdc28 and Cbk1. Substitution of these residues with non-phosphorylatable alanine altered the yeast phosphorylation profile and abrogated the characteristic transformation to the hyphal profile. Transcript profiling of the phosphorylation site mutant revealed that the hyphal phosphorylation profile is required for the expression of genes involved in pathogenesis, host interaction and biofilm formation. We confirmed that these changes in gene expression resulted in corresponding defects in pathogenic processes. Furthermore, we identified that Fkh2 interacts with the chromatin modifier Pob3 in a phosphorylation-dependent manner, thereby providing a possible mechanism by which the phosphorylation of Fkh2 regulates its specificity. Thus, we have discovered a novel cell cycle-independent phospho-regulatory event that subverts a key component of the cell cycle machinery to a role in the switch from commensalism to pathogenicity

Reduced short-term thermic effects of a meal in obese adolescent girls

Post-meal energy expenditure (TEM) was compared for 14 healthy obese (body fat = 45.3%, body mass index, BMI = 35.9 kg m −2 ) and 9 healthy nonobese (body fat = 20.7010, BMI = 17.8 kg M −2 ) adolescent girls. The test meal for both groups was a standard 3348.8-kJ, 0.473-1 chocolate milkshake of 15010 protein (casein), 40% fat (polyunsaturated/saturated ratio = 0.05; 75 mg cholesterol) and 45010 carbohydrate (lactose and sucrose). Glucose, insulin and resting energy expenditure (RMR) were measured at rest prior to meal consumption and 20, 40, 60, 90, and 120 min after the meal. Cumulative net TEM was calculated as the integrated area under the TEM curve with RMR as baseline. Reliability was assessed by retesting 4 subjects, and a placebo effect was tested by administering a flavored energy-free drink. Results indicated high reliability and no placebo effect. The meal resulted in a greater rise in insulin and glucose for the obese compared to the nonobese subjects ( P ⩽;0.05), and a significant TEM for both groups ( P ⩽0.05). The cumulative TEM (W kg −1 ) was 61.9% greater for the nonobese ( P < 0.01) when expressed relative to body mass, and 33.2010 greater for the nonobese ( P ⩽0.01) when expressed relative to the fat-free body mass. Expressed relative to the meal, the TEM was 25.5% less for the obese ( P <0.01). The data support an energy conservation hypothesis for obese female adolescents.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47424/1/421_2004_Article_BF00602361.pd