The Extended Dawid-Skene Model:Fusing Information from Multiple Data Schemas

While label fusion from multiple noisy annotations is a well understood concept in data wrangling (tackled for example by the Dawid-Skene (DS) model), we consider the extended problem of carrying out learning when the labels themselves are not consistently annotated with the same schema. We show that even if annotators use disparate, albeit related, label-sets, we can still draw inferences for the underlying full label-set. We propose the Inter-Schema AdapteR (ISAR) to translate the fully-specified label-set to the one used by each annotator, enabling learning under such heterogeneous schemas, without the need to re-annotate the data. We apply our method to a mouse behavioural dataset, achieving significant gains (compared with DS) in out-of-sample log-likelihood (-3.40 to -2.39) and F1-score (0.785 to 0.864).Comment: Updated with Author-Preprint version following Publication in P. Cellier and K. Driessens (Eds.): ECML PKDD 2019 Workshops, CCIS 1167, pp. 121 - 136, 202

A Bayesian re-assessment of two Phase II trials of gemcitabine in metastatic nasopharyngeal cancer

The Simon two-stage minimax design is a popular statistical design used in Phase II clinical trials. The analysis of the data arising from the design typically involves the use of frequentist statistics. This paper presents an alternative, Bayesian, approach to the design and analysis of Phase II clinical trials. In particular, we consider how a Bayesian approach could have affected the design, analysis and interpretation of two parallel Phase II trials of the National Cancer Centre Singapore, on the activity of gemcitabine in chemotherapy-naïve and in previously treated patients with metastatic nasopharyngeal carcinoma. We begin by explaining the Bayesian methodology and contrasting it with the frequentist approach. We then carry out a Bayesian analysis of the trial results. The conclusions drawn using the Bayesian approach were in general agreement with those obtained from the frequentist analysis. However they had the advantage of allowing for different and potentially more useful interpretations to be made regarding the trial results, as well as for the incorporation of external sources of information. In particular, using a Bayesian trial design, we were able to take into account the results of the parallel trial results when deciding whether to continue each trial beyond the interim stage

Prevalence and factors affecting home blood pressure documentation in routine clinical care: a retrospective study

<p>Abstract</p> <p>Background</p> <p>Home blood pressure (BP) is closely linked to patient outcomes. However, the prevalence of its documentation has not been examined. The objective of this study was to analyze the prevalence and factors affecting documentation of home BP in routine clinical care.</p> <p>Methods</p> <p>A retrospective study of 142,973 encounters of 9,840 hypertensive patients with diabetes from 2000 to 2005 was performed. The prevalence of recorded home BP and the factors associated with its documentation were analyzed. We assessed validity of home BP information by comparing the difference between home and office BP to previously published prospective studies.</p> <p>Results</p> <p>Home BP was documented in narrative notes for 2.08% of encounters where any blood pressure was recorded and negligibly in structured data (EMR flowsheets). Systolic and diastolic home BP in narrative notes were lower than office BP readings by 9.6 and 2.5 mm Hg, respectively (p < 0.0001 for both), consistent with prospective data. Probability of home BP documentation increased by 23.0% for each 10 mm Hg of office systolic BP (p < 0.0001), by 6.2% for each $10,000 in median income of zip code (p = 0.0055), and by 17.7% for each decade in the patient's age (p < 0.0001).</p> <p>Conclusions</p> <p>Home BP readings provide a valid representation of the patient's condition, yet are seldom documented despite their potential utility in both patient care and research. Strong association between higher patient income and home BP documentation suggests that the cost of the monitors may be a limiting factor; reimbursement of home BP monitoring expenses should be pursued.</p

Comparing oil based ointment versus standard practice for the treatment of moderate burns in Greece: a trial based cost effectiveness evaluation

<p>Abstract</p> <p>Background</p> <p>The local treatment of burn wounds has long been a subject of debate. The objective of this study was to compare the cost and the effectiveness of Moist Exposed Burn Ointment -MEBO versus a combination of <it>povidone iodine </it>plus <it>bepanthenol </it>cream for partial thickness burns.</p> <p>Methods</p> <p>The study was carried out in the Burn Center of a state hospital in Athens, Greece. 211 patients needing conservative therapy were prospectively selected according to the depth of the burn wound. The treatment was allocated according to the Stratified Randomization Design. The outcomes measured were mean cost of in-hospital stay, rate of complications, time of 50% wound healing, pain scores, in hospital stay diminution. We have adopted a societal perspective.</p> <p>Results</p> <p>In the total groups MEBO presented lower cost, (although not significantly different: p = 0.10) and better effectiveness. The data suggest that MEBO is the dominant therapy for superficial partial burn wound with significantly lower costs and significantly higher effectiveness due to a lesser time of recovery and consequently lower time of hospitalization and follow-up. MEBO presented similar percentages of complications with the comparator, lower pain levels and smaller time of no healthy appearance of the burn limits for superficial partial thickness burns.</p> <p>Conclusions</p> <p>The data suggested that topical application of MEBO may be considered for further investigation as a potential first-line treatment modality for superficial partial thickness burns.</p> <p>Trial registration</p> <p>The trial has been registered on the International Standard Randomised Controlled Trial Number Register (ISRCTN) and given the registration number <a href="http://www.controlled-trials.com/ISRCTN74058791">ISRCTN74058791</a>.</p

Nicotinic Acetylcholine Receptor Variants Are Related to Smoking Habits, but Not Directly to COPD

Genome-wide association studies identified single nucleotide polymorphisms (SNPs) in the nicotinic acetylcholine receptors (nAChRs) cluster as a risk factor for nicotine dependency and COPD. We investigated whether SNPs in the nAChR cluster are associated with smoking habits and lung function decline, and if these potential associations are independent of each other. The SNPs rs569207, rs1051730 and rs8034191 in the nAChR cluster were analyzed in the Vlagtwedde-Vlaardingen cohort (n = 1,390) that was followed for 25 years. We used GEE and LME models to analyze the associations of the SNPs with quitting or restarting smoking and with the annual FEV1 decline respectively. Individuals homozygote (CC) for rs569207 were more likely to quit smoking (OR (95%CI) = 1.58 (1.05–2.38)) compared to wild-type (TT) individuals. Individuals homozygote (TT) for rs1051730 were less likely to quit smoking (0.64 (0.42; 0.97)) compared to wild-type (CC) individuals. None of the SNPs was significantly associated with the annual FEV1 decline in smokers and ex-smokers. We show that SNPs in the nAChR region are associated with smoking habits such as quitting smoking, but have no significant effect on the annual FEV1 decline in smokers and ex-smokers, suggesting a potential role of these SNPs in COPD development via smoking habits rather than via direct effects on lung function

Tumor Volume Estimation and Quasi- Continuous Administration for Most Effective Bevacizumab Therapy

Bevacizumab is an exogenous inhibitor which inhibits the biological activity of human VEGF. Several studies have investigated the effectiveness of bevacizumab therapy according to different cancer types but these days there is an intense debate on its utility. We have investigated different methods to find the best tumor volume estimation since it creates the possibility for precise and effective drug administration with a much lower dose than in the protocol.We have examined C38 mouse colon adenocarcinoma and HT-29 human colorectal adenocarcinoma. In both cases, three groups were compared in the experiments. The first group did not receive therapy, the second group received one 200 μg bevacizumab dose for a treatment period (protocol-based therapy), and the third group received 1.1 μg bevacizumab every day (quasi-continuous therapy). Tumor volume measurement was performed by digital caliper and small animal MRI. The mathematical relationship between MRI-measured tumor volume and mass was investigated to estimate accurate tumor volume using caliper-measured data. A two-dimensional mathematical model was applied for tumor volume evaluation, and tumor- and therapy-specific constants were calculated for the three different groups. The effectiveness of bevacizumab administration was examined by statistical analysis.In the case of C38 adenocarcinoma, protocol-based treatment did not result in significantly smaller tumor volume compared to the no treatment group; however, there was a significant difference between untreated mice and mice who received quasi-continuous therapy (p = 0.002). In the case of HT-29 adenocarcinoma, the daily treatment with one-twelfth total dose resulted in significantly smaller tumors than the protocol-based treatment (p = 0.038). When the tumor has a symmetrical, solid closed shape (typically without treatment), volume can be evaluated accurately from caliper-measured data with the applied two-dimensional mathematical model.Our results provide a theoretical background for a much more effective bevacizumab treatment using optimized administration

CCR5 Haplotypes and Mother-to-Child HIV Transmission in Malawi

CCR5 and CCR2 gene polymorphisms (SNPs) have been associated with protection against HIV transmission in adults and with delayed progression to AIDS. The CCR5 Delta32 deletion and SNP -2459G are associated with reduced expression of the CCR5 protein.We investigated the association between infant CCR2/CCR5 diplotype and HIV mother to child transmission (MTCT) in Malawi. Blood samples from infants (n = 552) of HIV positive women who received nevirapine were genotyped using a post-PCR multiplex ligase detection reaction and haplotypes were identified based on 8 CCR2/CCR5 SNPs and the open reading frame 32 base pair deletion. Following verification of Hardy-Weinberg equilibrium, log linear regression was performed to examine the association between mutations and MTCT. Overall, protection against MTCT was weakly associated with two CCR5 SNPs, -2459G (Risk ratio [RR], 0.78; confidence interval [CI], 0.54-1.12), and the linked CCR5 -2135T (RR, 0.78; CI, 0.54-1.13). No child carried the CCR5 Delta32 SNP. Maternal Viral Load (MVL) was found to be an effect measure modifier. Among mothers with low MVL, statistically significant protection against MTCT was observed for -2459G (RR, 0.50; CI, 0.27-0.91), and -2135T (RR, 0.51; CI, 0.28-0.92). Statistically significant protection was not found at high MVL.Results from this study suggest that CCR5 SNPs -2459G and -2135T associated with reduced receptor expression protect against MTCT of HIV at low MVLs, whereas high MVLs may over-ride differences in coreceptor availability