Identification of patient subtypes based on protein expression for prediction of heart failure after myocardial infarction.

This study investigates the ability of high-throughput aptamer-based platform to identify circulating biomarkers able to predict occurrence of heart failure (HF), in blood samples collected during hospitalization of patients suffering from a first myocardial infarction (MI). REVE-1 (derivation) and REVE-2 (validation) cohorts included respectively 254 and 238 patients, followed up respectively 9 · 2 ± 4 · 8 and 7 · 6 ± 3 · 0 years. A blood sample collected during hospitalization was used for quantifying 4,668 proteins. Fifty proteins were significantly associated with long-term occurrence of HF with all-cause death as the competing event. k-means, an unsupervised clustering method, identified two groups of patients based on expression levels of the 50 proteins. Group 2 was significantly associated with a higher risk of HF in both cohorts. These results showed that a subset of 50 selected proteins quantified during hospitalization of MI patients is able to stratify and predict the long-term occurrence of HF.

The Optimal Sample Size for Usability Testing, From the Manufacturer's Perspective: A Value-of-Information Approach.

OBJECTIVES: For medical devices, a usability assessment is mandatory for market access; the objective is to detect potentially harmful use errors that stem from the device's design. The manufacturer assesses the final version of the device and determines the risk-benefit ratio for remaining errors. Nevertheless, the decision rule currently used to determine the sample size for this testing has statistical limitations and the lack of a clear decision-making perspective. METHODS: As an alternative, we developed a value-of-information analysis from the medical device manufacturer's perspective. The consequences of use errors not detected during usability testing and the errors' probability of occurrence were embedded in a loss function. The value of further testing was assessed as a reduction in the expected loss for the manufacturer. The optimal sample size was determined using the expected net benefit of sampling (ENBS) (the difference between the value provided by new participants and the cost of their inclusion). RESULTS: The value-of-information approach was applied to a real usability test of a needle-free adrenaline autoinjector. The initial estimate (performed on the first n = 20 participants) gave an optimal sample size of 100 participants and an ENBS of €255 453. This estimation was updated iteratively as new participants were included. After the inclusion of 90 participants, the ENBS was null for any sample size; hence, the cost of adding more participants outweighed the expected value of information, and therefore, the study could be stopped. CONCLUSIONS: On the basis of these results, our method seems to be highly suitable for sample size estimation in the usability testing of medical devices before market access.

Reject inference methods in credit scoring.

The granting process is based on the probability that the applicant will refund his/her loan given his/her characteristics. This probability, also called score, is learnt based on a dataset in which rejected applicants are excluded. Thus, the population on which the score is used is different from the learning population. Many "reject inference" methods try to exploit the data available from the rejected applicants in the learning process. However, most of these methods are empirical and lack of formalization of their assumptions, and of their expected theoretical properties. We formalize such hidden assumptions in a general missing data setting for some of the most common reject inference methods. It reveals that hidden modelling is mostly incomplete, thus prohibiting to compare existing methods within the general model selection mechanism (except by financing "non-fundable" applicants). So, we assess performance of the methods on both simulated data and real data (from CACF, a major European loan issuer). Unsurprisingly, no method seems uniformly dominant. Both these theoretical and empirical results not only reinforce the idea to carefully use the classical reject inference methods but also to invest in future research works for designing model-based reject inference methods (without financing "non-fundable" applicants).

Estimating the number of usability problems affecting medical devices: modelling the discovery matrix.

BACKGROUND: Usability testing of medical devices are mandatory for market access. The testings' goal is to identify usability problems that could cause harm to the user or limit the device's effectiveness. In practice, human factor engineers study participants under actual conditions of use and list the problems encountered. This results in a binary discovery matrix in which each row corresponds to a participant, and each column corresponds to a usability problem. One of the main challenges in usability testing is estimating the total number of problems, in order to assess the completeness of the discovery process. Today's margin-based methods fit the column sums to a binomial model of problem detection. However, the discovery matrix actually observed is truncated because of undiscovered problems, which corresponds to fitting the marginal sums without the zeros. Margin-based methods fail to overcome the bias related to truncation of the matrix. The objective of the present study was to develop and test a matrix-based method for estimating the total number of usability problems. METHODS: The matrix-based model was based on the full discovery matrix (including unobserved columns) and not solely on a summary of the data (e.g. the margins). This model also circumvents a drawback of margin-based methods by simultaneously estimating the model's parameters and the total number of problems. Furthermore, the matrix-based method takes account of a heterogeneous probability of detection, which reflects a real-life setting. As suggested in the usability literature, we assumed that the probability of detection had a logit-normal distribution. RESULTS: We assessed the matrix-based method's performance in a range of settings reflecting real-life usability testing and with heterogeneous probabilities of problem detection. In our simulations, the matrix-based method improved the estimation of the number of problems (in terms of bias, consistency, and coverage probability) in a wide range of settings. We also applied our method to five real datasets from usability testing. CONCLUSIONS: Estimation models (and particularly matrix-based models) are of value in estimating and monitoring the detection process during usability testing. Matrix-based models have a solid mathematical grounding and, with a view to facilitating the decision-making process for both regulators and device manufacturers, should be incorporated into current standards.

Circulating proteomic signature of early death in heart failure patients with reduced ejection fraction.

Heart failure (HF) remains a main cause of mortality worldwide. Risk stratification of patients with systolic chronic HF is critical to identify those who may benefit from advanced HF therapies. The aim of this study is to identify plasmatic proteins that could predict the early death (within 3 years) of HF patients with reduced ejection fraction hospitalized in CHRU de Lille. The subproteome targeted by an aptamer-based technology, the Slow Off-rate Modified Aptamer (SOMA) scan assay of 1310 proteins, was profiled in blood samples from 168 HF patients, and 203 proteins were significantly modulated between patients who died of cardiovascular death and patients who were alive after 3 years of HF evaluation (Wilcoxon test, FDR 5%). A molecular network was built using these 203 proteins, and the resulting network contained 2281 molecules assigned to 34 clusters annotated to biological pathways by Gene Ontology. This network model highlighted extracellular matrix organization as the main mechanism involved in early death in HF patients. In parallel, an adaptive Least Absolute Shrinkage and Selection Operator (LASSO) was performed on these 203 proteins, and six proteins were selected as candidates to predict early death in HF patients: complement C3, cathepsin S and F107B were decreased and MAPK5, MMP1 and MMP7 increased in patients who died of cardiovascular causes compared with patients living 3 years after HF evaluation. This proteomic signature of 6 circulating plasma proteins allows the identification of systolic HF patients with a risk of early death.

Statistical tests to compare motif count exceptionalities.

BACKGROUND: Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. RESULTS: We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. CONCLUSION: The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.