Immunophenotyping of acute leukemia and lymphoproliferative disorders: a consensus proposal of the European LeukemiaNet Work Package 10

The European LeukemiaNet (ELN), workpackage 10 (WP10) was designed to deal with diagnosis matters using morphology and immunophenotyping. This group aimed at establishing a consensus on the required reagents for proper immunophenotyping of acute leukemia and lymphoproliferative disorders. Animated discussions within WP10, together with the application of the Delphi method of proposals circulation, quickly led to post-consensual immunophenotyping panels for disorders on the ELN website. In this report, we established a comprehensive description of these panels, both mandatory and complementary, for both types of clinical conditions. The reason for using each marker, sustained by relevant literature information, is provided in detail. With the constant development of immunophenotyping techniques in flow cytometry and related software, this work aims at providing useful guidelines to perform the most pertinent exploration at diagnosis and for follow-up, with the best cost benefit in diseases, the treatment of which has a strong impact on health systems.

Package Patterns for Visual Architecture Recovery

Recovering the architecture is the first step towards reengineering a software system. Many reverse engineering tools use top-down exploration as a way of providing a visual and interactive process for architecture recovery. During the exploration process, the user navigates through various views on the system by choosing from several exploration operations. Although some sequences of these operations lead to views which, from the architectural point of view, are mode relevant than others, current tools do not provide a way of predicting which exploration paths are worth taking and which are not. In this article we propose a set of package patterns which are used for augmenting the exploration process with in formation about the worthiness of the various exploration paths. The patterns are defined based on the internal package structure and on the relationships between the package and the other packages in the system. To validate our approach, we verify the relevance of the proposed patterns for real-world systems by analyzing their frequency of occurrence in six open-source software projects.

Noisy kriging-based optimization methods: A unified implementation within the DiceOptim package

Kriging-based optimization relying on noisy evaluations of complex systems has recently motivated contributions from various research communities. Five strategies have been implemented in the DiceOptim package. The corresponding functions constitute a user-friendly tool for solving expensive noisy optimization problems in a sequential framework, while offering some flexibility for advanced users. Besides, the implementation is done in a unified environment, making this package a useful device for studying the relative performances of existing approaches depending on the experimental setup. An overview of the package structure and interface is provided, as well as a description of the strategies and some insight about the implementation challenges and the proposed solutions. The strategies are compared to some existing optimization packages on analytical test functions and show promising performances.

RNetCDF – A Package for Reading and Writing NetCDF Datasets

This paper describes the RNetCDF package (version 1.6), an interface for reading and writing files in Unidata NetCDF format, and gives an introduction to the NetCDF file format. NetCDF is a machine independent binary file format which allows storage of different types of array based data, along with short metadata descriptions. The package presented here allows access to the most important functions of the NetCDF C-interface for reading, writing, and modifying NetCDF datasets. In this paper, we present a short overview on the NetCDF file format and show usage examples of the package.

Patient information leaflets: informing or frightening? A focus group study exploring patients' emotional reactions and subsequent behavior towards package leaflets of commonly prescribed medications in family practices.

BACKGROUND The purpose of patient information leaflets (PILs) is to inform patients about the administration, precautions and potential side effects of their prescribed medication. Despite European Commission guidelines aiming at increasing readability and comprehension of PILs little is known about the potential risk information has on patients. This article explores patients' reactions and subsequent behavior towards risk information conveyed in PILs of commonly prescribed drugs by general practitioners (GPs) for the treatment of Type 2 diabetes, hypertension or hypercholesterolemia; the most frequent cause for consultations in family practices in Germany. METHODS We conducted six focus groups comprising 35 patients which were recruited in GP practices. Transcripts were read and coded for themes; categories were created by abstracting data and further refined into a coding framework. RESULTS Three interrelated categories are presented: (i) The vast amount of side effects and drug interactions commonly described in PILs provoke various emotional reactions in patients which (ii) lead to specific patient behavior of which (iii) consulting the GP for assistance is among the most common. Findings show that current description of potential risk information caused feelings of fear and anxiety in the reader resulting in undesirable behavioral reactions. CONCLUSIONS Future PILs need to convey potential risk information in a language that is less frightening while retaining the information content required to make informed decisions about the prescribed medication. Thus, during the production process greater emphasis needs to be placed on testing the degree of emotional arousal provoked in patients when reading risk information to allow them to undertake a benefit-risk-assessment of their medication that is based on rational rather than emotional (fearful) reactions.

gems: An R Package for Simulating from Disease Progression Models

Mathematical models of disease progression predict disease outcomes and are useful epidemiological tools for planners and evaluators of health interventions. The R package gems is a tool that simulates disease progression in patients and predicts the effect of different interventions on patient outcome. Disease progression is represented by a series of events (e.g., diagnosis, treatment and death), displayed in a directed acyclic graph. The vertices correspond to disease states and the directed edges represent events. The package gems allows simulations based on a generalized multistate model that can be described by a directed acyclic graph with continuous transition-specific hazard functions. The user can specify an arbitrary hazard function and its parameters. The model includes parameter uncertainty, does not need to be a Markov model, and may take the history of previous events into account. Applications are not limited to the medical field and extend to other areas where multistate simulation is of interest. We provide a technical explanation of the multistate models used by gems, explain the functions of gems and their arguments, and show a sample application.

The Martian Gas-Analytic Package for the Landing Platform Experiments of the ExoMars 2018

The paper describes the architecture of the Martian Gas Analytic Package, which is proposed for the Russian ExoMars Lander 2018.