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We present a finite-volume, genuinely fourth-order accurate numerical method for solving the equations of resistive relativistic magnetohydrodynamics in Cartesian coordinates. In our formulation, the magnetic field is evolved in time in terms of face-average values via the constrained-transport method, while the remaining variables (density, momentum, energy, and electric fields) are advanced as cell volume averages. Spatial accuracy employs fifth-order accurate WENO-Z reconstruction from point values (as described in a companion paper) to obtain left and right states at zone interfaces. Explicit flux evaluation is carried out by solving a Riemann problem at cell interfaces, using the Maxwell–Harten–Lax–van Leer with contact wave resolution. Time-stepping is based on the implicit–explicit Runge–Kutta (RK) methods, of which we consider both the third-order strong stability preserving SSP3(4,3,3) and a recent fourth-order additive RK scheme, to cope with the stiffness introduced by the source term in Ampere's law. Numerical benchmarks are presented in order to assess the accuracy and robustness of our implementation. [ABSTRACT FROM AUTHOR]

Software size estimation is a vital activity of software project planning and management. Early software size estimation is a challenging task due to the limited information available during the early phases of software development. The goal of this paper is to construct and validate early software size estimation models based on four analysis-to-design adjustment factor (ADAF)-adjusted analysis class diagram metrics (i.e. ADAF-adjusted number of classes, ADAF-adjusted number of attributes, ADAF-adjusted number of methods and ADAF-adjusted number of relationships) using stepwise multiple linear regression and leave-one-out cross-validation. Furthermore, the prediction accuracy of the best-performing proposed model is also compared with the model based on objective class points. The results of this comparison reveal that our proposed method reduces errors significantly (i.e. on average, 16% reduction in mean absolute residual and 24% reduction in mean squared error). [ABSTRACT FROM AUTHOR]

In this paper, we address modelling program development by multiple different programmers (or programming teams) who work in different settings (programming languages or reasoning frameworks) but follow a common specification. After consideration of some philosophical issues regarding program development, including its similarities and dissimilarities with scientific theorizing, we extend a logical framework built to describe scientific theorizing in relativist settings: our extensions add the ability of reasoning about programs, the iterative process of their generation and their specifications. We are thus able to use the framework in order to make a first step towards examining at an abstract level the problem of translatability between the programs produced by program generators, by defining a notion of translation between the outputs of program generators and proving that there is such a (trivial) translation when two program generators follow the same specification reliably (in a specific sense of reliability). [ABSTRACT FROM AUTHOR]

Mashups are web applications that expedite software development by reusing existing resources through integrating multiple application programming interfaces (APIs). Recommending the appropriate APIs plays a critical role in assisting developers in building such web applications easily and efficiently. The proliferation of publicly available APIs on the Internet has inspired the community to adopt various models to accomplish the recommendation task. Until present, considerable efforts have been made to recommend the optimal set of APIs, delivering fruitful results and achieving varying recommendation performance. This paper presents a timely review on the topic of API recommendations for mashup creation. Specifically, we investigate and compare not only traditional data mining approaches and recommendation techniques but also more recent approaches based on network representation learning and deep learning techniques. By analyzing the merits and pitfalls of existing approaches, we pinpoint a few promising directions to address the remaining challenges in the current research. This survey provides a timely comprehensive review of the API recommendation research and could be a useful reference for relevant researchers and practitioners. [ABSTRACT FROM AUTHOR]

Code review increases reliability and improves reproducibility of research. As such, code review is an inevitable step in software development and is common in fields such as computer science. However, despite its importance, code review is noticeably lacking in ecology and evolutionary biology. This is problematic as it facilitates the propagation of coding errors and a reduction in reproducibility and reliability of published results. To address this, we provide a detailed commentary on how to effectively review code, how to set up your project to enable this form of review and detail its possible implementation at several stages throughout the research process. This guide serves as a primer for code review, and adoption of the principles and advice here will go a long way in promoting more open, reliable, and transparent ecology and evolutionary biology. [ABSTRACT FROM AUTHOR]

ViewDEX (Viewer for Digital Evaluation of X-ray Images) is an image viewer compatible with Digital Imaging and Communications in Medicine (DICOM) that has been especially designed to facilitate image perception and observer performance studies within medical imaging. The software was first released in 2004 and since then a continuous development has been ongoing. One of the major drawbacks of previous versions of ViewDEX has been that they have lacked functionality enabling the possibility to evaluate multiple images and/or image stacks simultaneously. This functionality is especially requested by researchers working with modalities, where an image acquisition can result in multiple image stacks (e.g. axial, coronal and sagittal reformations in computed tomography). In ViewDEX 3.0 this functionality has been added and it is now possible to perform image evaluations of multiple images and/or image stacks simultaneously, by using multiple monitors and/or multiple image canvases in monitors. Additionally, some of the previously available functionality has been updated and improved. This paper describes the recent developments of ViewDEX 3.0. [ABSTRACT FROM AUTHOR]

In this paper, we present CALSAGOS : Clustering ALgorithmS Applied to Galaxies in Overdense Systems which is a PYTHON package developed to select cluster members and to search, find, and identify substructures. CALSAGOS is based on clustering algorithms, and was developed to be used in spectroscopic and photometric samples. To test the performance of CALSAGOS , we use the S-PLUS's mock catalogues, and we found an error of 1–6 per cent on member selection depending on the function that is used. Besides, CALSAGOS has a F 1-score of 0.8, a precision of 85 per cent and a completeness of 100 per cent in the identification of substructures in the outer regions of galaxy clusters (r > r 200). The F 1-score, precision, and completeness of CALSAGOS fall to 0.5, 75, and 40 per cent when we consider all substructure identifications (inner and outer) due to the function that searches, finds, and identifies the substructures works in 2D, and cannot resolve the substructures projected over others. [ABSTRACT FROM AUTHOR]

This work aimed to develop and validate software that calculates the shielding thickness required for a radiotherapy room with a linear accelerator utilising geometric and dosimetric data. The software "Radiotherapy Infrastructure Shielding Calculations" (RISC) was developed using MATLAB programming. It does not require the installation of the MATLAB platform, and the user only needs to download and install the application, which displays a graphical user interface (GUI). The GUI includes empty cells to insert numerical values for several parameters to calculate the proper shielding thickness. The GUI comprises two main interfaces, one for the primary and one for the secondary barrier calculation. The interface of the primary barrier is divided into four tabs: (a) primary radiation, (b) patient scattered and leakage radiation, (c) IMRT techniques and (d) the shielding cost calculations. The interface of the secondary barrier includes three tabs: (a) patient scattered and leakage radiation, (b) IMRT techniques and (c) the shielding cost calculations. Each tab consists of two sections: one for input and one for output of the necessary data. The RISC is based on the methods and formulae of the NCRP 151 and calculates the primary and secondary barrier thickness for ordinary concrete with a density of 2.35 g/cm3 and the cost for a radiotherapy room with a linear accelerator that performs conventional or IMRT techniques. Calculations can be performed for photon energies of 4, 6, 10, 15, 18, 20, 25 and 30 MV of a dual-energy linear accelerator, while instantaneous dose rate (IDR) calculations are also performed. The RISC has been validated using all comparative examples of NCRP 151 and the calculations from shielding reports of the Varian IX linear accelerator at Methodist Hospital of Willowbrook and Elekta Infinity at the University Hospital of Patras. The RISC is accompanied by two text files: (a) "Terminology," extensively describing all parameters, and (b) "User's Manual," providing useful instructions to the user. The RISC is user-friendly, simple, fast and precise, providing accurate shielding calculations and quickly and easily reproducing different shielding scenarios for a radiotherapy room with a linear accelerator. Additionally, it could be used during the educational process of shielding calculations by graduate students or trainee medical physicists. As a future work, the RISC will be updated with new features such as skyshine radiation, door shielding, and other types of machines and shielding materials. [ABSTRACT FROM AUTHOR]

Evaluation of phenotype-driven gene prioritization approaches for Mendelian diseases could facilitate the software development and method selection for the workflow configuration and clinical practice. In our original article, the performance of 10 well-recognized causal-gene prioritization methods was benchmarked using 305 cases from the deciphering developmental disorders (DDD) project and 209 in-house cases via a relatively unbiased methodology. The evaluation results showed that LIRICAL and AMELIE were two of the best methods in our benchmark experiments, and the possible integrative approach of these two methods may enhance the diagnostic efficiency. However, some methodological critiques were raised by the authors of Exomiser and PhenIX, so we revisited our benchmarking studies to answer their comments in this letter. [ABSTRACT FROM AUTHOR]