Abstract
Agent-based modeling (ABM) is a bottom-up modeling approach, where each entity of the system being modeled is uniquely represented as an independent decision-making agent. Large scale emergent behavior in ABMs is population sensitive. As such, the number of agents in a simulation should be able to reflect the reality of the system being modeled, which can be in the order of millions or billions of individuals in certain domains. A natural solution to reach acceptable scalability in commodity multi-core processors consists of decomposing models such that each component can be independently processed by a different thread in a concurrent manner. In this paper we present a multithreaded Java implementation of the PPHPC ABM, with two goals in mind: (1) compare the performance of this implementation with an existing NetLogo implementation; and, (2) study how different parallelization strategies impact simulation performance on a shared memory architecture. Results show that: (1) model parallelization can yield considerable performance gains; (2) distinct parallelization strategies offer specific trade-offs in terms of performance and simulation reproducibility; and, (3) PPHPC is a valid reference model for comparing distinct implementations or parallelization strategies, from both performance and statistical accuracy perspectives.

Abstract

Abstract
Agent-based modeling (ABM) is a bottom-up modeling approach, where each entity of the system being modeled is uniquely represented as an independent decision-making agent. ABMs are very sensitive to implementation details. Thus, it is very easy to inadvertently introduce changes which modify model dynamics. Such problems usually arise due to the lack of transparency in model descriptions, which constrains how models are assessed, implemented and replicated. In this paper, we present PPHPC, a model which aims to serve as a standard in agent based modeling research, namely, but not limited to, conceptual model specification, statistical analysis of simulation output, model comparison and parallelization studies. This paper focuses on the first two aspects (conceptual model specification and statistical analysis of simulation output), also providing a canonical implementation of PPHPC. The paper serves as a complete reference to the presented model, and can be used as a tutorial for simulation practitioners who wish to improve the way they communicate their ABMs.

Abstract
Tuberculosis is one of the major public health concerns. This highly contagious disease affects more than 10.4 million people, being a leading cause of morbidity by infection. Tuberculosis is diagnosed at the point-of-care by the Ziehl-Neelsen sputum smear microscopy test. Ziehl-Neelsen is laborious, prone to human error and infection risk, with a limit of detection of 10(4) cells/mL. In resource-poor nations, a more practical test, with lower detection limit, is paramount. This work uses a magnetoresistive biosensor to detect BCG bacteria for tuberculosis diagnosis. Herein we report: i) nanoparticle assembly method and specificity for tuberculosis detection; ii) demonstration of proportionality between BCG cell concentration and magnetoresistive voltage signal; application of multiplicative signal correction for systematic effects removal; iv) investigation of calibration effectiveness using chemometrics methods; and v) comparison with state-of-the-art point-of-care tuberculosis biosensors. Results present a clear correspondence between voltage signal and cell concentration. Multiplicative signal correction removes baseline shifts within and between biochip sensors, allowing accurate and precise voltage signal between different biochips. The corrected signal was used for multivariate regression models, which significantly decreased the calibration standard error from 0.50 to 0.03 log(10) (cells/mL). Results show that Ziehl-Neelsen detection limits and below are achievable with the magnetoresistive biochip, when pre-processing and chemometrics are used.

Abstract
This paper presents the positioning, navigation and awareness (PNA) system developed for the Underwater Robotic Mining System of the VAMOS! project [1]. It describes the main components of the VAMOS! system, the PNA sensors in each of those components, the global architecture of the PNA system, and its main subsystems: Position and Navigation, Real-time Mine Modeling, 3D Virtual reality HMI and Real-time grade system. General results and lessons learn during the first mining field trial in Lee Moor, Devon, UK during the months of September and October 2017 are presented.

Abstract
Labour shortage is a reality in agriculture. Farmers are asking for solutions to automate agronomic tasks, such as monitoring, pruning, spraying, and harvesting. The automation of these tasks requires, most of the time, the use of robotic arms to mimic human arms capabilities. The current robotic arm based solutions available, both in the market and in the scientific sphere, have several limitations, such as, low-speed manipulation, the path planning algorithms are not aware of the requirements of the agricultural tasks (robotic motion and manipulation synchronisation), and require active perception tuning to the end-target point. This work benchmarks algorithms from open manipulation planning library (OMPL) considering a cost-effective six-degree freedom manipulator in a simulated vineyard. The OMPL planners shown a very low performance under demanding pruning tasks. The best and most promising results are performed and obtained by BiTRRT. However, further work is needed to increase its performance and reduce planning time. This benchmark work helps the reader to understand the limitations of each algorithm and when to use them. © 2019, Springer Nature Switzerland AG.