Automated measurement of the spontaneous tail coiling of zebrafish embryos as a sensitive behavior endpoint using a workflow in KNIME

Neuroactive substances are the largest group of chemicals detected in European surface waters. Mixtures of neuroactive substances occurring at low concentrations can induce adverse neurological effects in humans and organisms in the environment. Therefore, there is a need to develop new screening tools to detect these chemicals. Measurement of behavior or motor effects in rodents and fish are usually performed to assess potential neurotoxicity for risk assessment. However, due to pain and stress inflicted on these animals, the scientific community is advocating for new alternative methods based on the 3R principle (reduce, replace and refine). As a result, the behavior measurement of early stages of zebrafish embryos such as locomotor response, photomotor response and spontaneous tail coiling are considered as a valid alternative to adult animal testing. In this study, we developed a workflow to investigate the spontaneous tail coiling (STC) of zebrafish embryos and to accurately measure the STC effect in the KNIME software. We validated the STC protocol with 3 substances (abamectin, chlorpyrifos-oxon and pyracostrobin) which have different mechanisms of action. The KNIME workflow combined with easy and cost-effective method of video acquisition makes this STC protocol a valuable method for neurotoxicity testing

Automating test oracles generation

Software systems play a more and more important role in our everyday life. Many relevant human activities nowadays involve the execution of a piece of software. Software has to be reliable to deliver the expected behavior, and assessing the quality of software is of primary importance to reduce the risk of runtime errors. Software testing is the most common quality assessing technique for software. Testing consists in running the system under test on a finite set of inputs, and checking the correctness of the results. Thoroughly testing a software system is expensive and requires a lot of manual work to define test inputs (stimuli used to trigger different software behaviors) and test oracles (the decision procedures checking the correctness of the results). Researchers have addressed the cost of testing by proposing techniques to automatically generate test inputs. While the generation of test inputs is well supported, there is no way to generate cost-effective test oracles: Existing techniques to produce test oracles are either too expensive to be applied in practice, or produce oracles with limited effectiveness that can only identify blatant failures like system crashes. Our intuition is that cost-effective test oracles can be generated using information produced as a byproduct of the normal development activities. The goal of this thesis is to create test oracles that can detect faults leading to semantic and non-trivial errors, and that are characterized by a reasonable generation cost. We propose two ways to generate test oracles, one derives oracles from the software redundancy and the other from the natural language comments that document the source code of software systems. We present a technique that exploits redundant sequences of method calls encoding the software redundancy to automatically generate test oracles named CCOracles. We describe how CCOracles are automatically generated, deployed, and executed. We prove the effectiveness of CCOracles by measuring their fault-finding effectiveness when combined with both automatically generated and hand-written test inputs. We also present Toradocu, a technique that derives executable specifications from Javadoc comments of Java constructors and methods. From such specifications, Toradocu generates test oracles that are then deployed into existing test suites to assess the outputs of given test inputs. We empirically evaluate Toradocu, showing that Toradocu accurately translates Javadoc comments into procedure specifications. We also show that Toradocu oracles effectively identify semantic faults in the SUT. CCOracles and Toradocu oracles stem from independent information sources and are complementary in the sense that they check different aspects of the system undertest

Real-time Motion Planning For Autonomous Car in Multiple Situations Under Simulated Urban Environment

Advanced autonomous cars have revolutionary meaning for the automobile industry. While more and more companies have already started to build their own autonomous cars, no one has yet brought a practical autonomous car into the market. One key problem of their cars is lacking a reliable active real-time motion planning system for the urban environment. A real-time motion planning system makes cars can safely and stably drive under the urban environment. The final goal for this project is to design and implement a reliable real-time motion planning system to reduce accident rates in autonomous cars instead of human drivers. The real-time motion planning system includes lane-keeping, obstacle avoidance, moving car avoidance, adaptive cruise control, and accident avoidance function. In the research, EGO vehicles will be built and equipped with an image processing unit, a LIDAR, and two ultrasonic sensors to detect the environment. These environment data make it possible to implement a full control program in the real-time motion planning system. The control program will be implemented and tested in a scaled-down EGO vehicle with a scaled-down urban environment. The project has been divided into three phases: build EGO vehicles, implement the control program of the real-time motion planning system, and improve the control program by testing under the scale-down urban environment. In the first phase, each EGO vehicle will be built by an EGO vehicle chassis kit, a Raspberry Pi, a LIDAR, two ultrasonic sensors, a battery, and a power board. In the second phase, the control program of the real-time motion planning system will be implemented under the lane-keeping program in Raspberry Pi. Python is the programming language that will be used to implement the program. Lane-keeping, obstacle avoidance, moving car avoidance, adaptive cruise control functions will be built in this control program. In the last phase, testing and improvement works will be finished. Reliability tests will be designed and fulfilled. The more data grab from tests, the more stability of the real-time motion planning system can be implemented. Finally, one reliable motion planning system will be built, which will be used in normal scale EGO vehicles to reduce accident rates significantly under the urban environment.No embargoAcademic Major: Electrical and Computer Engineerin

A Deep Learning Approach to Examine Ischemic ST Changes in Ambulatory ECG Recordings.

Patients with suspected acute coronary syndrome (ACS) are at risk of transient myocardial ischemia (TMI), which could lead to serious morbidity or even mortality. Early detection of myocardial ischemia can reduce damage to heart tissues and improve patient condition. Significant ST change in the electrocardiogram (ECG) is an important marker for detecting myocardial ischemia during the rule-out phase of potential ACS. However, current ECG monitoring software is vastly underused due to excessive false alarms. The present study aims to tackle this problem by combining a novel image-based approach with deep learning techniques to improve the detection accuracy of significant ST depression change. The obtained convolutional neural network (CNN) model yields an average area under the curve (AUC) at 89.6% from an independent testing set. At selected optimal cutoff thresholds, the proposed model yields a mean sensitivity at 84.4% while maintaining specificity at 84.9%

STOP-IT: strategic, tactical, operational protection of water infrastructure against cyberphysical threats

Water supply and sanitation infrastructures are essential for our welfare, but vulnerable to several attack types facilitated by the ever-changing landscapes of the digital world. A cyber-attack on critical infrastructures could for example evolve along these threat vectors: chemical/biological contamination, physical or communications disruption between the network and the supervisory SCADA. Although conceptual and technological solutions to security and resilience are available, further work is required to bring them together in a risk management framework, strengthen the capacities of water utilities to systematically protect their systems, determine gaps in security technologies and improve risk management approaches. In particular, robust adaptable/flexible solutions for prevention, detection and mitigation of consequences in case of failure due to physical and cyber threats, their combination and cascading effects (from attacks to other critical infrastructure, i.e. energy) are still missing. There is (i) an urgent need to efficiently tackle cyber-physical security threats, (ii) an existing risk management gap in utilities’ practices and (iii) an un-tapped technology market potential for strategic, tactical and operational protection solutions for water infrastructure: how the H2020 STOP-IT project aims to bridge these gaps is presented in this paper.Postprint (published version