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Stent graft visualization and planning tool for endovascular surgery using finite element analysis
(2014)
Purpose: A new approach to optimize stent graft selection for endovascular aortic repair is the use of finite element analysis. Once the finite element model is created and solved, a software module is needed to view the simulation results in the clinical work environment. A new tool for Interpretation of simulation results, named Medical Postprocessor, that enables comparison of different stent graft configurations and products was designed, implemented and tested. Methods Aortic endovascular stent graft ring forces and sealing states in the vessel landing zone of three different configurations were provided in a surgical planning software using the Medical Imaging Interaction Tool Kit (MITK) Software system. For data interpretation, software modules for 2D and 3D presentations were implemented. Ten surgeons evaluated the software features of the Medical Postprocessor. These surgeons performed usability tests and answered questionnaires based on their experience with the system.
Results: The Medical Postprocessor visualization system enabled vascular surgeons to determine the configuration with the highest overall fixation force in 16 ± 6 s, best proximal sealing in 56±24 s and highest proximal fixation force in 38 ± 12 s. The majority considered the multiformat data provided helpful and found the Medical Postprocessor to be an efficient decision support system for stent graft selection. The evaluation of the user interface results in an ISONORMconform user interface (113.5 points).
Conclusion: The Medical Postprocessor visualization Software tool for analyzing stent graft properties was evaluated by vascular surgeons. The results show that the software can assist the interpretation of simulation results to optimize stent graft configuration and sizing.
Intra-operative fluoroscopy-guided assistance system for transcatheter aortic valve implantation
(2014)
A new surgical assistance system has been developed to assist the correct positioning of the AVP during transapical TAVI. The developed assistance system automatically defines the target area for implanting the AVP under live 2-D fluoroscopy guidance. Moreover, this surgical assistance system works with low levels of contrast agent for the final deployment of AVP, reducing therefore long-term negative effects, such as renal failure in the elderly and high-risk patients.
To evaluate the quality of sleep, it is important to determine how much time was spent in each sleep stage during the night. The gold standard in this domain is an overnight polysomnography (PSG). But the recording of the necessary electrophysiological signals is extensive and complex and the environment of the sleep laboratory, which is unfamiliar to the patient, might lead to distorted results. In this paper, a sleep stage detection algorithm is proposed that uses only the heart rate signal, derived from electrocardiogram (ECG), as a discriminator. This would make it possible for sleep analysis to be performed at home, saving a lot of effort and money. From the heart rate, using the fast Fourier transformation (FFT), three parameters were calculated in order to distinguish between the different sleep stages. ECG data along with a hypnogram scored by professionals was used from Physionet database, making it easy to compare the results. With an agreement rate of 41.3%, this approach is a good foundation for future research.
In this paper a method for the generation of gSPM with ontology-based generalization was presented. The resulting gSPM was modeled with BPMN/BPMNsix in an efficient way and could be executed with BPMN workflow engines. In the next step the implementation of resource concepts, anatomical structures, and transition probabilities for workflow execution will be realized.
Empirical software engineering experts on the use of students and professionals in experiments
(2018)
Using students as participants remains a valid simplification of reality needed in laboratory contexts. It is an effective way to advance software engineering theories and technologies but, like any other aspect of study settings, should be carefully considered during the design, execution, interpretation, and reporting of an experiment. The key is to understand which developer population portion is being represented by the participants in an experiment. Thus, a proposal for describing experimental participants is put forward.
The focus of the developed maturity model was set on processes. The concept of the widespread CMM and its practices has been transferred to the perioperative domain and the concept of the new maturity model. Additional optimization goals and technological as well as networking-specific aspects enable a process- and object-focused view of the maturity model in order to ensure broad coverage of different subareas. The evaluation showed that the model is applicable to the perioperative field. Adjustments and extensions of the maturity model are future steps to improve the rating and classification of the new maturity model.
Background: Internationally, teledermatology has proven to be a viable alternative to conventional physical referrals. Travel cost and referral times are reduced while patient safety is preserved. Especially patients from rural areas benefit from this healthcare innovation. Despite these established facts and positive experiences from EU neighboring countries like the Netherlands or the United Kingdom, Germany has not yet implemented store-and-forward teledermatology in routine care.
Methods: The TeleDerm study will implement and evaluate store-and-forward teledermatology in 50 general practitioner (GP) practices as an alternative to conventional referrals. TeleDerm aims to confirm that the possibility of store-and-forward teledermatology in GP practices is going to lead to a 15% (n = 260) reduction in referrals in the intervention arm. The study uses a cluster-randomized controlled trial design. Randomization is planned for the cluster “county”. The main observational unit is the GP practice. Poisson distribution of referrals is assumed. The evaluation of secondary outcomes like acceptance, enablers and barriers uses a mixed methods design with questionnaires and interviews.
Discussion: Due to the heterogeneity of GP practice organization, patient management software, information technology service providers, GP personal technical affinity and training, we expect several challenges in implementing teledermatology in German GP routine care. Therefore, we plan to recruit 30% more GPs than required by the power calculation. The implementation design and accompanying evaluation is expected to deliver vital insights into the specifics of implementing telemedicine in German routine care.
Container virtualization evolved into a key technology for deployment automation in line with the DevOps paradigm. Whereas container management systems facilitate the deployment of cloud applications by employing container based artifacts, parts of the deployment logic have been applied before to build these artifacts. Current approaches do not integrate these two deployment phases in a comprehensive manner. Limited knowledge on application software and middleware encapsulated in container-based artifacts leads to maintainability and configuration issues. Besides, the deployment of cloud applications is based on custom orchestration solutions leading to lock in problems. In this paper, we propose a two-phase deployment method based on the TOSCA standard. We present integration concepts for TOSCA-based orchestration and deployment automation using container-based artifacts. Our two-phase deployment method enables capturing and aligning all the deployment logic related to a software release leading to better maintainability. Furthermore, we build a container management system, which is composed of a TOSCA-based orchestrator on Apache Mesos, to deploy container-based cloud applications automatically.
The relative pros and cons of using students or practitioners in experiments in empirical software engineering have been discussed for a long time and continue to be an important topic. Following the recent publication of “Empirical software engineering experts on the use of students and professionals in experiments” by Falessi, Juristo, Wohlin, Turhan, Münch, Jedlitschka, and Oivo (EMSE, February 2018) we received a commentary by Sjøberg and Bergersen. Given that the topic is of great methodological interest to the community and requires nuanced treatment, we invited two editorial board members, Martin Shepperd and Per Runeson, respectively, to provide additional views.
Back to the future: origins and directions of the “Agile Manifesto” – views of the originators
(2018)
In 2001, seventeen professionals set up the manifesto for agile software development. They wanted to define values and basic principles for better software development. On top of brought into focus, the manifesto has been widely adopted by developers, in software-developing organizations and outside the world of IT. Agile principles and their implementation in practice have paved the way for radical new and innovative ways of software and product development. In parallel, the understanding of the manifesto’s underlying principles evolved over time. This, in turn, may affect current and future applications of agile principles. This article presents results from a survey and an interview study in collaboration with the original contributors of the manifesto for agile software development. Furthermore, it comprises the results from a workshop with one of the original authors. This publication focuses on the origins of the manifesto, the contributors’ views from today’s perspective, and their outlook on future directions. We evaluated 11 responses from the survey and 14 interviews to understand the viewpoint of the contributors. They emphasize that agile methods need to be carefully selected and agile should not be seen as a silver bullet. They underline the importance of considering the variety of different practices and methods that had an influence on the manifesto. Furthermore, they mention that people should question their current understanding of "agile" and recommend reconsidering the core ideas of the manifesto.
In this paper, we deal with optimizing the monetary costs of executing parallel applications in cloud-based environments. Specifically, we investigate on how scalability characteristics of parallel applications impact the total costs of computations. We focus on a specific class of irregularly structured problems, where the scalability typically depends on the input data. Consequently, dynamic optimization methods are required for minimizing the costs of computation. For quantifying the total monetary costs of individual parallel computations, the paper presents a cost model that considers the costs for the parallel infrastructure employed as well as the costs caused by delayed results. We discuss a method for dynamically finding the number of processors for which the total costs based on our cost model are minimal. Our extensive experimental evaluation gives detailed insights into the performance characteristics of our approach.
Parallel applications are the computational backbone of major industry trends and grand challenges in science. Whereas these applications are typically constructed for dedicated High Performance Computing clusters and supercomputers, the cloud emerges as attractive execution environment, which provides on-demand resource provisioning and a pay-per-use model. However, cloud environments require specific application properties that may restrict parallel application design. As a result, design trade-offs are required to simultaneously maximize parallel performance and benefit from cloud-specific characteristics.
In this paper, we present a novel approach to assess the cloud readiness of parallel applications based on the design decisions made. By discovering and understanding the implications of these parallel design decisions on an application’s cloud readiness, our approach supports the migration of parallel applications to the cloud.We introduce an assessment procedure, its underlying meta model, and a corresponding instantiation to structure this multi-dimensional design space. For evaluation purposes, we present an extensive case study comprising three parallel applications and discuss their cloud readiness based on our approach.
Software evolvability is an important quality attribute, yet one difficult to grasp. A certain base level of it is allegedly provided by service- and microservice-based systems, but many software professionals lack systematic understanding of the reasons and preconditions for this. We address this issue via the proxy of architectural modifiability tactics. By qualitatively mapping principles and patterns of Service Oriented Architecture (SOA) and microservices onto tactics and analyzing the results, we cannot only generate insights into service-oriented evolution qualities, but can also provide a modifiability comparison of the two popular service-based architectural styles. The results suggest that both SOA and microservices possess several inherent qualities beneficial for software evolution. While both focus strongly on loose coupling and encapsulation, there are also differences in the way they strive for modifiability (e.g. governance vs. evolutionary design). To leverage the insights of this research, however, it is necessary to find practical ways to incorporate the results as guidance into the software development process.
Purpose: Gliomas are the most common and aggressive type of brain tumors due to their infiltrative nature and rapid progression. The process of distinguishing tumor boundaries from healthy cells is still a challenging task in the clinical routine. Fluid attenuated inversion recovery (FLAIR) MRI modality can provide the physician with information about tumor infiltration. Therefore, this paper proposes a new generic deep learning architecture, namely DeepSeg, for fully automated detection and segmentation of the brain lesion using FLAIR MRI data.
Methods: The developed DeepSeg is a modular decoupling framework. It consists of two connected core parts based on an encoding and decoding relationship. The encoder part is a convolutional neural network (CNN) responsible for spatial information extraction. The resulting semantic map is inserted into the decoder part to get the full-resolution probability map. Based on modified U-Net architecture, different CNN models such as residual neural network (ResNet), dense convolutional network (DenseNet), and NASNet have been utilized in this study.
Results: The proposed deep learning architectures have been successfully tested and evaluated on-line based on MRI datasets of brain tumor segmentation (BraTS 2019) challenge, including s336 cases as training data and 125 cases for validation data. The dice and Hausdorff distance scores of obtained segmentation results are about 0.81 to 0.84 and 9.8 to 19.7 correspondingly.
Conclusion: This study showed successful feasibility and comparative performance of applying different deep learning models in a new DeepSeg framework for automated brain tumor segmentation in FLAIR MR images. The proposed DeepSeg is open source and freely available at https://github.com/razeineldin/DeepSeg/.
Elasticity is considered to be the most beneficial characteristic of cloud environments, which distinguishes the cloud from clusters and grids. Whereas elasticity has become mainstream for web-based, interactive applications, it is still a major research challenge how to leverage elasticity for applications from the high-performance computing (HPC) domain, which heavily rely on efficient parallel processing techniques. In this work, we specifically address the challenges of elasticity for parallel tree search applications. Well-known meta-algorithms based on this parallel processing technique include branch-and-bound and backtracking search. We show that their characteristics render static resource provisioning inappropriate and the capability of elastic scaling desirable. Moreover, we discuss how to construct an elasticity controller that reasons about the scaling behavior of a parallel system at runtime and dynamically adapts the number of processing units according to user-defined cost and efficiency thresholds. We evaluate a prototypical elasticity controller based on our findings by employing several benchmarks for parallel tree search and discuss the applicability of the proposed approach. Our experimental results show that, by means of elastic scaling, the performance can be controlled according to user-defined thresholds, which cannot be achieved with static resource provisioning.
Background
The actual task of electrocardiographic examinations is to increase the reliability of diagnosing the condition of the heart. Within the framework of this task, an important direction is the solution of the inverse problem of electrocardiography, based on the processing of electrocardiographic signals of multichannel cardio leads at known electrode coordinates in these leads (Titomir et al. Noninvasiv electrocardiotopography, 2003), (Macfarlane et al. Comprehensive Electrocardiology, 2nd ed. (Chapter 9), 2011).
Results
In order to obtain more detailed information about the electrical activity of the heart, we carry out a reconstruction of the distribution of equivalent electrical sources on the heart surface. In this area, we hold reconstruction of the equivalent sources during the cardiac cycle at relatively low hardware cost. ECG maps of electrical potentials on the surface of the torso (TSPM) and electrical sources on the surface of the heart (HSSM) were studied for different times of the cardiac cycle. We carried out a visual and quantitative comparison of these maps in the presence of pathological regions of different localization. For this purpose we used the model of the heart electrical activity, based on cellular automata.
Conclusions
The model of cellular automata allows us to consider the processes of heart excitation in the presence of pathological regions of various sizes and localization. It is shown, that changes in the distribution of electrical sources on the surface of the epicardium in the presence of pathological areas with disturbances in the conduction of heart excitation are much more noticeable than changes in ECG maps on the torso surface.
Context
Microservices as a lightweight and decentralized architectural style with fine-grained services promise several beneficial characteristics for sustainable long-term software evolution. Success stories from early adopters like Netflix, Amazon, or Spotify have demonstrated that it is possible to achieve a high degree of flexibility and evolvability with these systems. However, the described advantageous characteristics offer no concrete guidance and little is known about evolvability assurance processes for microservices in industry as well as challenges in this area. Insights into the current state of practice are a very important prerequisite for relevant research in this field.
Objective
We therefore wanted to explore how practitioners structure the evolvability assurance processes for microservices, what tools, metrics, and patterns they use, and what challenges they perceive for the evolvability of their systems.
Method
We first conducted 17 semi-structured interviews and discussed 14 different microservice-based systems and their assurance processes with software professionals from 10 companies. Afterwards, we performed a systematic grey literature review (GLR) and used the created interview coding system to analyze 295 practitioner online resources.
Results
The combined analysis revealed the importance of finding a sensible balance between decentralization and standardization. Guidelines like architectural principles were seen as valuable to ensure a base consistency for evolvability and specialized test automation was a prevalent theme. Source code quality was the primary target for the usage of tools and metrics for our interview participants, while testing tools and productivity metrics were the focus of our GLR resources. In both studies, practitioners did not mention architectural or service-oriented tools and metrics, even though the most crucial challenges like Service Cutting or Microservices Integration were of an architectural nature.
Conclusions
Practitioners relied on guidelines, standardization, or patterns like Event-Driven Messaging to partially address some reported evolvability challenges. However, specialized techniques, tools, and metrics are needed to support industry with the continuous evaluation of service granularity and dependencies. Future microservices research in the areas of maintenance, evolution, and technical debt should take our findings and the reported industry sentiments into account.
The cloud evolved into an attractive execution environment for parallel applications, which make use of compute resources to speed up the computation of large problems in science and industry. Whereas Infrastructure as a Service (IaaS) offerings have been commonly employed, more recently, serverless computing emerged as a novel cloud computing paradigm with the goal of freeing developers from resource management issues. However, as of today, serverless computing platforms are mainly used to process computations triggered by events or user requests that can be executed independently of each other and benefit from on-demand and elastic compute resources as well as per-function billing. In this work, we discuss how to employ serverless computing platforms to operate parallel applications. We specifically focus on the class of parallel task farming applications and introduce a novel approach to free developers from both parallelism and resource management issues. Our approach includes a proactive elasticity controller that adapts the physical parallelism per application run according to user-defined goals. Specifically, we show how to consider a user-defined execution time limit after which the result of the computation needs to be present while minimizing the associated monetary costs. To evaluate our concepts, we present a prototypical elastic parallel system architecture for self-tuning serverless task farming and implement two applications based on our framework. Moreover, we report on performance measurements for both applications as well as the prediction accuracy of the proposed proactive elasticity control mechanism and discuss our key findings.
Context:
Test-driven development (TDD) is an agile software development approach that has been widely claimed to improve software quality. However, the extent to which TDD improves quality appears to be largely dependent upon the characteristics of the study in which it is evaluated (e.g., the research method, participant type, programming environment, etc.). The particularities of each study make the aggregation of results untenable.
Objectives:
The goal of this paper is to: increase the accuracy and generalizability of the results achieved in isolated experiments on TDD, provide joint conclusions on the performance of TDD across different industrial and academic settings, and assess the extent to which the characteristics of the experiments affect the quality-related performance of TDD.
Method:
We conduct a family of 12 experiments on TDD in academia and industry. We aggregate their results by means of meta-analysis. We perform exploratory analyses to identify variables impacting the quality-related performance of TDD.
Results:
TDD novices achieve a slightly higher code quality with iterative test-last development (i.e., ITL, the reverse approach of TDD) than with TDD. The task being developed largely determines quality. The programming environment, the order in which TDD and ITL are applied, or the learning effects from one development approach to another do not appear to affect quality. The quality-related performance of professionals using TDD drops more than for students. We hypothesize that this may be due to their being more resistant to change and potentially less motivated than students.
Conclusion:
Previous studies seem to provide conflicting results on TDD performance (i.e., positive vs. negative, respectively). We hypothesize that these conflicting results may be due to different study durations, experiment participants being unfamiliar with the TDD process, or case studies comparing the performance achieved by TDD vs. the control approach (e.g., the waterfall model), each applied to develop a different system. Further experiments with TDD experts are needed to validate these hypotheses.