Utilizing traceable software artifacts to improve bug localization

Die Entwicklung von Softwaresystemen ist eine komplexe Aufgabe. Qualitätssicherung versucht auftretenden Softwarefehler (bugs) in Systemen zu vermeiden, jedoch können Fehler nie ausgeschlossen werden. Sobald ein Softwarefehler entdeckt wird, wird typischerweise ein Fehlerbericht (bug report) erstellt. Dieser dient als Ausgangspunkt für den Entwickler den Fehler im Quellcode der Software zu finden und zu beheben (bug fixing). Fehlerberichte sowie weitere Softwareartefakte, z.B. Anforderungen und der Quellcode selbst, werden in Software Repositories abgelegt. Diese erlauben die Artefakte mit trace links zur Nachvollziehbarkeit (traceability) zu verknüpfen. Oftmals ist die Erstellung der trace links im Entwicklungsprozess vorgeschrieben. Dazu zählen u.a. die Luftfahrt- und Automobilindustrie, sowie die Entwicklung von medizinischen Geräten. Das Auffinden von Softwarefehlern in großen Systemen mit tausenden Artefakten ist eine anspruchsvolle, zeitintensive und fehleranfällige Aufgabe, welche eine umfangreiche Projektkenntnis erfordert. Deswegen wird seit Jahren aktiv an der Automatisierung dieses Prozesses geforscht. Weiterhin wird die manuelle Erstellung und Pflege von trace links als Belastung empfunden und sollte weitgehend automatisiert werden. In dieser Arbeit wird ein neuartiger Algorithmus zum Auffinden von Softwarefehlern vorgestellt, der aktiv die erstellten trace links ausnutzt. Die Artefakte und deren Beziehungen dienen zur Erstellung eines Nachvollziehbarkeitsgraphen, welcher analysiert wird um fehlerhafte Quellcodedateien anhand eines Fehlerberichtes zu finden. Jedoch muss angenommen werden, dass nicht alle notwendigen trace links zwischen den Softwareartefakten eines Projektes erstellt wurden. Deswegen wird ein vollautomatisierter, projektunabhängiger Ansatz vorgestellt, der diese fehlenden trace links erstellt (augmentation). Die Grundlage zur Entwicklung dieses Algorithmus ist der typische Entwicklungsprozess eines Softwareprojektes. Die entwickelten Ansätze wurden mit mehr als 32.000 Fehlerberichten von 27 Open-Source Projekten evaluiert und die Ergebnisse zeigen, dass die Einbeziehung von traceability signifikant das Auffinden von Fehlern im Quellcode verbessert. Weiterhin kann der entwickelte Augmentation Algorithmus zuverlässig fehlende trace links erstellen.The development of software systems is a very complex task. Quality assurance tries to prevent defects – software bugs – in deployed systems, but it is impossible to avoid bugs all together, especially during development. Once a bug is observed, typically a bug report is written. It guides the responsible developer to locate the bug in the project's source code, and once found to fix it. The bug reports, along with other development artifacts such as requirements and the source code are stored in software repositories. The repositories also allow to create relationships – trace links – among contained artifacts. Establishing this traceability is demanded in many domains, such as safety related ones like the automotive and aviation industry, or in development of medical devices. However, in large software systems with thousands of artifacts, especially source code files, manually locating a bug is time consuming, error-prone, and requires extensive knowledge of the project. Thus, automating the bug localization process is actively researched since many years. Further, manually creating and maintaining trace links is often considered as a burden, and there is the need to automate this task as well. Multiple studies have shown, that traceability is beneficial for many software development tasks. This thesis presents a novel bug localization algorithm utilizing traceability. The project's artifacts and trace links are used to create a traceability graph. This graph is then analyzed to locate defective source code files for a given bug report. Since the existing trace link set of a project is possibly incomplete, another algorithm is prosed to augment missing links. The algorithm is fully automated, project independent, and derived from a project's development workflow. An evaluation on more than 32,000 bug reports from 27 open-source projects shows, that incorporating traceability information into bug localization significantly improves the bug localization performance compared to two state of the art algorithms. Further, the trace link augmentation approach reliably constructs missing links and therefore simplifies the required trace maintenance

ROCK signalling induced gene expression changes in mouse pancreatic ductal adenocarcinoma cells

The RhoA and RhoC GTPases act via the ROCK1 and ROCK2 kinases to promote actomyosin contraction, resulting in directly induced changes in cytoskeleton structures and altered gene transcription via several possible indirect routes. Elevated activation of the Rho/ROCK pathway has been reported in several diseases and pathological conditions, including disorders of the central nervous system, cardiovascular dysfunctions and cancer. To determine how increased ROCK signalling affected gene expression in pancreatic ductal adenocarcinoma (PDAC) cells, we transduced mouse PDAC cell lines with retroviral constructs encoding fusion proteins that enable conditional activation of ROCK1 or ROCK2, and subsequently performed RNA sequencing (RNA-Seq) using the Illumina NextSeq 500 platform. We describe how gene expression datasets were generated and validated by comparing data obtained by RNA-Seq with RT-qPCR results. Activation of ROCK1 or ROCK2 signalling induced significant changes in gene expression that could be used to determine how actomyosin contractility influences gene transcription in pancreatic cancer

Targeting ROCK activity to disrupt and prime pancreatic cancer for chemotherapy

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease; the identification of novel targets and development of effective treatment strategies are urgently needed to improve patient outcomes. Remodeling of the pancreatic stroma occurs during PDAC development, which drives disease progression and impairs responses to therapy. The actomyosin regulatory ROCK1 and ROCK2 kinases govern cell motility and contractility, and have been suggested to be potential targets for cancer therapy, particularly to reduce the metastatic spread of tumor cells. However, ROCK inhibitors are not currently used for cancer patient treatment, largely due to the overwhelming challenge faced in the development of anti-metastatic drugs, and a lack of clarity as to the cancer types most likely to benefit from ROCK inhibitor therapy. In 2 recent publications, we discovered that ROCK1 and ROCK2 expression were increased in PDAC, and that increased ROCK activity was associated with reduced survival and PDAC progression by enabling extracellular matrix (ECM) remodeling and invasive growth of pancreatic cancer cells. We also used intravital imaging to optimize ROCK inhibition using the pharmacological ROCK inhibitor fasudil (HA-1077), and demonstrated that short-term ROCK targeting, or ‘priming’, improved chemotherapy efficacy, disrupted cancer cell collective movement, and impaired metastasis. This body of work strongly indicates that the use of ROCK inhibitors in pancreatic cancer therapy as ‘priming’ agents warrants further consideration, and provides insights as to how transient mechanical manipulation, or fine-tuning the ECM, rather than chronic stromal ablation might be beneficial for improving chemotherapeutic efficacy in the treatment of this deadly disease

Using Evidence to Address Psychosocial Impairments Post-Stroke: A Guide for Occupational Therapy

Introduction: Following a stroke, individuals experience a wide variety of physical and psychosocial impairments. While physical impairments are commonly given attention by medical practitioners, psychosocial impairments are often overlooked or undiagnosed. (Hildebrand, 2015). Unfortunately, the same is true in occupational therapy, where physical and psychosocial issues have not been receiving the same amount of attention, physical issues being addressed far more than psychosocial issues (Gillen, 2014). The purpose of this scholarly project is to provide occupational therapists a guide to use of current evidence-based assessments and interventions to address psychosocial impairments following stroke. The guide focuses on evidence-based assessments, and interventions appropriate to a wide variety of occupational therapy settings. Methodology: The review of the literature supported the need for a therapy guide translating current research literature for occupational therapists to address interventions and assessments specific to psychosocial impairments post-stroke. The Model of Human Occupation’s six steps of therapeutic reasoning were selected to structure the guide and emphasize the need to consider the individual as a collaborator in the intervention process. Results: The product includes assessments and evidence based interventions that therapists can use throughout the therapeutic reasoning process. The guide focuses on evidence based assessments that can be used by occupational therapists to assess common psychosocial issues that occur after a patient experiences a stroke. The interventions included in this guide have been published in the Occupational Therapy Practice Guidelines for Adults with Stroke (Wolf & Nilsen, 2015). These interventions came from the work of Mary Hildebrand’s (2014), Effectiveness of Interventions for Adults With Psychosocial or Emotional Impairment After Stroke: An Evidence-Based Review. This guide, including assessment and interventions, is guided by the Model of Human Occupation (MOHO), specifically, MOHO’s 6 steps of therapeutic reasoning. Conclusions & Significance: A product has been created to guide occupational therapists through the therapeutic process in order to encourage treatment of not only physical but also psychosocial impairments that accompany a stroke. A potential limitation for this product is that the interventions included are evidence based and have been tested by researchers in the past outside of the profession of occupational therapy. The product does not offer interventions that may be effective but just have not yet been tested in research. Future improvements to this product could include testing the specific evidence-based interventions in the profession of occupational therapy. Further, other intervention options that are not yet considered evidence-based can be tested and added to the product in order to increase options for clients and therapists

High-Pressure Phase Transition of the Oxonitridosilicate Chloride Ce4[Si4O3+xN7-x]Cl1-xOx with x = 0.12 and 0.18

The high-pressure behaviour of the oxonitridosilicate chlorides Ce4[Si4O3þxN7-x]Cl1-xOx, x = 0.12 and 0.18, is investigated by in situ powder synchrotron X-ray diffraction. Pressures up to 28 GPa are generated using the diamond-anvil cell technique. A reversible phase transition of first order occurs at pressures between 8 and 10 GPa. Within this pressure range the high- and the low-pressure phases are observed concomitantly. At the phase transition the unit cell volume is reduced by about 5%, and the cubic symmetry (space group P213) is reduced to orthorhombic (space group P212121) following a translationengleiche group-subgroup relationship of index 3. A fit of a third-order Birch-Murnaghan equation of state to the p-V data results in a bulk modulus B0 = 124(5) GPa with its pressure derivative B0 = 5(1) at V0 = 1134.3(4) Å3 for the low-pressure phase and in B0 = 153(10) GPa with B0 = 3.0(6) at V0 = 1071(3) Å3 for the high-pressure phase. The orthorhombic phase shows an anisotropic axial compression with the a axis (which is the shortest axis) being more compressible (k(a) = 0.0143(4) 1/GPa) than the b and c axes (k(b) = 0.0045(2), k(c) = 0.0058(2) 1/GPa). The experimental results confirm an earlier prediction of the pressureinduced instability of isotypic Ce4[Si4O4N6]O, and also show that the bulk modulus was predicted reasonably well

Did You Remember to Test Your Tokens?

Authentication is a critical security feature for confirming the identity of a system's users, typically implemented with help from frameworks like Spring Security. It is a complex feature which should be robustly tested at all stages of development. Unit testing is an effective technique for fine-grained verification of feature behaviors that is not widely-used to test authentication. Part of the problem is that resources to help developers unit test security features are limited. Most security testing guides recommend test cases in a "black box" or penetration testing perspective. These resources are not easily applicable to developers writing new unit tests, or who want a security-focused perspective on coverage. In this paper, we address these issues by applying a grounded theory-based approach to identify common (unit) test cases for token authentication through analysis of 481 JUnit tests exercising Spring Security-based authentication implementations from 53 open source Java projects. The outcome of this study is a developer-friendly unit testing guide organized as a catalog of 53 test cases for token authentication, representing unique combinations of 17 scenarios, 40 conditions, and 30 expected outcomes learned from the data set in our analysis. We supplement the test guide with common test smells to avoid. To verify the accuracy and usefulness of our testing guide, we sought feedback from selected developers, some of whom authored unit tests in our dataset.Comment: In 17th International Conference on Mining Software Repositories (MSR) 2020, Technical Track, Virtual. 11 page

A one-step procedure to probe the viscoelastic properties of cells by Atomic Force Microscopy

The increasingly recognised importance of viscoelastic properties of cells in pathological conditions requires rapid development of advanced cell microrheology technologies. Here, we present a novel Atomic Force Microscopy (AFM)-microrheology (AFM2) method for measuring the viscoelastic properties in living cells, over a wide range of continuous frequencies (0.005 Hz ~ 200 Hz), from a simple stress-relaxation nanoindentation. Experimental data were directly analysed without the need for pre-conceived viscoelastic models. We show the method had an excellent agreement with conventional oscillatory bulk-rheology measurements in gels, opening a new avenue for viscoelastic characterisation of soft matter using minute quantity of materials (or cells). Using this capability, we investigate the viscoelastic responses of cells in association with cancer cell invasive activity modulated by two important molecular regulators (i.e. mutation of the p53 gene and Rho kinase activity). The analysis of elastic (G′(ω)) and viscous (G″(ω)) moduli of living cells has led to the discovery of a characteristic transitions of the loss tangent (G″(ω)/G′(ω)) in the low frequency range (0.005 Hz ~ 0.1 Hz) that is indicative of the capability for cell restructuring of F-actin network. Our method is ready to be implemented in conventional AFMs, providing a simple yet powerful tool for measuring the viscoelastic properties of living cells

Tissue-selective expression of a conditionally-active ROCK2-estrogen receptor fusion protein

The serine/threonine kinases ROCK1 and ROCK2 are central mediators of actomyosin contractile force generation that act downstream of the RhoA small GTP-binding protein. As a result, they have key roles in regulating cell morphology and proliferation, and have been implicated in numerous pathological conditions and diseases including hypertension and cancer. Here we describe the generation of a gene-targeted mouse line that enables CRE-inducible expression of a conditionally-active fusion between the ROCK2 kinase domain and the hormone-binding domain of a mutated estrogen receptor (ROCK2:ER). This two-stage system of regulation allows for tissue-selective expression of the ROCK2:ER fusion protein, which then requires administration of estrogen analogues such as tamoxifen or 4-hydroxytamoxifen to elicit kinase activity. This conditional gain-of-function system was validated in multiple tissues by crossing with mice expressing CRE recombinase under the transcriptional control of cytokeratin14 (K14), murine mammary tumor virus (MMTV) or cytochrome P450 Cyp1A1 (Ah) promoters, driving appropriate expression in the epidermis, mammary or intestinal epithelia respectively. Given the interest in ROCK signaling in normal physiology and disease, this mouse line will facilitate research into the consequences of ROCK activation that could be used to complement conditional knockout models

Open Peer Review: An Innovation in Scientific Publishing

This research observes the emerging open peer review journals. In scientific publishing, transparency in peer review is a growing topic of interest for online journals. The traditional blind refereeing process has been criticized for lacking transparency. Although the idea of open peer review (OPR) has been explored since 1980s, it is only in this decade that OPR journals are born. Towards a more open publishing model, the peer review process--once accessible only to the editors and referees—is now available to public. The published article and its review history are being integrated into one entity; readers can submit or post comments to extend the peer process. This preliminary study observed four pioneer OPR journals representing pre-publication OPR and post-publication OPR. Data collection focuses on publication’s lifecycle from its submission to peer approval. Preliminary results include comparisons of the level of openness and nature of interactions during refereeing process