Syndromic craniosynostosis is most commonly associated with mutations in Fibroblast Growth Factor Receptor genes (FGFR)-1, 2 and 3. Clinical and animal reports suggest a link between FGFR-associated craniosynostosis and defects in the gastrointestinal tract (GIT). Objective: to determine whether GIT malformations occur more frequently in the craniosynostosis population with a known FGFR mutation when compared to the general population. Methods: A retrospective chart review of patients diagnosed with Crouzon, Pfeiffer or Apert syndromes between 1990 and 2011 was performed at the Hospital for Sick Children in Toronto. Thirty-two charts meeting inclusion criteria were analyzed for any history of GIT abnormalities. Results: Three out of 32 patients had documented intestinal/bowel malrotations while 7 had gastroesophageal reflux disease. All patients had documented FGFR2 mutations, a finding in line with previous studies and published case reports. Conclusions: Results suggest an association between FGFR-associated craniosynostosis and GIT malformations.

ARF6 et ARF1 sont des petites GTPases de la famille des ARF(s) qui régulent plusieurs voies de signalisation comprenant, la formation et le mouvement des vésicules, la transformation des lipides membranaires et la réorganisation du cytosquelette d’actine. À ce jour, le rôle de la protéine ARF6 et de la protéine ARF1 dans la signalisation des récepteurs couplés aux protéines G (RCPG) et des récepteurs à activité tyrosine kinase (RTK) dans les cellules endothéliales est encore très peu étudié. Le but de cette étude a été de caractériser le rôle de la protéine ARF6 dans la migration des cellules endothéliales induite par l’endothéline-1, ainsi que le rôle de la protéine ARF1 dans la sécrétion du monoxyde d’azote (NO) stimulées par le VEGF. Dans cette étude, nous montrons qu’ARF6 est essentielle à la migration des cellules endothéliales induite par l’endotheline-1. L’inhibition de l’expression d’ARF6 par interférence à l’ARN entraîne une activation marquée de la kinase FAK et son association constitutive avec Src. Par ailleurs, cette inhibition affecte l’association entre GIT1 et la kinase FAK. Ceci se traduit par une inhibition du désassemblage des contacts focaux et une augmentation de l’adhésion cellulaire menant à une diminution de la motilité. De plus, nos résultats montrent que la protéine ARF1 est essentielle à l’activation d’eNOS et à la sécrétion du NO suite à l’activation du VEGFR2 dans les cellules endothéliales BAEC. En effet, l’inhibition de l’expression d’ARF1 par interférence à l’ARN entraîne une inhibition du recrutement de la kinase Akt à la membrane plasmique et une inhibition de son activation induite par le VEGF. L’inhibition de l’activation de la kinase Akt par le VEGF conduit à une inhibition de l’activation de eNOS et de la sécrétion du NO. Dans l’ensemble, nos résultats montrent que les protéines ARF6 et ARF1 sont essentielles à la signalisation de l’ETB et du VEGFR2 pour les processus menant à la migration cellulaire et à la sécrétion du NO respectivement, deux évènements essentiels à l’angiogenèse. / ARF6 and ARF1 are small GTPases of the ARF family(s) that regulate several signalling pathways including vesicles trafficking, lipid membrane remodelling and actin cytoskeleton reorganization. To date, the role of ARF6 and ARF1 in GPCR and RTK signalling, in endothelial cells, is little known. In this thesis, we aimed to characterize the role of ARF6 in the migration of endothelial cells induced by Enodothelin-1, and the role of ARF1 in the secretion of NO induced by VEGF. We show that ARF6 is essential for endothelial cell migration induced by endothelin-1. Inhibition of ARF6 expression using RNA interference markedly impaired basal and ET-1 stimulated cell migration. In this condition, FAK is found constitutively associated with Src. In contrast, depletion of ARF6 impairs the ability of GIT1 to form an agonist-promoted complex with FAK, thereby preventing disassembly of focal adhesions. As a consequence, adhesion of ARF6-depleted endothelial cells is increased and their motility is reduced. Furthermore, our result shows that ARF1 GTPase is essential for the activation of eNOS and the secretion of NO following VEGFR2 activation in endothelial cells. Inhibition of ARF1 expression using RNA interference markedly impaired the recruitment of Akt to the plasma membrane and its phosphorylation by the VEGF. As a consequence, the inhibition of Akt leads to an inhibition of eNOS, a well known downstream target, which in turn leads to inhibition of NO production. All together, our results indicate that ARF6 and ARF1 are essential for the ETB and the VEGFR2 signalling leading to cell migration and NO secretion respectively, two required steps for angiogenesis.

Det är sedan länge känt, både bland företag och i den akademiska världen, att det krävs strukturerade arbetsmetoder för att lyckas med storskalig programvaruutveckling. Vilka metoder som fungerar bäst är det svårt att göra ett generellt uttalande om eftersom detta till stor del är situationsberoende. Det existerar en ansenlig mängd metoder och processer som finns beskrivna i detalj av deras förespråkare, men ingen metod fungerar felfritt i alla situationer. I den här rapporten beskrivs de metoder en projektgrupp tillämpade under ett kandidatarbete i programvaruutveckling, och konsekvenserna dessa fick för den slutgiltiga produkten. Gruppen har kommit fram till att värde har skapats för kunden genom att implementera kundens begärda system, en interaktiv webbapplikation. Underhållbarhet har uppnåtts genom att följa en kodstandard, tillämpa parprogrammering och kodgranskningar samt publicera koden som öppen källkod. Att under möten diskutera gruppmedlemmarnas välmående bidrog till bättre sammanhållning och stämning och därmed ett bättre slutresultat. Många av gruppens svårigheter hade lösts om gruppen haft ett dedikerat kontor. Förhoppningen är att de erfarenheter och den kunskap som gruppen tillgodogjort sig under projektet, och dokumenterat i den här rapporten, ska komma till nytta för både projektmedlemmarna och rapportens läsare.

This thesis discusses the extraction of information from version control systems. Its goal is to describe the implementation of a software application that facilitates this type of extraction, focusing on the version control system Git. The theoretical part of the thesis identifies and analyses data stored in repositories. It also evaluates the tools available on the market using specific criteria. The practical part specifies development requirements, describes the resulting software application, and contains a how-to manual for extending the application and implementing one's own metrics that lead to gaining information. The application is developed in the CoffeeScript programming language and Node.js engine. It contains several example metrics. The output is a graphical user interface with interactive graphs served by a built-in HTTP server. Another output option is a machine-readable export to a file.

Dependency problems for developers are like sneezing for people with pollen allergies during the spring, an everyday problem. This is especially true when working in multi-repositories. The dependency problems that occur do so as a byproduct of enabling developers to work on different components of a project in smaller teams, where everything is version controlled.Nearly all developers use version control systems, such as Git, Mercurial, or Subversion. While version control systems have helped developers for nearly 40 years and are constantly getting updated, there are still functionalities that do not exist. One example of that is having a good way of managing dependencies and allowing developers to download projects without having to handle dependency problems manually. The solutions that version control systems offer to help manage dependencies (e.g., Git’s submodules or Mercurial’s subrepositories), do not enable developers a fail-safe download or build the project if it contains dependency problems.In this study, a case study was conducted at Saab Training and Simulation to explore methods for dependency management as well as discuss and highlight some of the problems that emerge when working with dependencies in multi-repositories.An argument can be made that the functionality of dependency management systems, both package managers and version control systems’ solutions are not up to date on how dependencies are used in the development, during this time.In this paper, a novel approach to dependency management is introduced with the possibility to describe the dependencies dynamically by providing the utility to describes usages of a repository (such as simulation of hardware or the main project). As well as discussing the necessary functionalities that are required to handle such a system.By re-opening the dialog about dependency management as well as describing problems that arise in such environments, the goal is to inspire further research within these areas.

Collaboration is one of the most important topics regarding the evolution of the World Wide Web and thus also for the Web of Data. In scenarios of distributed collaboration on datasets it is necessary to provide support for multiple different versions of datasets to exist simultaneously, while also providing support for merging diverged datasets. In this paper we present an approach that uses SPARQL 1.1 in combination with the version control system Git, that creates commits for all changes applied to an RDF dataset containing multiple named graphs. Further the operations provided by Git are used to distribute the commits among collaborators and merge diverged versions of the dataset. We show the advantages of (public) Git repositories for RDF datasets and how this represents a way to collaborate on RDF data and consume it. With SPARQL 1.1 and Git in combination, users are given several opportunities to participate in the evolution of RDF data.

Finding the most relevant candidate for a position represents an ubiquitous challenge for organisations. It can also be arduous for a candidate to explain on a concise resume what they have experience with. Due to the fact that the candidate usually has to select which experience to expose and filter out some of them, they might not be detected by the person carrying out the search, whereas they were indeed having the desired experience. In the field of software engineering, developing one's experience usually leaves traces behind: the code one produced. This project explores approaches to tackle the screening challenges with an automated way of extracting experience directly from code by defining common lexical patterns in code for different experience fields, using topic modeling. Two different techniques were compared. On one hand, Latent Dirichlet Allocation (LDA) is a generative statistical model which has proven to yield good results in topic modeling. On the other hand Non-Negative Matrix Factorization (NMF) is simply a singular value decomposition of a matrix representing the code corpus as word counts per piece of code.The code gathered consisted of 30 random repositories from all the collaborators of the open-source Ruby-on-Rails project on GitHub, which was then applied common natural language processing transformation steps. The results of both techniques were compared using respectively perplexity for LDA, reconstruction error for NMF and topic coherence for both. The two first represent how well the data could be represented by the topics produced while the later estimates the hanging and fitting together of the elements of a topic, and can depict human understandability and interpretability. Given that we did not have any similar work to benchmark with, the performance of the values obtained is hard to assess scientifically. However, the method seems promising as we would have been rather confident in assigning labels to 10 of the topics generated. The results imply that one could probably use natural language processing methods directly on code production in order to extend the detected fields of experience of a developer, with a finer granularity than traditional resumes and with fields definition evolving dynamically with the technology.

Denna kandidatrapport är skriven av åtta studenter i kursen Kandidatprojekt i mjukvaruutveckling, TDDD96, vid Linköpings universitet under våren 2020. Kandidatrapporten inkluderar en sammanfattning av det arbete som utförts i projektet. Till projektet tillhörde ett uppdrag på beställning av Digitala resursenheten vid Linköpings universitet. Uppdraget var att skapa en webbapplikation där examinatorer och handledare för kurser vid Linköpings universitet på ett enkelt och intuitivt sätt kan beställa mjukvara till sina respektive kurser. Projektgruppen jobbade agilt och byggde projektet i Python samt JavaScript. Applikationen nådde alla mål satta tillsammans mellan kunden och projektgruppen och resulterade i en fungerande produkt som kunde utökas och modifieras enligt kundens behov. Till kandidatrapporten inkluderas även individuella bidrag skrivna av vardera gruppmedlem som djupdykt inom ett specifikt ämne eller område.

Denna kandidatrapport behandlar resultatet av ett kandidatarbete i kursen TDDD96:Kandidatprojekt i programvarutvekling som ges av Linköpings universitet. Projektet heter TestCoverage Visualizer (TCV) och beställdes av Saab Aeronautics. Uppdraget handlade omatt skapa ett visualiseringsverktyg för resultaten av deras testfiler.Projektet genomfördes av åtta studenter under våren 2021. Gruppen använde sig avScrum vid utvecklingen och utvecklade i språken JavaScript och Python. Projektet resulterade i en webbapplikation med en backend och frontend samt en tillhörande parser sommed hjälp av reguljära uttryck kan parsa testfiler och sparade dem i databasen. Resultatenvisades grafiskt på frontend:en med hjälp av mätare och grafer.I kandidatrapporten inkluderades även individuella bidrag skrivna av respektive projektmedlem som fördjupar sig i något ämne eller område som har något med projektet attgöra.

Software development is a process fraught with unpredictability, in part because software is created by people. Human interactions add complexity to development processes, and collaborative development can become a liability if not properly understood and managed. Recent years have seen an increase in the use of data mining techniques on publicly-available repository data with the goal of improving software development processes, and by extension, software quality. In this thesis, we introduce the concept of author entropy as a metric for quantifying interaction and collaboration (both within individual files and across projects), present results from two empirical observational studies of open-source projects, identify and analyze authorship and collaboration patterns within source code, demonstrate techniques for visualizing authorship patterns, and propose avenues for further research.