Creating a readable language for checking XML

Today sharing data is done everywhere. Doctors might want to share patient journal information. Patient journals may contain sensitive information that doctors do not want to share. The journals needs to be checked before they are shared. In this thesis, data and journals are coded in XML and checking journals and data is the same as validating XML. Validating XML documents is usually done by following rules from a validator. A validator processes XML documents and checks that the XML documents follows the validation rules. The issue with most validators today is that they cannot compare arbitrary elements in the XML document with each other and there are no mathematical operations to supply these comparisons. Sometimes there is a need to verify the validation rules. This might be done by someone who has little programming skills. The validator has to be readable so that this someone can verify that the validator matches the requirements. This thesis attempts to solve the issue with existing solutions by creating a readable language for validating XML documents. The solution is done in three steps: investigating similar solutions, implementing a validator, and testing the readability of the validator with a usability test.Idag delar man mycket information med varandra och ibland behöver vi se till att rätt sorts information delas. Tänk om man t. ex råkar skicka sitt personnummer istället för telefonnummer till någon? Detta examensarbetet handlar om att utveckla ett enkelt verktyg som bekräftar att information som delas är rätt formad. Eftersom det blir viktigare att vara säker på att information som delas är formad på rätt sätt så kommer fler människor att komma i kontakt med att bekräfta information innan de delar den. Det finns en del verktyg som kan bekräfta information åt dig men i vissa fall räcker inte dessa verktyg. Ett tillämpningsområde är sjukhusjournaler. En läkare kanske vill dela med sig av ett specifikt fall, i t. ex utbildningssyfte, genom att skicka en patientjournal till en kollega. En patientjournal innehåller mycket information om en patient som en läkare kanske inte kan eller vill dela, exempelvis patientens identitet. Alltså använder läkaren ett program genererat med verktyget från detta examensarbetet för att bekräfta att all privat (och annan potentiellt onödig) information inte finns med i journalen som läkaren tänker skicka. Företaget som examensarbetet utfördes på, Advenica, har ett testfall som kräver mer komplexa beräkningar än vad dagens verktyg klarar av. Om det är viktigt att information bekräftas på ett säkert sätt är det viktigt att någon ser på verktyget så att det gör det som den verkligen ska göra. Idag är de flesta verktygen svårläsliga vilket gör det svårt att förstå om det som verktyget gör är korrekt. Examensarbetet resulterade i ett verktyg som skapar program som bekräftar om information som ska delas är formad på rätt sätt. Verktyget används genom att någon, en programmerare med kunskap i ämnet, skriver regler som sen används för att generera ett program som bekräftar information. Reglerna är gjorda för att vara lättläsliga så människor utan programmeringsbakgrund kan förstå och kontrollera att reglerna är korrekt skrivna. De behöver inte skriva reglerna själva, det gör programmeraren. Programmen som genereras tar informationen och säger till användaren om informationen är formad på rätt sätt. Om informationen inte är formad på rätt sätt måste användaren ändra informationen tills programmet accepterar informationen. Verktyget som utvecklas har två egenskaper som inte andra verktyg har: komplexa matematiska beräkningar, när man bekräftar information, samt att reglerna som verktyget tar är lättläsliga. Med hjälp av matematiska beräkningar kan man se att informationen stämmer överens med mer komplexa krav. Exempelvis kan man beräkna sträckan mellan två koordinater på jorden med hjälp av de matematiska beräkningarna. Eftersom verktygets regler är lätta att kontrollera så är det enkelt att låta en utomstående person se på reglerna och säga om det är rätt regler för rätt syfte

Change as a Service: Challenges and Effects of a New Paradigm for Library Systems and Content Infrastructure

The infrastructure for supplying information resources to higher education and research has gone through dramatic changes the last 15 years. The amount of electronic resources available and library systems that handle them have multiplied leaving libraries in a challenging situation. We are coping with a changing definition of library collections, changing business models for owning and accessing materials as well as a shift in the architecture of library systems. The Library at Chalmers University of Technology spent close to 98% of the media budget in 2010 on electronic resources and has been spending more than 50% of the budget on electronic resources for over 10 years. So far the library has not been able to lower total cost of ownership for library systems or information resources since there has been few changes to existing systems or subscriptions. Instead we have been trying to cope with the development by introducing new systems and more electronic resources leaving us with complex workflows and dependencies. As we look to new unified services for libraries where information resources and systems are merged in a ― as a service environment there is a need for libraries to re-evaluate the current situation and what led up to it. Chalmers university library has initiated a system survey with the ambition of reviewing current workflows, quantifying and defining the crucial elements of todays systems with the goal of finding what we actually need in the near future. The evaluation is still in progress but this paper summarizes Chalmers evaluation so far, highlighting key findings, trends and possible strategies for the future

Introducing Agile Principles and Management to a Library Organization

Libraries are pressured to adapt to changing conditions due to user demands, behavior, emerging technologies and a need for cost-efficient solutions. Software companies have turned to agile development to stay competitive and to deliver working solutions in a short timeframe. Agile processes are built upon co-operation, iterative workflows and delivering working solutions with a high business value. Agile development and management in an agile organization constitutes a controlled framework of principles with a promise to ensure that the organization focuses on the right things and is able to adapt to new needs. The Library at Chalmers University of Technology in Sweden introduced agile software development in 2011 as a part of the work with the institutional repository. Following the success of introducing Scrum to system developers the formation of cross-disciplinary teams for other projects involved librarians. One of the projects for a cross-disciplinary team was to develop a brand new website. Drawing upon the experience of Scrum and with a focus on User Experience design (UX) the team was able to define an agile methodology involving different competences at the library. As other projects formed and adopted the principles of Scrum and agile the methodology spread throughout the library organization as it was re-organized. Managing an agile oriented organization can be challenging. Senior management has been forced to work with allocating resources, input to prioritization, sprint planning and judging business value thus forcing a transparency to appear in the organization and exposing its operations. Chalmers Library is still exploring the possibilities and challenges of working with agile development and management. It is an iterative and evolving process, but the benefits far outweigh the drawbacks as the organization can learn and respond to change, re-prioritize how resources are allocated, avoid knowledge silos, build strong teams and identify uncertainties early. As of January 1st 2014 the library organization changed and introduced agile principles throughout all operations

Diversity and Relatedness Enhance Survival in Colour Polymorphic Grasshoppers

Evolutionary theory predicts that different resource utilization and behaviour by alternative phenotypes may reduce competition and enhance productivity and individual performance in polymorphic, as compared with monomorphic, groups of individuals. However, firm evidence that members of more heterogeneous groups benefit from enhanced survival has been scarce or lacking. Furthermore, benefits associated with phenotypic diversity may be counterbalanced by costs mediated by reduced relatedness, since closely related individuals typically are more similar. Pygmy grasshoppers (Tetrix subulata) are characterized by extensive polymorphism in colour pattern, morphology, behaviour and physiology. We studied experimental groups founded by different numbers of mothers and found that survival was higher in low than in high density, that survival peaked at intermediate colour morph diversity in high density, and that survival was independent of diversity in low density where competition was less intense. We further demonstrate that survival was enhanced by relatedness, as expected if antagonistic and competitive interactions are discriminately directed towards non-siblings. We therefore also performed behavioural observations and staged encounters which confirmed that individuals recognized and responded differently to siblings than to non-siblings. We conclude that negative effects associated with competition are less manifest in diverse groups, that there is conflicting selection for and against genetic diversity occurring simultaneously, and that diversity and relatedness may facilitate the productivity and ecological success of groups of interacting individuals

Exploration of Extracellular Vesicle miRNAs, Targeted mRNAs and Pathways in Prostate Cancer : Relation to Disease Status and Progression

Simple Summary Prostate cancer lacks non-invasive specific biomarkers for aggressive disease. Urinary extracellular vesicles (uEV) could provide such markers; however, due to technical challenges, little is known regarding the pathogenesis pathways reflected in uEV. We performed a miRNA, target mRNA and pathway study focused on uEV, exploring the differences between cancer (1) status groups (Gleason score) and (2) progression groups. The uEV provided a surprisingly comprehensive presentation of differentially expressed miRNAs, target mRNAs and pathogenesis pathways. The miRNAs associated with prostate cancer status or progression were mostly unique, but still targeted overlapping sets of signalling, resistance, hormonal and immune pathways. Interestingly, mRNA targets of the key miRNAs (miR-892a, miR-223-3p, miR-146a-5p) were widely expressed in both uEV and plasma EV from PCa patients. The study thus suggests that uEV carry a vast presentation of PCa status and progression-linked RNAs that are worth further exploration in large personalized medicine trials. Background: Prostate cancer (PCa) lacks non-invasive specific biomarkers for aggressive disease. We studied the potential of urinary extracellular vesicles (uEV) as a liquid PCa biopsy by focusing on the micro RNA (miRNA) cargo, target messenger RNA (mRNA) and pathway analysis. Methods: We subjected uEV samples from 31 PCa patients (pre-prostatectomy) to miRNA sequencing and matched uEV and plasma EV (pEV) from three PCa patients to mRNA sequencing. EV quality control was performed by electron microscopy, Western blotting and particle and RNA analysis. We compared miRNA expression based on PCa status (Gleason Score) and progression (post-prostatectomy follow-up) and confirmed selected miRNAs by quantitative PCR. Expression of target mRNAs was mapped in matched EV. Results: Quality control showed typical small uEV, pEV, RNA and EV-protein marker enriched samples. Comparisons between PCa groups revealed mostly unique differentially expressed miRNAs. However, they targeted comprehensive and largely overlapping sets of cancer and progression-associated signalling, resistance, hormonal and immune pathways. Quantitative PCR confirmed changes in miR-892a (Gleason Score 7 vs. >= 8), miR-223-3p (progression vs. no progression) and miR-146a-5p (both comparisons). Their target mRNAs were expressed widely in PCa EV. Conclusions: PCa status and progression-linked RNAs in uEV are worth exploration in large personalized medicine trials.Peer reviewe

Exploration of Extracellular Vesicle miRNAs, Targeted mRNAs and Pathways in Prostate Cancer: Relation to Disease Status and Progression

Background: Prostate cancer (PCa) lacks non-invasive specific biomarkers for aggressive disease. We studied the potential of urinary extracellular vesicles (uEV) as a liquid PCa biopsy by focusing on the micro RNA (miRNA) cargo, target messenger RNA (mRNA) and pathway analysis. Methods: We subjected uEV samples from 31 PCa patients (pre-prostatectomy) to miRNA sequencing and matched uEV and plasma EV (pEV) from three PCa patients to mRNA sequencing. EV quality control was performed by electron microscopy, Western blotting and particle and RNA analysis. We compared miRNA expression based on PCa status (Gleason Score) and progression (post-prostatectomy follow-up) and confirmed selected miRNAs by quantitative PCR. Expression of target mRNAs was mapped in matched EV. Results: Quality control showed typical small uEV, pEV, RNA and EV-protein marker enriched samples. Comparisons between PCa groups revealed mostly unique differentially expressed miRNAs. However, they targeted comprehensive and largely overlapping sets of cancer and progression-associated signalling, resistance, hormonal and immune pathways. Quantitative PCR confirmed changes in miR-892a (Gleason Score 7 vs. ≥8), miR-223-3p (progression vs. no progression) and miR-146a-5p (both comparisons). Their target mRNAs were expressed widely in PCa EV. Conclusions: PCa status and progression-linked RNAs in uEV are worth exploration in large personalized medicine trials

Exploration of Extracellular Vesicle miRNAs, Targeted mRNAs and Pathways in Prostate Cancer : Relation to Disease Status and Progression

Simple Summary Prostate cancer lacks non-invasive specific biomarkers for aggressive disease. Urinary extracellular vesicles (uEV) could provide such markers; however, due to technical challenges, little is known regarding the pathogenesis pathways reflected in uEV. We performed a miRNA, target mRNA and pathway study focused on uEV, exploring the differences between cancer (1) status groups (Gleason score) and (2) progression groups. The uEV provided a surprisingly comprehensive presentation of differentially expressed miRNAs, target mRNAs and pathogenesis pathways. The miRNAs associated with prostate cancer status or progression were mostly unique, but still targeted overlapping sets of signalling, resistance, hormonal and immune pathways. Interestingly, mRNA targets of the key miRNAs (miR-892a, miR-223-3p, miR-146a-5p) were widely expressed in both uEV and plasma EV from PCa patients. The study thus suggests that uEV carry a vast presentation of PCa status and progression-linked RNAs that are worth further exploration in large personalized medicine trials. Background: Prostate cancer (PCa) lacks non-invasive specific biomarkers for aggressive disease. We studied the potential of urinary extracellular vesicles (uEV) as a liquid PCa biopsy by focusing on the micro RNA (miRNA) cargo, target messenger RNA (mRNA) and pathway analysis. Methods: We subjected uEV samples from 31 PCa patients (pre-prostatectomy) to miRNA sequencing and matched uEV and plasma EV (pEV) from three PCa patients to mRNA sequencing. EV quality control was performed by electron microscopy, Western blotting and particle and RNA analysis. We compared miRNA expression based on PCa status (Gleason Score) and progression (post-prostatectomy follow-up) and confirmed selected miRNAs by quantitative PCR. Expression of target mRNAs was mapped in matched EV. Results: Quality control showed typical small uEV, pEV, RNA and EV-protein marker enriched samples. Comparisons between PCa groups revealed mostly unique differentially expressed miRNAs. However, they targeted comprehensive and largely overlapping sets of cancer and progression-associated signalling, resistance, hormonal and immune pathways. Quantitative PCR confirmed changes in miR-892a (Gleason Score 7 vs. >= 8), miR-223-3p (progression vs. no progression) and miR-146a-5p (both comparisons). Their target mRNAs were expressed widely in PCa EV. Conclusions: PCa status and progression-linked RNAs in uEV are worth exploration in large personalized medicine trials.Peer reviewe