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  • 301.
    Alemayehu, Brook
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik.
    Johnsons, Fredrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik.
    Maskininlärning inom kommersiella fastigheter: Prediktion av framtida hyresvakanser2018Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    The purpose of this thesis is to investigate the possibilities of predicting vacancies in the real estate market by using machine learning models in terms of classification. These models were mainly based on data from contracts between a Swedish real estate company and their tenants. Attributes such as annual renting cost and rental area for each contract were supplemented with additional data regarding financial and geographical information about the tenants. The data was stored in three different formats with the first having binary classes which aim is to predict if the tenant is moving out within a year or more. The format of the second and third version were both multi classification problems that aims to classify if the tenants might terminate their contract within a specific interval with the length of three and six months.

    Based on the results from Microsoft Azure Machine Learning Studio, it is discovered that the multi classification problems perform rather poorly due to the classes being unbalanced. Regarding the  performance of the binary model, a more satisfying result was obtained but not to the extend to say that the model can be used to determine a vacancy with high accuracy. It should rather be used as a risk analysis tool to detect if a tenant is showing tendencies that could result in a future vacancy. A major pitfall of this thesis was the lack of data and the financial information not being specific enough. The performance of the models will likely increase with a larger dataset and more accurate financial information. 

  • 302.
    Alenius, Fabian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    Authentication and Authorization: Achieving Single Sign-on in an Erlang Environment2010Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Forcing users to enter their credentials every time they want to use a service is associated with several problems. Common problems include lowered user productivity, increased administration costs and security issues. As companies and organizations are adding more services to their networks, it is becoming an increasingly important problem. By allowing users to sign on once and centralizing access control decisions, it is possible to reduce or completely mitigate this problem. This paper describes how a service written in Erlang was modified to allow for single sign-on and centralized access control.

  • 303. Alenljung, Beatrice
    et al.
    Andreasson, Rebecca
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Lowe, Robert
    Billing, Erik
    Lindblom, Jessica
    Conveying Emotions by Touch to the Nao Robot: A User Experience Perspective2018Inngår i: Multimodal Technologies and Interaction, ISSN 2414-4088, Vol. 2, nr 4, artikkel-id 82Artikkel i tidsskrift (Fagfellevurdert)
  • 304. Alenljung, Beatrice
    et al.
    Lindblom, Jessica
    Andreasson, Rebecca
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Ziemke, Tom
    User experience in social human–robot interaction2017Inngår i: International Journal of Ambient Computing and Intelligence (IJACI), ISSN 1941-6237, E-ISSN 1941-6245, Vol. 8, nr 2, s. 12-31Artikkel i tidsskrift (Fagfellevurdert)
  • 305.
    Alenlöv, Johan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    Olsson, Jimmy
    Particle-based adaptive-lag online marginal smoothing in general state-space models2019Inngår i: IEEE Transactions on Signal Processing, ISSN 1053-587X, E-ISSN 1941-0476, Vol. 67, nr 21, s. 5571-5582Artikkel i tidsskrift (Fagfellevurdert)
  • 306.
    Alessandro, Martini
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    Biosensorsystem för övervakning av vattenkvalitet2012Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    Sweden's drinking water quality is considered to be high partly due to a high quality of the raw water and a well developed sewage infrastructure. Despite this, there is water contamination that could be prevented by installation of a sophisticated early warning system. Some of the major players in the production of drinking water have already invested in different types of early warning systems to ensure drinking water of high quality. There are various forms of early warning systems where automatic monitoring of E. Coli is an interesting alternative. Today's technology allows for this type of measurement, but it is often expensive and sometimes slow.

    This work aims to investigate whether the phenomenon of Extraordinary Optical Transmission (EOT) can be used as the technology of sensors for real-time measurement of indicators of fecal contaminated water. EOT is a transmissions peak which arises due to plasmon resonance. The study was conducted by performing verification measurements by spectrophotometry to detect the EOT. After this biomeasurements where done to show that the surface of the sample can be functionalized to provide the opportunity to choose which analytes should be detected.

    The verifying measurements showed that EOT was detected for one of the five samples where the hole size was 400 nm and the hole spacing was 600 nm. This is due to the high signal strength and to the fact that the phenomenon occurred within the measurement range of the instruments. Samples where designated with the name sPa where s indicates hole size in nm and a hole spacing in nm. The signal strength of the sample 140P600 and 200P600 was too low to determine whether EOT occurred. For samples 400P1000 and 600P1000 calculations showed that EOT occurred outside the measurement range, which meant that EOT could not be measured. Sample 400P600 was chosen to implement bio-measurements wherein the surface was functionalized with biotin Bovine serum albumin (B-BSA) to later bind with fluidMAG Streptavidin. Both B-BSA and streptavidin was bound as shown by the kinetic measurements. 

  • 307.
    Alex, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för människa-datorinteraktion.
    Business Navigator: Användarcentrerad utveckling av framtidens internetbank2010Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    This thesis deals with an iterative user-centered IT-development project in a bank setting. The aim is to present a solution for deployment of future Internet banking for small businesses. The project features a design of IT-related concepts and ideas with a strong emphasis on scenario-based design and the usage of patterns as a documentation tool.

    The project plan featured an iterative framework and was carried out by a group of designers in collaboration with a reference group representing the future users of the system. This group consisted of company managers and bank employees, all from the small town of Åtvidaberg in Sweden.

    The method used in the development process was Scrum. A total of three sprints were completed with user meetings at the end of every sprint. In these meetings, focus groups were utilized to obtain information from the users. Throughout the process patterns were used to document important concepts and ideas as well as to create project outlines. In meetings with the reference group there was extensive usage of scenario based design.

    The outcome of the project was a prototype demonstrating some of the desired functions in the future software as well as a large pattern map showing the entire project as a whole with all the concepts and ideas that were discovered during the process.

    Patterns were successfully used for documentation as well as development and helped to enhance the communication within the group of designers. Also, scenario based design worked well in the context to bridge the gap between developers and users throughout the project.

  • 308. Alexander, Perry
    et al.
    Flener, PierreUppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    Proceedings ASE 2000. The Fifteenth IEEE International Conference on Automated Software Engineering, 20002000Konferanseproceedings (Annet vitenskapelig)
  • 309. Alexander, Perry
    et al.
    Flener, PierreUppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi. Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för ekologi och evolution, Datalogi. CSD.
    Special Issue on ASE'002003Collection/Antologi (Annet vitenskapelig)
  • 310. Alexander, Sylvia
    et al.
    Amillo, June
    Roger, Boyle
    Martyn, Clark
    Daniels, Mats
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. Datorteknik.
    Laxer, Cary
    Loose, Ken
    Case studies in admission to and early performance in computer science degrees2003Inngår i: ACM SIGCSE Bulletin, ISSN 0097-8418, Vol. 35, nr 4, s. 149-153Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Changing conditions for teaching increase our motivation to understand the teaching and learning process. First time investigators of educational settings often feel uncertain about what aspects are involved and how to design a meaningful investigation. This paper develops and describes an applied research model with the ob jective of providing computer science (CS) academics of with a structured overview of the inter-disciplinary research components of CS education research.

    The paper argues that adopting such a model has the potential to enhance the maturity, significance and applicability of CS education research studies by placing them in a more complete research context. This helps to make the outcomes more readily transportable to other teaching and learning situations.

    One aim of publicizing the model is to help inspire the growing numbers of people who are becoming interested in CS education research. In addition we hope to simplify the task of gaining a rapid understanding of the research design issues and options that are typically involved.

  • 311.
    Alghamdi, Fayiq
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi. Al-Baha University .
    Why Computer Science teachers in Saudi Arabia Learn on Their Own: Impulse for Self-Directed Professional Development in CS teachingManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The research investigates the self-directed learning of CS teaching among Computer Science (CS) teachers in Saudi Arabia schools as a way of their professional development. The researchers developed a questionnaire with a 42-items inspiring from the previous literature and the purpose of the research question: How CS teachers were influenced by self-directed professional development in CS teaching? The questionnaires evaluated by the virtual honesty, Factor analysis and Alpha-Cronbach. Then, it distributed to 16 education offices and responses were received from 352 participants. The data shows that CS female teachers are more engaged in self-directed learning than CS male teachers. Also, the participants agreed on the total of average scores of the survey on learners’ self-directedness in the workplaces and self- reflection, planning, reasons and professional development for CS teachers. The recommendation made supported the CS teaching internet material recourses and make them easy and accessibility for all CS teachers community.

  • 312.
    Alghamdi, Fayiq
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi. Al-Baha University, Al Baha, Saudi Arabia.
    Why do female students choose to study CS in the Kingdom of Saudi Arabia?2017Inngår i: Proc. 5th International Conference on Learning and Teaching in Computing and Engineering, IEEE Computer Society, 2017, s. 49-53Konferansepaper (Fagfellevurdert)
    Abstract [en]

    We know that female students in computer science, CS, are fewer than male students in Western countries. What is not well understood is the high rate of Saudi female students in CS. This article explores why female students choose to study CS in the Kingdom of Saudi Arabia, KSA. Data was collected through structured interviews with ten female students in three different universities in the KSA. The content analysis approach was used. This study determines the students' experiences in studying CS. The findings of this study are a first step in paying more attention to the system of women's education in the KSA. Motivation and expectation regarding CS were investigated. Results showed that the reasons behind the engagement of Saudi female students in CS are government support, family influence, and a stable workplace. The results could help to improve the CS curriculum and program of preparation for CS teachers in the KSA.

  • 313.
    Alghamdi, Fayiq
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Women in computing in Saudi Arabia2016Inngår i: Proc. 3rd ACM-W Europe Celebration of Women in Computing, 2016, , s. 4s. 1-3Konferansepaper (Annet vitenskapelig)
  • 314.
    Alghamdi, Fayiq
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Nylén, Aletta
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Pears, Arnold
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Changing the Educational Epistemologies of Computer Science Teachers: A Case Study of the Kingdom of Saudi Arabia2018Inngår i: 2018 IEEE Frontiers in Education Conference (FIE), Piscataway, NJ: IEEE, 2018Konferansepaper (Fagfellevurdert)
    Abstract [en]

    This paper explores the attitudes of Computer Sci- ence (CS) teachers in the Kingdom of Saudi Arabia (KSA) who are confronted by the Saudi Teaching Competencies Standards (STCS). The STCS is a response to a substantial need to develop both subject-specific pedagogical ability as well as teachers subject area knowledge. The Ministry of Education in the KSA is encouraging teachers to improve their practices to achieve the new quality requirements for education. This paper presents the results of an investigation of CS teachers’ views on educational belief changes in the KSA schools. The paper addresses how and why CS teachers adopt new educational beliefs in their teaching. The paper presents the results of the investigation of the CS teachers views on educational belief changes in the KSA schools and the STCS policy document guidelines. Research in the area of changing educational epistemology in teaching CS identifies six factors that influence teachers, these are personal pedagogical beliefs, peer learning, curriculum, self-directed learning, student feedback and the STCS. A mixed method study approach was adopted in this work. Content analysis has been applied to the interview transcript and thematic coding analysis to the government policy document (STCS). The results provide a valuable case study in the KSA and emphasize the weak relationship between educational epistemology change and the STCS norms. The findings show that the STCS should provide stronger guidance for CS teachers to keep changing beliefs in teaching CS. The STCS should offer supporting official resources to CS teachers to help them in changing their beliefs in regard to teaching CS.

  • 315.
    Alghamdi, Fayiq
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Nylén, Aletta
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Pears, Arnold
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Teachers’ Awards - an Incentive for Pedagogical Development in Saudi Arabia2019Konferansepaper (Fagfellevurdert)
    Abstract [en]

    This work-in-progress paper presents a study on

    how K-12 Computer Science teachers in Saudi Arabia have

    changed their pedagogy as a result of engaging in one year of

    professional development leading up to applying for a teacher’s

    award. The results are based on thematic analysis of fourteen

    interviews with teachers that have been awarded either the

    ’Education Excellence Award’ or the ’Microsoft Expert in Education’.

    The study focuses on how preparing for and getting

    the teaching award has influenced them focusing on changes

    in their pedagogical development and subsequent practices. The

    work provides an in-depth description of several aspects of

    the Saudi Arabian teaching culture. It explores and discusses

    the affordances of mechanisms used to strengthen pedagogical

    competence in a teacher community, paying extra attention to

    awards. This study identifies four main factors that motivate

    teachers to engage in pedagogical development in teaching

    Computer Science. The research suggests that awards can be an

    efficient motivator in establishing a culture of excellence among

    Computer Science teachers.

  • 316.
    Alghamdi, Fayiq
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Pears, Arnold
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Nylén, Aletta
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Computer science teachers perspectives on competencies: A case study in the Kingdom of Saudi Arabia2018Inngår i: Informatics in Schools. Fundamentals of Computer Science and Software Engineering, Springer, 2018, s. 129-140Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The Kingdom of Saudi Arabia (KSA) has recently adopted the Saudi Teaching Competencies Standard (STCS). This paper tries to answer how these competencies are achieved, how they are maintained, and what support exists to support teaching CS competently in the KSA. This paper presents the results of an investigation of teacher awareness of, and attitudes to, the STCS in the Kingdom. Through the study reported here, we address an urgent need in the Kingdom to understand teacher preparedness in terms of CS teaching competencies. The study draws on interviews with ten CS teachers in five different cities in the KSA. A thematic coding analysis approach was used. This study explores the CS teaching competencies held by teachers in three areas of CS teaching, focusing on connection to society, professional practice and professional development. The results of the study highlight the CS teaching competencies that CS teachers feel they currently grasp well in the KSA. By enhancing awareness of what teachers currently do well we contribute to the adjustment and improvement of the STCS and help to build a program which addresses the current in-service training needs of CS teachers. The outcomes also help to raise awareness of the challenges of implementing the Computer Education curriculum in KSA schools.

  • 317.
    Algvere, Caroline
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    Bull, Victoria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    Trodin, Matilda
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    Wallner, Vanja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    En interaktiv webbapplikation för elever med inlärningsproblematik2018Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Almost one out of five Swedish students finish 9th grade without the option to continue their education due to not passing compulsory courses. Unfortunately, students with ADHD or autism often fall into this category. The opportunity to get extra support for the students who are at risk of not passing their courses is guaranteed by law, but the schools often fail to fulfill these rights. Todays education is seldom adjusted to meet the needs of the individual. Our ambition was to create a web application to be used as a mean of supporting teachers in their teaching and students in their learning. The functionality of the application is divided into two different views; the one of the teachers and the one of the students. The teachers can create assignments with different types of questions for their students. Some examples are multiple choice questions, drag-and-drop questions, questions that require a written answer and questions based on images. The teachers can in that way vary their assignments depending on what suits the student. They can also provide leads on how to solve a question which the students can activate if they want the question explained more thoroughly step-by-step. The resulting product has a lot of potential for development and needs to be connected to a data base before it can be used in a big scale.

  • 318.
    Alhalaweh, Amjad
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Alzghoul, Ahmad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Bergström, Christel A. S.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Molecular Drivers of Crystallization Kinetics for Drugs in Supersaturated Aqueous Solutions2019Inngår i: Journal of Pharmaceutical Sciences, ISSN 0022-3549, E-ISSN 1520-6017, Vol. 108, nr 1, s. 252-259Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this study, we explore molecular properties of importance in solution-mediated crystallization occurring in supersaturated aqueous drug solutions. Furthermore, we contrast the identified molecular properties with those of importance for crystallization occurring in the solid state. A literature data set of 54 structurally diverse compounds, for which crystallization kinetics from supersaturated aqueous solutions and in melt-quenched solids were reported, was used to identify molecular drivers for crystallization kinetics observed in solution and contrast these to those observed for solids. The compounds were divided into fast, moderate, and slow crystallizers, and in silico classification was developed using a molecular K-nearest neighbor model. The topological equivalent of Grav3 (related to molecular size and shape) was identified as the most important molecular descriptor for solution crystallization kinetics; the larger this descriptor, the slower the crystallization. Two electrotopological descriptors (the atom-type E-state index for -Caa groups and the sum of absolute values of pi Fukui(+) indices on C) were found to separate the moderate and slow crystallizers in the solution. The larger these descriptors, the slower the crystallization. With these 3 descriptors, the computational model correctly sorted the crystallization tendencies from solutions with an overall classification accuracy of 77% (test set).

  • 319.
    Alhalaweh, Amjad
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Alzghoul, Ahmad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Kaialy, Waseem
    Mahlin, Denny
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Bergström, Christel A. S.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Computational predictions of glass-forming ability and crystallization tendency of drug molecules2014Inngår i: Molecular Pharmaceutics, ISSN 1543-8384, E-ISSN 1543-8392, Vol. 11, nr 9, s. 3123-3132Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Amorphization is an attractive formulation technique for drugs suffering from poor aqueous solubility as a result of their high lattice energy. Computational models that can predict the material properties associated with amorphization, such as glass-forming ability (GFA) and crystallization behavior in the dry state, would be a time-saving, cost-effective, and material-sparing approach compared to traditional experimental procedures. This article presents predictive models of these properties developed using support vector machine (SVM) algorithm. The GFA and crystallization tendency were investigated by melt-quenching 131 drug molecules in situ using differential scanning calorimetry. The SVM algorithm was used to develop computational models based on calculated molecular descriptors. The analyses confirmed the previously suggested cutoff molecular weight (MW) of 300 for glass-formers, and also clarified the extent to which MW can be used to predict the GFA of compounds with MW < 300. The topological equivalent of Grav3_3D, which is related to molecular size and shape, was a better descriptor than MW for GFA; it was able to accurately predict 86% of the data set regardless of MW. The potential for crystallization was predicted using molecular descriptors reflecting Hückel pi atomic charges and the number of hydrogen bond acceptors. The models developed could be used in the early drug development stage to indicate whether amorphization would be a suitable formulation strategy for improving the dissolution and/or apparent solubility of poorly soluble compounds.

  • 320.
    Alhalaweh, Amjad
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Alzghoul, Ahmad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Mahlin, Denny
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Bergström, Christel A. S.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Physical stability of drugs after storage above and below the glass transition temperature: Relationship to glass-forming ability2015Inngår i: International Journal of Pharmaceutics, ISSN 0378-5173, E-ISSN 1873-3476, Vol. 495, nr 1, s. 312-317Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Amorphous materials are inherently unstable and tend to crystallize upon storage. In this study, we investigated the extent to which the physical stability and inherent crystallization tendency of drugs are related to their glass-forming ability (GFA), the glass transition temperature (T-g) and thermodynamic factors. Differential scanning calorimetry was used to produce the amorphous state of 52 drugs [ 18 compounds crystallized upon heating (Class II) and 34 remained in the amorphous state (Class III)] and to perform in situ storage for the amorphous material for 12 h at temperatures 20 degrees C above or below the T-g. A computational model based on the support vector machine (SVM) algorithm was developed to predict the structure-property relationships. All drugs maintained their Class when stored at 20 degrees C below the T-g. Fourteen of the Class II compounds crystallized when stored above the T-g whereas all except one of the Class III compounds remained amorphous. These results were only related to the glass-forming ability and no relationship to e. g. thermodynamic factors was found. The experimental data were used for computational modeling and a classification model was developed that correctly predicted the physical stability above the T-g. The use of a large dataset revealed that molecular features related to aromaticity and pi-pi interactions reduce the inherent physical stability of amorphous drugs.

  • 321.
    Ali Arslan, Mehmet
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    Generation and Bioinformatic Analysis of Synthetic Ago HITS-CLIP Data2013Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    Micro-RNAs (miRNAs) have been discovered to regulate messenger RNA (mRNA) translation and degradation. Various recent studies have been focused on miRNA target prediction, in order to get a better understanding of the rules and nature of miRNA regulation over mRNAs. In this project we aim to create a software module to identify miRNA target sites on mRNAs. As basis to this project, we refer to a study that identified a platform for miRNA-mRNA interaction in protein-RNA complexes in mouse brain (AGO HITS-CLIP study). We propose a probabilistic model of the data from this study, and generate synthetic sample data according to this model, in order to create a test bed for a discovery module. Our discovery module analyzes the sample data to identify peak regions where the interaction density is high. We present results both on synthetic sample data and data from the AGO HITS-CLIP study to evaluate our module.

  • 322.
    Alimehr, Leila
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    The Performance of Sequence Alignment Algorithms2013Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    This thesis deals with sequence alignment algorithms. The sequence alignment is a mutual arrange of two or more sequences in order to study their similarity and dissimilarity. Four decades after the seminal work by Needleman and Wunsch in 1970, these methods still need more explorations.

    We start out with a review of a sequence alignment, and its generalization to multiple alignments, although the focus of this thesis is on the evaluation of the new alignment algorithms. The research presented here in has stepped into the different algorithms that are in terms of the dynamic programming. In the study of sequence alignment algorithms, two powerful techniques have been invented. According to the simulations, the new algorithms are shown to be extremely efficient for the comparing DNA sequences. All the sequence alignment algorithmsare compared in terms of the distance. We use the programming language R for the implementation and simulation of the algorithms discussed in this thesis.

  • 323.
    Alipour, Mehdi
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Carlson, Trevor E.
    Black-Schaffer, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Kaxiras, Stefanos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Maximizing limited resources: A limit-based study and taxonomy of out-of-order commit2019Inngår i: Journal of Signal Processing Systems, ISSN 1939-8018, E-ISSN 1939-8115, Vol. 91, nr 3-4, s. 379-397Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Out-of-order execution is essential for high performance, general-purpose computation, as it can find and execute useful work instead of stalling. However, it is typically limited by the requirement of visibly sequential, atomic instruction executionin other words, in-order instruction commit. While in-order commit has a number of advantages, such as providing precise interrupts and avoiding complications with the memory consistency model, it requires the core to hold on to resources (reorder buffer entries, load/store queue entries, physical registers) until they are released in program order. In contrast, out-of-order commit can release some resources much earlier, yielding improved performance and/or lower resource requirements. Non-speculative out-of-order commit is limited in terms of correctness by the conditions described in the work of Bell and Lipasti (2004). In this paper we revisit out-of-order commit by examining the potential performance benefits of lifting these conditions one by one and in combination, for both non-speculative and speculative out-of-order commit. While correctly handling recovery for all out-of-order commit conditions currently requires complex tracking and expensive checkpointing, this work aims to demonstrate the potential for selective, speculative out-of-order commit using an oracle implementation without speculative rollback costs. Through this analysis of the potential of out-of-order commit, we learn that: a) there is significant untapped potential for aggressive variants of out-of-order commit; b) it is important to optimize the out-of-order commit depth for a balanced design, as smaller cores benefit from reduced depth while larger cores continue to benefit from deeper designs; c) the focus on implementing only a subset of the out-of-order commit conditions could lead to efficient implementations; d) the benefits of out-of-order commit increases with higher memory latency and in conjunction with prefetching; e) out-of-order commit exposes additional parallelism in the memory hierarchy.

  • 324.
    Alipour, Mehdi
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Carlson, Trevor E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Kaxiras, Stefanos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    A Taxonomy of Out-of-Order Instruction Commit2017Inngår i: 2017 Ieee International Symposium On Performance Analysis Of Systems And Software (Ispass), Los Alamitos: IEEE Computer Society, 2017, s. 135-136Konferansepaper (Fagfellevurdert)
    Abstract [en]

    While in-order instruction commit has its advantages, such as providing precise interrupts and avoiding complications with the memory consistency model, it requires the core to hold on to resources (reorder buffer entries, load/store queue entries, registers) until they are released in program order. In contrast, out-of-order commit releases resources much earlier, yielding improved performance without the need for additional hardware resources. In this paper, we revisit out-of-order commit from a different perspective, not by proposing another hardware technique, but by introducing a taxonomy and evaluating three different micro-architectures that have this technique enabled. We show how smaller processors can benefit from simple out-oforder commit strategies, but that larger, aggressive cores require more aggressive strategies to improve performance.

  • 325.
    Alipour, Mehdi
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Carlson, Trevor E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Kaxiras, Stefanos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Exploring the performance limits of out-of-order commit2017Inngår i: Proc. 14th Computing Frontiers Conference, New York: ACM Press, 2017, s. 211-220Konferansepaper (Fagfellevurdert)
  • 326.
    Alipour, Mehdi
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Kumar, Rakesh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Kaxiras, Stefanos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Black-Schaffer, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Delay and Bypass: Ready and Criticality Aware Instruction Scheduling in Out-of-Order Processors2020Inngår i: The 26th IEEE International Symposium on High-Performance Computer Architecture (HPCA) / [ed] IEEE, 2020Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Flexible instruction scheduling is essential for performance in out-of-order processors. This is typically achieved by using CAM-based Instruction Queues (IQs) that provide complete flexibility in choosing ready instructions for execution, but at the cost of significant scheduling energy.

    In this work we seek to reduce the instruction scheduling energy by reducing the depth and width of the IQ. We do so by classifying instructions based on their readiness and criticality, and using this information to bypass the IQ for instructions that will not benefit from its expensive scheduling structures and delay instructions that will not harm performance. Combined, these approaches allow us to offload a significant portion of the instructions from the IQ to much cheaper FIFO-based scheduling structures without hurting performance. As a result we can reduce the IQ depth and width by half, thereby saving energy.

    Our design, Delay and Bypass (DNB), is the first design to explicitly address both readiness and criticality to reduce scheduling energy. By handling both classes we are able to achieve 95% of the baseline out-of-order performance while only using 33% of the scheduling energy. This represents a significant improvement over previous designs which addressed only criticality or readiness (91%/89% performance at 74%/53% energy).

  • 327.
    Alipour, Mehdi
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation.
    Kumar, Rakesh
    Norwegian Univ Sci & Technol, Dept Comp Sci, Trondheim, Norway.
    Kaxiras, Stefanos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Black-Schaffer, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    FIFOrder MicroArchitecture: Ready-Aware Instruction Scheduling for OoO Processors2019Inngår i: 2019 Design, Automation & Test in Europe Conference & Exhibition (DATE), IEEE, 2019, s. 716-721Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The number of instructions a processor's instruction queue can examine (depth) and the number it can issue together (width) determine its ability to take advantage of the ILP in an application. Unfortunately, increasing either the width or depth of the instruction queue is very costly due to the content-addressable logic needed to wakeup and select instructions out-of-order. This work makes the observation that a large number of instructions have both operands ready at dispatch, and therefore do not benefit from out-of-order scheduling. We leverage this to place such ready-at-dispatch instructions in separate, simpler, in-order FIFO queues for scheduling. With such additional queues, we can reduce the size and width of the expensive out-of-order instruction queue, without reducing the processor's overall issue width and depth. Our design, FIFOrder, is able to steer more than 60% of instructions to the cheaper FIFO queues, providing a 50% energy savings over a traditional out-of-order instruction queue design, while delivering 8% higher performance.

  • 328.
    Alirezaie, Marjan
    et al.
    Örebro University.
    Renoux, Jennifer
    Örebro University.
    Köckemann, Uwe
    Örebro University.
    Kristoffersson, Annica
    Örebro University.
    Karlsson, Lars
    Örebro University.
    Blomqvist, Eva
    SICS East.
    Tsiftes, Nicolas
    SICS.
    Voigt, Thiemo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorarkitektur och datorkommunikation. SICS.
    Loutfi, Amy
    Örebro University.
    An Ontology-based Context-aware System for Smart Homes: E-care@ home2017Inngår i: Sensors, ISSN 1424-8220, E-ISSN 1424-8220, Vol. 17, nr 7Artikkel i tidsskrift (Fagfellevurdert)
  • 329.
    Allalou, Amin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Methods for 2D and 3D Quantitative Microscopy of Biological Samples2011Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    New microscopy techniques are continuously developed, resulting in more rapid acquisition of large amounts of data. Manual analysis of such data is extremely time-consuming and many features are difficult to quantify without the aid of a computer. But with automated image analysis biologists can extract quantitative measurements and increases throughput significantly, which becomes particularly important in high-throughput screening (HTS). This thesis addresses automation of traditional analysis of cell data as well as automation of both image capture and analysis in zebrafish high-throughput screening. 

    It is common in microscopy images to stain the nuclei in the cells, and to label the DNA and proteins in different ways. Padlock-probing and proximity ligation are highly specific detection methods that  produce point-like signals within the cells. Accurate signal detection and segmentation is often a key step in analysis of these types of images. Cells in a sample will always show some degree of variation in DNA and protein expression and to quantify these variations each cell has to be analyzed individually. This thesis presents development and evaluation of single cell analysis on a range of different types of image data. In addition, we present a novel method for signal detection in three dimensions. 

    HTS systems often use a combination of microscopy and image analysis to analyze cell-based samples. However, many diseases and biological pathways can be better studied in whole animals, particularly those that involve organ systems and multi-cellular interactions. The zebrafish is a widely-used vertebrate model of human organ function and development. Our collaborators have developed a high-throughput platform for cellular-resolution in vivo chemical and genetic screens on zebrafish larvae. This thesis presents improvements to the system, including accurate positioning of the fish which incorporates methods for detecting regions of interest, making the system fully automatic. Furthermore, the thesis describes a novel high-throughput tomography system for screening live zebrafish in both fluorescence and bright field microscopy. This 3D imaging approach combined with automatic quantification of morphological changes enables previously intractable high-throughput screening of vertebrate model organisms.

    Delarbeid
    1. A detailed analysis of 3D subcellular signal localization
    Åpne denne publikasjonen i ny fane eller vindu >>A detailed analysis of 3D subcellular signal localization
    Vise andre…
    2009 (engelsk)Inngår i: Cytometry Part A, ISSN 1552-4922, Vol. 75A, nr 4, s. 319-328Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Detection and localization of fluorescent signals in relation to other subcellular structures is an important task in various biological studies. Many methods for analysis of fluorescence microscopy image data are limited to 2D. As cells are in fact 3D structures, there is a growing need for robust methods for analysis of 3D data. This article presents an approach for detecting point-like fluorescent signals and analyzing their subnuclear position. Cell nuclei are delineated using marker-controlled (seeded) 3D watershed segmentation. User-defined object and background seeds are given as input, and gradient information defines merging and splitting criteria. Point-like signals are detected using a modified stable wave detector and localized in relation to the nuclear membrane using distance shells. The method was applied to a set of biological data studying the localization of Smad2-Smad4 protein complexes in relation to the nuclear membrane. Smad complexes appear as early as 1 min after stimulation while the highest signal concentration is observed 45 min after stimulation, followed by a concentration decrease. The robust 3D signal detection and concentration measures obtained using the proposed method agree with previous observations while also revealing new information regarding the complex formation.

    Emneord
    3D image analysis, fluorescence signal segmentation, subcellular positioning, Smad detection
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-98014 (URN)10.1002/cyto.a.20663 (DOI)000264513800006 ()
    Tilgjengelig fra: 2009-02-05 Laget: 2009-02-05 Sist oppdatert: 2018-01-13bibliografisk kontrollert
    2. Single-cell A3243G mitochondrial DNA mutation load assays for segregation analysis
    Åpne denne publikasjonen i ny fane eller vindu >>Single-cell A3243G mitochondrial DNA mutation load assays for segregation analysis
    Vise andre…
    2007 (engelsk)Inngår i: Journal of Histochemistry and Cytochemistry, ISSN 0022-1554, E-ISSN 1551-5044, Vol. 55, nr 11, s. 1159-1166Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Segregation of mitochondrial DNA (mtDNA) is an important underlying pathogenic factor in mtDNA mutation accumulation in mitochondrial diseases and aging, but the molecular mechanisms of mtDNA segregation are elusive. Lack of high-throughput single-cell mutation load assays lies at the root of the paucity of studies in which, at the single-cell level, mitotic mtDNA segregation patterns have been analyzed. Here we describe development of a novel fluorescence-based, non-gel PCR restriction fragment length polymorphism method for single-cell A3243G mtDNA mutation load measurement. Results correlated very well with a quantitative in situ Padlock/rolling circle amplification–based genotyping method. In view of the throughput and accuracy of both methods for single-cell A3243G mtDNA mutation load determination, we conclude that they are well suited for segregation analysis.

    Emneord
    A3243G mtDNA, Aging, Heteroplasmy, Mitochondrial diseases, Mutation load, Padlock probing, PCR-RFLP, Segregation
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-12658 (URN)10.1369/jhc.7A7282.2007 (DOI)000250320100009 ()17679731 (PubMedID)
    Tilgjengelig fra: 2008-01-09 Laget: 2008-01-09 Sist oppdatert: 2017-12-11bibliografisk kontrollert
    3. BlobFinder, a tool for fluorescence microscopy image cytometry
    Åpne denne publikasjonen i ny fane eller vindu >>BlobFinder, a tool for fluorescence microscopy image cytometry
    2009 (engelsk)Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 94, nr 1, s. 58-65Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Images can be acquired at high rates with modern fluorescence microscopy hardware, giving rise to a demand for high-speed analysis of image data. Digital image cytometry, i.e., automated measurements and extraction of quantitative data from images of cells, provides valuable information for many types of biomedical analysis. There exists a number of different image analysis software packages that can be programmed to perform a wide array of useful measurements. However, the multi-application capability often compromises the simplicity of the tool. Also, the gain in speed of analysis is often compromised by time spent learning complicated software. We provide a free software called BlobFinder that is intended for a limited type of application, making it easy to use, easy to learn and optimized for its particular task. BlobFinder can perform batch processing of image data and quantify as well as localize cells and point like source signals in fluorescence microscopy images, e.g., from FISH, in situ PLA and padlock probing, in a fast and easy way.

    Emneord
    Image cytometry, Single cell analysis, FISH, Software
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-87971 (URN)10.1016/j.cmpb.2008.08.006 (DOI)000264282400006 ()18950895 (PubMedID)
    Tilgjengelig fra: 2009-01-22 Laget: 2009-01-16 Sist oppdatert: 2018-06-26bibliografisk kontrollert
    4. Robust signal detection in 3D fluorescence microscopy
    Åpne denne publikasjonen i ny fane eller vindu >>Robust signal detection in 3D fluorescence microscopy
    2010 (engelsk)Inngår i: Cytometry. Part A, ISSN 1552-4922, Vol. 77A, nr 1, s. 86-96Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Robust detection and localization of biomolecules inside cells is of great importance to better understand the functions related to them. Fluorescence microscopy and specific staining methods make biomolecules appear as point-like signals on image data, often acquired in 3D. Visual detection of such point-like signals can be time consuming and problematic if the 3D images are large, containing many, sometimes overlapping, signals. This sets a demand for robust automated methods for accurate detection of signals in 3D fluorescence microscopy. We propose a new 3D point-source signal detection method that is based on Fourier series. The method consists of two parts, a detector, which is a cosine filter to enhance the point-like signals, and a verifier, which is a sine filter to validate the result from the detector. Compared to conventional methods, our method shows better robustness to noise and good ability to resolve signals that are spatially close. Tests on image data show that the method has equivalent accuracy in signal detection in comparison to Visual detection by experts. The proposed method can be used as an efficient point-like signal detection tool for various types of biological 3D image data.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-98015 (URN)10.1002/cyto.a.20795 (DOI)000273384700011 ()
    Tilgjengelig fra: 2009-02-05 Laget: 2009-02-05 Sist oppdatert: 2011-11-04bibliografisk kontrollert
    5. High-throughput in vivo optical projection tomography of small vertebrates
    Åpne denne publikasjonen i ny fane eller vindu >>High-throughput in vivo optical projection tomography of small vertebrates
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-159203 (URN)
    Tilgjengelig fra: 2011-09-25 Laget: 2011-09-25 Sist oppdatert: 2011-11-04
    6. Fully automated cellular-resolution vertebrate screening platform with parallel animal processing
    Åpne denne publikasjonen i ny fane eller vindu >>Fully automated cellular-resolution vertebrate screening platform with parallel animal processing
    Vise andre…
    2012 (engelsk)Inngår i: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 12, nr 4, s. 711-716Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The zebrafish larva is an optically-transparent vertebrate model with complex organs that is widelyused to study genetics, developmental biology, and to model various human diseases. In this article, wepresent a set of novel technologies that significantly increase the throughput and capabilities of ourpreviously described vertebrate automated screening technology (VAST). We developed a robustmulti-thread system that can simultaneously process multiple animals. System throughput is limitedonly by the image acquisition speed rather than by the fluidic or mechanical processes. We developedimage recognition algorithms that fully automate manipulation of animals, including orienting andpositioning regions of interest within the microscope’s field of view. We also identified the optimalcapillary materials for high-resolution, distortion-free, low-background imaging of zebrafish larvae.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-159202 (URN)10.1039/c1lc20849g (DOI)000299380800007 ()
    Tilgjengelig fra: 2011-09-25 Laget: 2011-09-25 Sist oppdatert: 2018-01-12bibliografisk kontrollert
    7. Image based measurements of single cell mtDNA mutation load MTD 2007
    Åpne denne publikasjonen i ny fane eller vindu >>Image based measurements of single cell mtDNA mutation load MTD 2007
    Vise andre…
    2007 (engelsk)Inngår i: Medicinteknikdagarna 2007, 2007Konferansepaper, Publicerat paper (Annet (populærvitenskap, debatt, mm))
    Abstract [en]

    Cell cultures as well as cells in tissue always display a certain degree of variability,and measurements based on cell averages will miss important information contained in a heterogeneous population. These differences among cells in a population may be essential to quantify when looking at, e.g., protein expression and mutations in tumor cells which often show high degree of heterogeneity.

    Single nucleotide mutations in the mithochondrial DNA (mtDNA) can accumulate and later be present in large proportions of the mithocondria causing devastating diseases. To study mtDNA accumulation and segregation one needs to measure the amount of mtDNA mutations in each cell in multiple serial cell culture passages. The different degrees of mutation in a cell culture can be quantified by making measurements on individual cells as an alternative to looking at an average of a population. Fluorescence microscopy in combination with automated digital image analysis provides an efficient approach to this type of single cell analysis.

    Image analysis software for these types of applications are often complicated and not easy to use for persons lacking extensive knowledge in image analysis, e.g., laboratory personnel. This paper presents a user friendly implementation of an automated method for image based measurements of mtDNA mutations in individual cells detected with padlock probes and rolling-circle amplification (RCA). The mitochondria are present in the cell’s cytoplasm, and here each cytoplasm has to be delineated without the presence of a cytoplasmic stain. Three different methods for segmentation of cytoplasms are compared and it is shown that automated cytoplasmic delineation can be performed 30 times faster than manual delineation, with an accuracy as high as 87%. The final image based measurements of mitochondrial mutation load are also compared to, and show high agreement with, measurements made using biochemical techniques.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-12745 (URN)
    Tilgjengelig fra: 2008-01-11 Laget: 2008-01-11 Sist oppdatert: 2018-01-12bibliografisk kontrollert
    8. Increasing the dynamic range of in situ PLA
    Åpne denne publikasjonen i ny fane eller vindu >>Increasing the dynamic range of in situ PLA
    Vise andre…
    2011 (engelsk)Inngår i: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 8, nr 11, s. 892-893Artikkel i tidsskrift, Editorial material (Fagfellevurdert) Published
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-159199 (URN)10.1038/nmeth.1743 (DOI)000296891800004 ()
    Tilgjengelig fra: 2011-09-25 Laget: 2011-09-25 Sist oppdatert: 2017-12-08bibliografisk kontrollert
    9. High-throughput cellular-resolution in vivo vertebrate screening
    Åpne denne publikasjonen i ny fane eller vindu >>High-throughput cellular-resolution in vivo vertebrate screening
    Vise andre…
    2011 (engelsk)Inngår i: Proc. 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 2011Konferansepaper, Publicerat paper (Fagfellevurdert)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-159201 (URN)
    Tilgjengelig fra: 2011-09-25 Laget: 2011-09-25 Sist oppdatert: 2011-11-04
  • 330.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Curic, Vladimir
    Pardo-Martin, Carlos
    Massachusetts Institute of Technology, USA.
    Yanik, Mehmet Fatih
    Massachusetts Institute of Technology, USA.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Approaches for increasing throughput andinformation content of image-based zebrafishscreens2011Inngår i: Proceeding of SSBA 2011, 2011Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Microscopy in combination with image analysis has emerged as one of the most powerful and informativeways to analyze cell-based high-throughput screening (HTS) samples in experiments designed to uncover novel drugs and drug targets. However, many diseases and biological pathways can be better studied in whole animals, particularly diseases and pathways that involve organ systems and multicellular interactions, such as organ development, neuronal degeneration and regeneration, cancer metastasis, infectious disease progression and pathogenesis. The zebrafish is a wide-spread and popular vertebrate model of human organfunction and development, and it is unique in the sense that large-scale in vivo genetic and chemical studies are feasible due in part to its small size, optical transparency,and aquatic habitat. To improve the throughput and complexity of zebrafish screens, a high-throughput platform for cellular-resolution in vivo chemical and genetic screens on zebrafish larvae has been developed at Yanik lab at Research Laboratory of Electronics, MIT, USA. The system loads live zebrafish from reservoirs or multiwell plates, positions and rotates them for high-speed confocal imaging of organs,and dispenses the animals without damage. We present two improvements to the described system, including automation of positioning of the animals and a novel approach for brightfield microscopy tomographic imaging of living animals.

  • 331.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    Pinidiyaarachchi, Amalka
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    Robust signal detection in 3D fluorescence microscopy2010Inngår i: Cytometry. Part A, ISSN 1552-4922, Vol. 77A, nr 1, s. 86-96Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Robust detection and localization of biomolecules inside cells is of great importance to better understand the functions related to them. Fluorescence microscopy and specific staining methods make biomolecules appear as point-like signals on image data, often acquired in 3D. Visual detection of such point-like signals can be time consuming and problematic if the 3D images are large, containing many, sometimes overlapping, signals. This sets a demand for robust automated methods for accurate detection of signals in 3D fluorescence microscopy. We propose a new 3D point-source signal detection method that is based on Fourier series. The method consists of two parts, a detector, which is a cosine filter to enhance the point-like signals, and a verifier, which is a sine filter to validate the result from the detector. Compared to conventional methods, our method shows better robustness to noise and good ability to resolve signals that are spatially close. Tests on image data show that the method has equivalent accuracy in signal detection in comparison to Visual detection by experts. The proposed method can be used as an efficient point-like signal detection tool for various types of biological 3D image data.

  • 332.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    van de Rijke, Frans
    Jahangir Tafrechi, Roos
    Raap, Anton
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    Image based measurements of single cell mtDNA mutation load MTD 20072007Inngår i: Medicinteknikdagarna 2007, 2007Konferansepaper (Annet (populærvitenskap, debatt, mm))
    Abstract [en]

    Cell cultures as well as cells in tissue always display a certain degree of variability,and measurements based on cell averages will miss important information contained in a heterogeneous population. These differences among cells in a population may be essential to quantify when looking at, e.g., protein expression and mutations in tumor cells which often show high degree of heterogeneity.

    Single nucleotide mutations in the mithochondrial DNA (mtDNA) can accumulate and later be present in large proportions of the mithocondria causing devastating diseases. To study mtDNA accumulation and segregation one needs to measure the amount of mtDNA mutations in each cell in multiple serial cell culture passages. The different degrees of mutation in a cell culture can be quantified by making measurements on individual cells as an alternative to looking at an average of a population. Fluorescence microscopy in combination with automated digital image analysis provides an efficient approach to this type of single cell analysis.

    Image analysis software for these types of applications are often complicated and not easy to use for persons lacking extensive knowledge in image analysis, e.g., laboratory personnel. This paper presents a user friendly implementation of an automated method for image based measurements of mtDNA mutations in individual cells detected with padlock probes and rolling-circle amplification (RCA). The mitochondria are present in the cell’s cytoplasm, and here each cytoplasm has to be delineated without the presence of a cytoplasmic stain. Three different methods for segmentation of cytoplasms are compared and it is shown that automated cytoplasmic delineation can be performed 30 times faster than manual delineation, with an accuracy as high as 87%. The final image based measurements of mitochondrial mutation load are also compared to, and show high agreement with, measurements made using biochemical techniques.

  • 333.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    van de Rijke, Frans M.
    Jahangir Tafrechi, Roos
    Raap, Anton K.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Image Based Measurements of Single Cell mtDNA Mutation Load2007Inngår i: Image Analysis, Proceedings / [ed] Ersboll BK, Pedersen KS, 2007, s. 631-640Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Cell cultures as well as cells in tissue always display a certain degree of variability, and measurements based on cell averages will miss important information contained in a heterogeneous population. This paper presents automated methods for image based measurements of mitochondiral DNA (mtDNA) mutations in individual cells. The mitochondria are present in the cell’s cytoplasm, and each cytoplasm has to be delineated. Three different methods for segmentation of cytoplasms are compared and it is shown that automated cytoplasmic delineation can be performed 30 times faster than manual delineation, with an accuracy as high as 87%. The final image based measurements of mitochondrial mutation load are also compared to, and show high agreement with, measurements made using biochemical techniques.

  • 334.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Wu, Yuelong
    Ghannad-Rezaie, Mostafa
    Eimon, Peter M.
    Yanik, Mehmet Fatih
    Automated deep-phenotyping of the vertebrate brain2017Inngår i: eLIFE, E-ISSN 2050-084X, Vol. 6, artikkel-id e23379Artikkel i tidsskrift (Fagfellevurdert)
  • 335.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    BlobFinder, a tool for fluorescence microscopy image cytometry2009Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 94, nr 1, s. 58-65Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Images can be acquired at high rates with modern fluorescence microscopy hardware, giving rise to a demand for high-speed analysis of image data. Digital image cytometry, i.e., automated measurements and extraction of quantitative data from images of cells, provides valuable information for many types of biomedical analysis. There exists a number of different image analysis software packages that can be programmed to perform a wide array of useful measurements. However, the multi-application capability often compromises the simplicity of the tool. Also, the gain in speed of analysis is often compromised by time spent learning complicated software. We provide a free software called BlobFinder that is intended for a limited type of application, making it easy to use, easy to learn and optimized for its particular task. BlobFinder can perform batch processing of image data and quantify as well as localize cells and point like source signals in fluorescence microscopy images, e.g., from FISH, in situ PLA and padlock probing, in a fast and easy way.

  • 336.
    Allalou, Amin