| 1. |
- Asghar, Naveed, et al.
(author)
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Tick-borne encephalitis virus sequenced directly from questing and blood-feeding ticks reveals quasispecies variance.
- 2014
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In: PLOS ONE. - San Francisco, USA : Public Library of Science (PLoS). - 1932-6203. ; 9:7
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Journal article (peer-reviewed)abstract
- The increased distribution of the tick-borne encephalitis virus (TBEV) in Scandinavia highlights the importance of characterizing novel sequences within the natural foci. In this study, two TBEV strains: the Norwegian Mandal 2009 (questing nymphs pool) and the Swedish Saringe 2009 (blood-fed nymph) were sequenced and phylogenetically characterized. Interestingly, the sequence of Mandal 2009 revealed the shorter form of the TBEV genome, similar to the highly virulent Hypr strain, within the 3' non-coding region (3'NCR). A different genomic structure was found in the 3'NCR of Saringe 2009, as in-depth analysis demonstrated TBEV variants with different lengths within the poly(A) tract. This shows that TBEV quasispecies exists in nature and indicates a putative shift in the quasispecies pool when the virus switches between invertebrate and vertebrate environments. This prompted us to further sequence and analyze the 3'NCRs of additional Scandinavian TBEV strains and control strains, Hypr and Neudoerfl. Toro 2003 and Habo 2011 contained mainly a short (A)3C(A)6 poly(A) tract. A similar pattern was observed for the human TBEV isolates 1993/783 and 1991/4944; however, one clone of 1991/4944 contained an (A)3C(A)11 poly(A) sequence, demonstrating that quasispecies with longer poly(A) could be present in human isolates. Neudoerfl has previously been reported to contain a poly(A) region, but to our surprise the re-sequenced genome contained two major quasispecies variants, both lacking the poly(A) tract. We speculate that the observed differences are important factors for the understanding of virulence, spread, and control of the TBEV.
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| 2. |
- Begum, Marjahan, et al.
(author)
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Designing a Pedagogical Framework for Developing Abstraction Skills
- 2024
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In: PROCEEDINGS OF THE 2024 CONFERENCE INNOVATION AND TECHNOLOGY IN COMPUTER SCIENCE EDUCATION, VOL 2, ITICSE 2024. - : ASSOC COMPUTING MACHINERY. - 9798400706035 ; , s. 769-770
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Conference paper (peer-reviewed)abstract
- The Abstraction is a fundamental skill and concept in computer science and it is also a difficult skill to teach. The purpose of the working group is to analyse different perspectives of abstraction's conceptualisation and ways of teaching the skill. Therefore as a result of the working group we will be first identifying how abstraction is discussed and defined in key literature. As a team we will agree on the perspectives and models we will like to explore in teaching context. Finally we will work with computing educators and computing education researchers to design a pedagogical framework that will enable the development of the abstraction skills.
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| 3. |
- Begum, Marjahan, et al.
(author)
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Empirical Evaluation of a Differentiated Assessment of Data Structures: The Role of Prerequisite Skills
- 2023
-
In: Informatics in Education. An International Journal. - Vilnius : Vilnius University. - 1648-5831 .- 2335-8971. ; 23, s. 57-99
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Journal article (peer-reviewed)abstract
- There can be many reasons why students fail to answer correctly to summative tests in advanced computer science courses: often the cause is a lack of prerequisites or misconceptions about topics presented in previous courses. One of the ITiCSE 2020 working groups investigated the possibility of designing assessments suitable for differentiating between fragilities in prerequisites (in particular, knowledge and skills related to introductory programming courses) and advanced topics. This paper reports on an empirical evaluation of an instrument focusing on data structures, among those proposed by the ITiCSE working group. The evaluation aimed at understanding what fragile knowledge and skills the instrument is actually able to detect and to what extent it is able to differentiate them. Our results support that the instrument is able to distinguish between some specific fragilities (e.g., value vs. reference semantics), but not all of those claimed in the original report. In addition, our findings highlight the role of relevant skills at a level between prerequisite and advanced skills, such as program comprehension and reasoning about constraints. We also suggest ways to improve the questions in the instrument, both by improving the distractors of the multiple choice questions, and by slightly changing the content or phrasing of the questions. We argue that these improvements will increase the effectiveness of the instrument in assessing prerequisites as a whole, but also to pinpoint specific fragilities.
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| 4. |
- Björn, Camilla, et al.
(author)
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It's Okay Because I Worked Really Hard! : Student Justifications for Questionable Collaboration while Solving Computer Labs
- 2022
-
In: Proceedings. - : Institute of Electrical and Electronics Engineers (IEEE).
-
Conference paper (peer-reviewed)abstract
- In this full research paper we examine questionable collaboration from a student perspective. Collaborating while solving computer lab assignments is often considered an important part when learning computer science, as it allows students to discuss their work, while also practicing working together. However, it also introduces risks, such as students collaborating in ways negatively impacting their learning outcomes and leading to inaccurate grading. Hence it is important to work towards reducing the use of these poor collaborative practices. In order to ameliorate the problem with academic misconduct, we need to understand students' justifications for deviating from acceptable practices. In this paper we therefore investigate how students justify their collaborative practices during computer lab assignments in situations they experience as questionable. The justifications were collected through 15 semi-structured interviews with students experienced in pair programming, majoring in computer science and other technical fields from two large well-known European universities.The justifications from the interviews were analysed using phenomenography resulting in seven categories: external pressure, lack of interest, spending time on the assignment, understanding the end product, contributing to the process, learning from the assignment and reflecting on the purpose of the learning. These describe in which situations students might deviate from the rules and can be used by institutions to prevent such behavior.
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| 5. |
- Björn, Camilla, et al.
(author)
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It’s Okay Because I Worked Really Hard! – Student Justifications for Questionable Collaboration while Solving Computer Labs
- 2022
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In: 2022 IEEE Frontiers in Education Conference (FIE). - Uppsala, Sweden : Institute of Electrical and Electronics Engineers (IEEE). - 9781665462440 - 9781665462457
-
Conference paper (peer-reviewed)abstract
- In this full research paper we examine questionable collaboration from a student perspective. Collaborating while solving computer lab assignments is often considered an important part when learning computer science, as it allows students to discuss their work, while also practicing working together. However, it also introduces risks, such as students collaborating in ways negatively impacting their learning outcomes and leading to inaccurate grading. Hence it is important to work towards reducing the use of these poor collaborative practices. In order to ameliorate the problem with academic misconduct, we need to understand students’ justifications for deviating from acceptable practices. In this paper we therefore investigate how students justify their collaborative practices during computer lab assignments in situations they experience as questionable. The justifications were collected through 15 semi-structured interviews with students experienced in pair programming, majoring in computer science and other technical fields from two large well-known European universities.The justifications from the interviews were analysed using phenomenography resulting in seven categories: external pressure, lack of interest, spending time on the assignment, understanding the end product, contributing to the process, learning from the assignment and reflecting on the purpose of the learning. These describe in which situations students might deviate from the rules and can be used by institutions to prevent such behavior.
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| 6. |
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| 7. |
- Haglund, Pontus, et al.
(author)
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Grasping the Unseen: TA Insights into Teaching Subtle Concepts in Computer Science
- 2024
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In: PROCEEDINGS OF THE 2024 CONFERENCE INNOVATION AND TECHNOLOGY IN COMPUTER SCIENCE EDUCATION, VOL 1, ITICSE 2024. - : ASSOC COMPUTING MACHINERY. - 9798400706004 ; , s. 157-163
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Conference paper (peer-reviewed)abstract
- Conquering fundamental programming concepts that subtly affect program behavior is a challenge for Computer Science (CS) students. Learning parameter passing, aliasing, scope, and references, how they work and being able to reason about them, is crucial for CS students. In this qualitative study we explore how these concepts are taught from the perspective of Teaching Assistants (TAs). Using phenomenographic analysis we find several areas that could be improved regarding the activities and assessments that students are exposed to during their studies. These findings include issues with consistent grading, the training of TAs, the support structures offered to TAs, and variations in the perceived focus on these concepts. Finally, our results highlight a need to explore how proficient TAs are with these concepts.
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| 8. |
- Haglund, Pontus, et al.
(author)
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Understanding Students’ Failure to use Functions as a Tool for Abstraction – An Analysis of Questionnaire Responses and Lab Assignments in a CS1 Python Course
- 2021
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In: Informatics in Education. An International Journal. - : Vilnius University Press. - 1648-5831 .- 2335-8971. ; 20:4, s. 583-614
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Journal article (peer-reviewed)abstract
- Controlling complexity through the use of abstractions is a critical part of problem solving in programming. Thus, becoming proficient with procedural and data abstraction through the use of user-defined functions is important. Properly using functions for abstraction involves a number of other core concepts, such as parameter passing, scope and references, which are known to be difficult. Therefore, this paper aims to study students proficiency with these core concepts, and students ability to apply procedural and data abstraction to solve problems. We collected data from two years of an introductory Python course, both from a questionnaire and from two lab assignments. The data shows that students had difficulties with the core concepts, and a number of issues solving problems with abstraction. We also investigate the impact of using a visualization tool when teaching the core concepts.
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| 9. |
- Lindblom, Pontus, et al.
(author)
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Determining factors for successful vaccination against tick-borne encephalitis virus in older individuals
- 2014
-
Other publication (other academic/artistic)abstract
- We performed a cross-sectional study including 533 persons (median age 61) from the highly TBE endemic Åland Islands in the archipelago between Sweden and Finland. Blood samples, questionnaires and vaccination records were obtained from all study participants. The aim was to investigate if there was any association between TBEV antibody titer and 14 healthrelated factors: [age, gender, number of vaccine doses (0-5), time since last vaccine dose, previous TBE disease, vaccination against other flaviviruses, ≥2 tick-bites during the previous 3 months, pet-ownership, asthma, smoking, allergy, diabetes, medication, and previous tumor]. Measurement of TBEV IgG antibodies was performed using two commercial ELISA assays (Enzygnost and Immunozym), and a third in-house rapid fluorescent focus inhibition test was used to measure TBEV neutralizing antibodies. The age of the person and the number of vaccine doses were the two most important factors determining successful vaccination. The response to each vaccine dose declined linearly with increased age. A 35 year age difference corresponds to a vaccine dose increment from 3 to 4 to achieve the same response. Participants receiving medication and participants previously vaccinated against other flaviviruses had lower TBEV antibody titers on average, while those with self-reported asthma had higher titers. By comparing the 3 serological assays we show that the Enzygnost and Immunozym assay differ due to choice of cutoffs, but not in overall accuracy.
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| 10. |
- Lindblom, Pontus, 1982-
(author)
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Epidemiological and Ecological Studies of Tick-borne Encephalitis Virus
- 2014
-
Doctoral thesis (other academic/artistic)abstract
- Ticks are blood-sucking parasites that are an inconvenience for both humans and animals. The tick by itself is normally harmless unless they attack in excessive numbers. The harm from ticks stems from them being excellent vectors for other parasites, in the form of bacteria and virus that via the ticks are provided a bridge to move across the blood streams of different animals, including humans.One of the most pathogenic tick-borne disease for humans is caused by a flavivirus, the tick-borne encephalitis virus (TBEV). Each year approximately 10 000 individuals on the Eurasian continent develop neurological disease, in the form of meningitis, encephalitis, myelitis and radiculitis, following a bite by a TBEV infected tick.To evaluate the risk of TBEV infection after a tick-bite, we have developed a study to investigate ticks that have bitten humans and to follow up the tick-bitten humans to investigate if they get infected, and if they develop symptoms, and further trace the virus back to the tick that is infected with TBEV. Ticks, blood samples, and questionnaires were collected in collaboration with 34 primary health care centers in Sweden and on the Åland Islands during 2008 and 2009.Several demographical and biological factors were investigated regarding the interaction between ticks and humans. The main finding was that men removed the ticks later than women, and that both older men and older women removed the ticks later than younger individuals. This could in part explain why older individuals in general, and men in particular, are at greater risk of acquiring tick-borne encephalitis (TBE).Furthermore, the prevalence of TBEV in ticks that have bitten humans were investigated, in order to correlate the copy number of TBEV in the tick and the tick feeding-time to the risk of developing symptomatic and asymptomatic infection. This entailed the development of new methodology for tick analysis and TBEV real-time PCR. The result showed a very low risk of TBEV infection in the studied areas, only 5 of 2167 investigated ticks contained TBEV. Three of the individuals bitten by TBEV infected ticks were vaccinated and did not develop symptoms of TBEV infection. One unvaccinated individual got bitten by a tick containing 1800 virus copies, with a feeding-time of 12-24h, and interestingly showed no signs of infection. Another unvaccinated individual got bitten by a tick containing 7.7 million virus copies, with a feedingtime of >60h. This individual developed symptoms consistent with a 1st phase of TBE, including fever and headache, but did not develop the 2nd neurological phase of TBEV infection. Despite only finding 5 ticks infected with TBEV, a correlation between the virus load in the tick and the tick feeding-time was observed. In 2 other individuals, TBEV antibody seroconversion was detected during the 3 month study period, one without symptoms, while the other experienced symptoms consistent with the 1st phase of TBE. These observations support the hypothesis that a higher virus amount in the tick and a longer feeding time increases the risk of TBEV infection.To further examine TBEV in ticks that have bitten humans and find factors that may predict the risk of human infection and development of TBE, we characterized several TBEV strains genetically. Including TBEV strains isolated from ticks that have bitten human, from questing field-collected ticks, and TBEV strains isolated from patients with TBE. In one of the ticks detached from a human after >60h of feeding, there was a heterogeneous population of TBEV quasispecies with varying poly(A) length in the 3’ untranslated region of the genome was observed. These variations might have implications for differences in virulence between TBEV strains, and the heterogeneous quasispecies population observed could be the virus adapting from replication in tick cells to mammalian cells.We also investigated the response to TBEV vaccination in relation to 14 health-related factors in a population of older individuals on the Åland Islands. Blood samples, questionnaires, and vaccination records were collected from 533 individuals. Three different serological assays to characterize antibody response to TBEV vaccination were used. The main finding was that the number of vaccine doses in relation to age was the most important factor determining successful vaccination. The response to each vaccination dose declined linearly with age, and as much as 47% of individuals 50 years or older that had taken 3 vaccine doses were seronegative, compared to 23% that had taken 4 doses and 6% with 5 doses. Comparison between the serological assays revealed that the cutoffs determining the balance between sensitivity and specificity differed, but not the overall accuracy.Taken together, these results contribute to a better understanding of the TBEV epidemiology and can provide tools in the prevention of TBE.
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| 11. |
- Lindblom, Pontus, et al.
(author)
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Factors Determining Immunological Response to Vaccination against Tick-Borne Encephalitis Virus in Older Individuals
- 2014
-
In: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 9:6, s. e0100860-
-
Journal article (peer-reviewed)abstract
- We performed a cross-sectional study including 533 individuals (median age 61) from the highly TBE endemic A land Islands in the archipelago between Sweden and Finland. Blood samples, questionnaires and vaccination records were obtained from all study participants. The aim was to investigate if there was any association between TBEV antibody titer and 12 health-related factors. Measurement of TBEV IgG antibodies was performed using two commercial ELISA assays (Enzygnost and Immunozym), and a third in-house rapid fluorescent focus inhibition test was used to measure TBEV neutralizing antibodies. The age of the individual and the number of vaccine doses were the two most important factors determining the immunological response to vaccination. The response to each vaccine dose declined linearly with increased age. A 35 year age difference corresponds to a vaccine dose increment from 3 to 4 to achieve the same immunological response. Participants previously vaccinated against other flaviviruses had lower odds of being seropositive for neutralizing TBEV antibodies on average, while participants with self-reported asthma had higher odds of being seropositive. By comparing the 3 serological assays we show that the Enzygnost and Immunozym assay differ due to choice of cutoffs, but not in overall accuracy.
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| 12. |
- Lindblom, Pontus, et al.
(author)
-
Tick-borne encephalitis virus in ticks detached from humans and follow-up of serological and clinical response.
- 2014
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In: Ticks and Tick Borne Diseases. - Jena, Germany : Elsevier. - 1877-959X. ; 5:1, s. 21-28
-
Journal article (peer-reviewed)abstract
- The risk of tick-borne encephalitis virus (TBEV) infection after a tick bite remains largely unknown. To address this, we investigated the presence of TBEV in ticks detached from humans in an attempt to relate viral copy number, TBEV subtype, and tick feeding time with the serological and clinical response of the tick-bitten participants. Ticks, blood samples, and questionnaires were collected from tick-bitten humans at 34 primary health care centers in Sweden and in the Aland Islands (Finland). A total of 2167 ticks was received from 1886 persons in 2008-2009. Using a multiplex quantitative real-time PCR, 5 TBEV-infected ticks were found (overall prevalence 0.23%, copy range <4 X 10(2)-7.7 X 10(6) per tick). One unvaccinated person bitten by a tick containing 7.7 x 10(6) TBEV copies experienced symptoms. Another unvaccinated person bitten by a tick containing 1.8 x 10(3) TBEV copies developed neither symptoms nor TBEV antibodies. The remaining 3 persons were protected by vaccination. In contrast, despite lack of TBEV in the detached ticks, 2 persons developed antibodies against TBEV, one of whom reported symptoms. Overall, a low risk of TBEV infection was observed, and too few persons got bitten by TBEV-infected ticks to draw certain conclusions regarding the clinical outcome in relation to the duration of the blood meal and virus copy number. However, this study indicates that an antibody response may develop without clinical symptoms, that a bite by an infected tick not always leads to an antibody response or clinical symptoms, and a possible correlation between virus load and tick feeding time. (C) 2013 Elsevier GmbH. All rights reserved.
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| 13. |
- Strömbäck, Filip, et al.
(author)
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The Progression of Students’ Ability to Work With Scope, Parameter Passing and Aliasing
- 2023
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In: ACE '23. - New York, NY, USA : Association for Computing Machinery. - 9781450399418 ; , s. 39-48
-
Conference paper (peer-reviewed)abstract
- Students need the ability to reason about the behavior of programs when working with advanced concepts like concurrency and abstraction. To achieve this, students require core programming skills that allow them to trace and predict the outcome of a program. While previous research indicates that teachers cannot expect students to acquire all core programming skills after their introductory CS course, less is known of students’ progression in later years. In this study, we investigate 397 students’ ability to predict the outcome of short computer programs. The participants are from different programs and progressions in their studies. We find that students, regardless of program and year, struggle with predicting the outcome of short programs that require an accurate mental model of some less readily apparent concepts, such as references. Further, we discover that there is no significant improvement in the first three years. Finally, we propose further avenues of research to improve these learning outcomes.
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| 14. |
- Wilhelmsson, Peter, et al.
(author)
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A prospective study on the incidence of Borrelia burgdorferi sensu lato infection after a tick bite in Sweden and On the Åland Islands, Finland (2008-2009)
- 2016
-
In: Ticks and Tick-borne Diseases. - : Elsevier. - 1877-959X .- 1877-9603. ; 7:1, s. 71-79
-
Journal article (peer-reviewed)abstract
- Lyme borreliosis (LB) is a common and increasing tick-borne disease in Europe. The risk of acquiring a Borrelia infection after a tick bite is not fully known. Therefore, we investigated the incidence of Borrelia infection after a bite by a Borrelia-infected tick and if the Borrelia load and/or the duration of tick-feeding influenced the risk of infection. During 2008-2009, ticks and blood samples were collected from 1546 tick-bitten persons from Sweden and the Åland Islands, Finland. Follow-up blood samples were taken 3 months after the tick bite. The duration of tick feeding was microscopically estimated and Borrelia was detected and quantified in ticks by real-time PCR. Anti-Borrelia antibodies were detected in sera using ELISA tests and immunoblot. Five percent (78/1546) of the study participants developed Borrelia infection (LB diagnosis and/or seroconversion) after a tick bite (45% bitten by Borrelia-infected ticks and 55% bitten by uninfected ticks). Of these, 33 developed LB (whereof 9 also seroconverted) while 45 participants seroconverted only. Experience of non-specific symptoms was more frequently reported by Borrelia-infected participants compared to uninfected participants. All who seroconverted removed "their" ticks significantly later than those who did not. The Borrelia load in the ticks did not explain the risk of seroconversion. Regional and sex differences in the Borrelia seroprevalence were found. The risk of developing a Borrelia infection after a bite by a Borrelia-infected tick is small but increases with the duration of tick feeding.
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| 15. |
- Wilhelmsson, Peter, et al.
(author)
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A prospective study on the incidence of Borrelia infection after a tick bite in Sweden and on the Åland Islands, Finland (2008-2009)
- 2016
-
In: Ticks and Tick-borne Diseases. - : Elsevier. - 1877-959X .- 1877-9603. ; 7:1, s. 71-79
-
Journal article (peer-reviewed)abstract
- Lyme borreliosis (LB) is a common and increasing tick-borne disease in Europe. The risk of acquiring a Borrelia infection after a tick bite is not fully known. Therefore, we investigated the incidence of Borrelia infection after a tick bite and if the Borrelia load and/or the duration of tick-feeding influenced the risk of infection. During 2008-2009, ticks and blood samples were collected from 1546 tick-bitten persons from Sweden and the Åland Islands, Finland. Follow-up blood samples were taken three months after the tick bite. The duration of tick feeding was microscopically estimated and Borrelia was detected and quantified in ticks by real-time PCR. Anti-Borrelia antibodies were detected in sera using ELISA assays and immunoblot.Even though 28 % of the participants were bitten by a Borrelia-positive tick, only 7.5% (32/428) of them developed a Borrelia infection, half of them LB. All who seroconverted removed “their” ticks significantly later than those who did not. The Borrelia load in the ticks did not explain the risk of seroconversion. Regional as well as gender differences in the Borrelia seroprevalence were found. The risk of developing a Borrelia infection after a bite by a Borrelia-infected tick is small but increases with the duration of tick feeding.
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