| 1. |
- Jansson, Malin, 1988-
(författare)
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Spontaneous online tutoring : Students’ support of their own and other students’ process of inquiry in online text-based tutoring
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The use of online technologies has made education more accessible. In online education, there are increased expectations for students to be self-directed and take responsibility for their learning. Research has also shown that students can benefit from learning from each other. The purpose of this thesis is to explore how students support their own and other students’ process of inquiry in online text-based tutoring sessions. To enable the analysis of the conversations, a coding scheme for transcript analysis of online tutoring was introduced based on the Relationship of Inquiry framework, which is an adaptation of the Community of Inquiry framework.This thesis consists of four papers. The first paper focuses on the development of the RoI coding scheme, which is used in two of the following papers. In the second paper, the coding scheme is further revised regarding the aspect of students’ teaching presence and how it connects to students’ support of their own and other students’ inquiry process. In the third paper, students’ support of their own and other students’ process of inquiry in online text-based tutoring sessions is studied further, and their messages are analyzed with the revised coding scheme. The fourth paper adopts an inductive approach and analyzes how students take responsibility for their own and their peers’ problem-solving through thematic analysis. The findings show that in online tutoring sessions, students may spontaneously take on the role of a tutor. Through their expressions of teaching presence by, for example, explaining their issues and their previous steps, or answering other students’ questions and giving suggestions, students support their own as well as other students’ inquiry process. The findings indicate that students acquire metacognitive development, through self- and co-regulation, with their expressions of teaching and cognitive presence. Furthermore, the findings show that the coding scheme with fixed categories may not show the full picture of interactions in an online learning environment. Additional analysis reveals that students’ expressions focus on different levels of learning while supporting the problem-solving process. Lastly, this thesis offers guidance on how to create online tutoring sessions where students take responsibility for their learning and are encouraged to help one another.
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| 2. |
- Pelosi, Benedetta
(författare)
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The labyrinth of protein classification: a pipeline forselection and classification of biological data
- 2022
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Recent progress in fundamental biological sciences and medicine has considerably increased the quantity ofdata that can be studied and processed. The main limitation now is not retrieving data, but rather extractinguseful biological insights from the large datasets accumulated. More recent advances have provided detailedhigh-density data regarding metabolism (metabolomics) and protein expression (proteomics). Clearly, no single analytic methods, can provide a comprehensive understanding. Rather, the ability to link available datatogether in a coherent manner is required to obtain a complete view. The improving application of MachineLearning (ML) techniques provides the means to make continuous progress in processing complex data sets.A brief discussion is offered on the advantages of ML, the state-of-the-art in Deep Learning (DL) for proteinpredictions and the importance of ML in biological data processing. Noise stemming from incorrect classification or arbitrary/ambiguous labelling of data may arise when ML techniques are applied to large datasets. Furthermore, the stochasticity of biological systems needs to be considered for correctly evaluating theoutputs. Here we show the potential of a workflow to respond biological questions taking into consideration aperturbation of the biological data. For controlling the applicability of models and maximizing the predictivity, in silico filtering schemescan usefully be applied as an “Ockham’s razor” before using any ML technique. After reviewing differentDL approaches for protein prediction purposes, this work shows that a computational approach in filteringsteps is a valuable tool for proteins classification when biological features are not fully annotated or reviewed.The in silico approach has identified putative proline transporters in fungi and plants as well as carotenoidbiosynthetic gene products in the plant family Brassicaceae. The proposed method is suitable for extractingfeatures of classification and then maximizing the use of a DL approach.
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| 3. |
- Antonson, Hans, 1963-
(författare)
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Landskap och ödesbölen : Jämtland före, under och efter den medeltida agrarkrisen
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This study examines landscape change in the Province of Jämtland during c. 1000–1750 AD. Settlement and arable cultivation are two of the most important sources in this study. They are therefore treated in depth, particularly farmsteads that were deserted during the late medieval agrarian crisis, so-called ödesbölen, and their fossil field-traces. The dissertation contains four major investigations. In the first investigation 610 possible ödesbölen were identified. The desertion was estimated at 50 per cent. The second investigation had its focus on the geographic location, and the conclusion was that the ödesbölen may have been deserted when the climate turned colder in the 14th century. The third investigation concerned medieval agriculture. Using historical maps and detailed mapping of fossil field traces it was established that the annually cultivated acreage decreased from the High Middle Ages until early modern times. This probably means that the agrarian crisis caused a change in the agrarian regime, from predominant arable farming to predominant stock-raising. The fourth investigation was whether the ownership or the use of the ödesbölen created obstacles to recolonization when the crisis subsided. This turned out not to be so in the case of ownership, but may have been so with regard to communal forest grazing. According to historical maps the ödesbölen in Jämtland were finally recolonized about 200 years later than for example in southern Sweden. The reasons probably were wars and a worse climate. The dissertation is capped off with both a model and a description of landscape change in Jämtland. Characteristic for the development of the landscape has been fluctuations in settlement. The ödesbölen are part of a pattern in which they are colonized, deserted, recolonized and again deserted in a cyclical course of events. The openness of the landscape is not part of this course of events.
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| 4. |
- Bag, Pushan, 1993-
(författare)
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How could Christmas trees remain evergreen? : photosynthetic acclimation of Scots pine and Norway spruce needles during winter
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plants and other green organisms harvest sunlight by green chlorophyll pigments and covertit to chemical energy (sugars) and oxygen in a process called photosynthesis providing the foundation for life on Earth. Although it is unanimously believed that oceanic phytoplanktons are the main contributors to the global photosynthesis, the contribution of coniferous boreal forests distributed across vast regions of the northern hemisphere cannot be undermined. Hence boreal forests account signifificantly for social, economical and environmental sustainability. Not only do conifers thrive in the tundra regions with extreme climate, but they also maintain their needles green over the boreal winter. A question remains; what makes them so resilient? In this respect, we aimed to understand the remarkable winter adaptation strategies in two dominant boreal coniferous species,i.e., Pinus sylvestris and Picea abies. First, we mapped the transcriptional landscape in Norway spruce (Picea abies) needles over the annual cycle. Transcriptional changes in the nascent needles reflflected a sequence of developmental processes and active vegetative growth during early summer and summer. Later after maturation, transcriptome reflflected activated defense against biotic factors and acclimationin response to abiotic environmental cues such as freezing temperatures during winter. Secondly, by monitoring the photosynthetic performance of Scot pine needles, we found that the trees face extreme stress during the early spring (Feb-Mar) when sub-zero temperatures are accompanied by high solar radiation. At this time, drastic changes occur in the thylakoid membranes of the chloroplast that allows the mixing of photosystem I and photosystem II that typically remain laterally segregated. This triggers direct energy transfer from PSII to PSI and thus protects PSII from damage. Furthermore, we found that this loss of lateral segregation may be a consequence of triple phosphorylationof Lhcb1 (Light harvesting complex1 of photosystem II). The structural changes in thylakoid membranes also lead to changes inthe thylakoid macro domain organisationand pigment protein composition. Furthermore, we discovered that while PSII is protected by direct energy transfer, the protection of PSI is provided through photoreduction of oxygen by flavodiiron proteins, which in turn allows P700 to stay in an oxidised state necessary for direct energy transfer. These coordinated cascades of changes concomitantly protect both PSI and PSII to maintain the needles green over the winter.
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| 5. |
- Courtois-Moreau, Charleen, Laetitia, 1978-
(författare)
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Programmed Cell Death in Xylem Development
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Concerns about climate changes and scarcity of fossil fuels are rising. Hence wood is becoming an attractive source of renewable energy and raw material and these new dimensions have prompted increasing interest in wood formation in trees, in both the scientific community and wider public. In this thesis, the focus is on a key process in wood development: programmed cell death (PCD) in the development of xylem elements. Since secondary cell wall formation is dependent, inter alia, upon the life time of xylem elements, the qualitative features of wood will be affected by PCD in xylem, about which there is little information. This thesis focuses on the anatomical, morphological and transcriptional features of PCD during xylem development in both the stem of hybrid aspen, Populus tremula (L.) x tremuloides (Michx.) and the hypocotyl of the herbaceous model system Arabidopsis thaliana (L. Heynh.). In Populus, the progressive removal of organelles from the cytoplasm before the time of death (vacuolar bursts) and the slowness of the cell death process, illustrated by DNA fragmentation assays (such as TUNEL and Comet assays), have been ascertained in the xylem fibres by microscopic analyses. Furthermore, candidate genes for the regulation of fibre cell death were identified either from a Populus EST library obtained from woody tissues undergoing fibre cell death or from microarray experiments in Populus stem, and further assessed in an in silico comparative transcriptomic analysis of Arabidopsis thaliana. These candidate genes were either putative novel regulators of fibre cell death or members of previously described families of cell death-related genes, such as autophagy-related genes. The induction of the latter and the previous microscopic observations suggest the importance of autophagy in the degradation of the cytoplasmic contents specifically in the xylem fibres. Vacuolar bursts in the vessels were the only previously described triggers of PCD in the xylem, which induce the very rapid degradation of the nuclei and surrounding cytoplasmic contents, therefore unravelling a unique previously unrecorded type of PCD in the xylem fibres, principally involving autophagy. Arabidopsis is an attractive alternative model plant for exploring some aspects of wood formation, such as the characterisation of negative regulators of PCD. Therefore, the anatomy of Arabidopsis hypocotyls was also investigated and the ACAULIS5 (ACL5) gene, encoding an enzyme involved in polyamine biosynthesis, was identified as a key regulator of xylem specification, specifically in the vessel elements, though its negative effect on the cell death process. Taken together, PCD in xylem development seems to be a highly specific process, involving unique cell death morphology and molecular machinery. In addition, the technical challenges posed by the complexity of the woody tissues examined highlighted the need for specific methods for assessing PCD and related phenomena in wood.
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| 6. |
- Damkjaer, Jakob, 1976-
(författare)
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Phosphorylation in State Transition : Less cause more effect
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Study of the Arabidopsis thaliana knockout mutant lacking Lhcb3 (koLhcb3) have revealed a close similarity to the wild type plants. Growth rate, NPQ, qP, Φ(PSII), circular dichroism spectra, pigment composition and content of LCHII trimers have been found to be unaffected by this mutation. The proteomic analysis shows only some minor increases in the amount of Lhcb1 and Lhcb2. PAM fluorometry revealed a significant increase in the rate of the state 1 to state 2 state transition in the koLhcb3. None the less, the extent of state transition is identical to wild type. Alterations in the PSII-LHCII supercomplex structure have been demonstrated as well. The M-trimer was found to be rotated ~21° CCW. This altered binding of the LHCII M-trimer is likely the cause of the altered affinity resulting in the increased rate of state transition. Proteomic analysis of the phosphorylation of LHCII revealed a significant increase in state 1 and 2 LHCII phosphorylation relative to wild type. Investigation whether phosphorylation or the altered LHCII binding is the cause of the accelerated rate of state transition have not been conclusive so far. A Lhcb6 depleted mutant (koLhcb6) showed a significant alteration of the PSII-LHCII supercomplex structure and photosynthetic acclimation processes. The LHCII M-trimer is depleted in the PSII-LHCII supercomplexes causing the state transition process to be “stuck” in state 2 and the mutants ability to preform NPQ is inhibited as well. The Lhcb6 protein was concluded to be essential for the binding of the LHCII M-trimer to the PSII core as well as energy transfer. The depletion of LHCII M-trimer was linked to the reduced ability to photoacclimate using NPQ as well.
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| 7. |
- Erlandsson, Mikael, 1979-
(författare)
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What's in your mind? : Collegial Verbalisation – An ecological approach to knowledge elicitation
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Knowledge elicitation of the work of professional operators, using traditional methods such as concurrent or retrospective verbalization is problematic. Concurrent verbalization distracts the operators from their primary task, and the operators have difficulties in verbalizing about their automated work tasks. Retrospective verbalization on the other hand, suffers from rationalization problems. An operator might give a perfectly good explanation of some action taken and might also be completely confident about truth of the verbalized information, when it in fact is incorrect. To overcome some of these problems, this thesis presents a new complementary verbalization method called Collegial Verbalization (CV).The CV-method utilizes the shared knowledge among work colleagues to improve the quality of the resulting information. The method consists roughly of the following steps; (1) Video tape subjects while they are working. (2) Play back interesting events to the subject’s colleagues individually and let them verbalize on the subject’s actions. (3) Compare the colleagues’ verbal reports to each other to find similarities, differences, etc. Throughout my research I have formulated, defined and assessed the new method in detail. The method has been applied to study train drivers, high-speed ferry operators, train traffic dispatchers and the medical staff at intensive care units.Comparative studies have shown; (1) that CV-protocols can be used as an independent source of data, (2) that colleagues produce reports with similar characteristics of retrospective verbal reports, (3) that the CV-method can produce more information than retrospective verbalization, because of the advantage of using multiple narrators. When the intention is to gather data as input to design, rather than establishing the original thought processes form the time of the studied events, the CV-method can also produce more reliable information than retrospective verbalization, because of the advantage of using multiple narrators.Based on these results, I have concluded that the CV-method has a clear advantage as a complementary information acquisition method, when studying the work of professional operators. The thesis ends with a discussion about several additional possible applications for the CV-method, such as applied team learning or psychological research in the field of decision making.
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| 8. |
- Hrastinski, Stefan, Professor, 1980-, et al.
(författare)
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Examining the Development of K-12 Students' Cognitive Presence over Time : The Case of Online Mathematics Tutoring
- 2023
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Ingår i: ONLINE LEARNING. - : The Online Learning Consortium. - 2472-5749. ; 27:3, s. 252-270
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Tidskriftsartikel (refereegranskat)abstract
- In this article, we focus on the cognitive presence element of the Community of Inquiry (CoI) framework. Cognitive presence consists of four categories: Triggering Event, Exploration, Integration, and Resolution. These categories have been described as phases following an idealized logical sequence, although the phases should not be seen as immutable. Few studies have empirically examined how the four categories develop over time during the inquiry process. This article uses learning analytics methods to study transitions between the categories in K-12 online mathematics tutoring. It was statistically most probable that the tutoring sessions started with Triggering Event (95%) and then transitioned to Exploration (51%). The transitions from Exploration to Integration (18%) and Integration to Resolution (21%) achieved statistical significance but were less likely. In fact, it was more likely that the tutoring sessions transitioned from Integration to Exploration (39%) and Resolution to Exploration (36%). In conclusion, the findings suggest that the idealized logical sequence is evident in the data but that other transitions occur as well; especially Exploration recurs throughout the sessions. It seems challenging for students to reach the Integration and Resolution categories. As the CoI framework is commonly adopted in practice, it is important that tutors and educators understand that the categories of cognitive presence will often not play out in idealized ways, underlining their role in supporting how the inquiry process unfolds. In order to gain an improved understanding of the inquiry process, future research is suggested to investigate how the presences and categories of the CoI framework develop over time in different educational settings.
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| 9. |
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| 10. |
- Jansson, Malin, et al.
(författare)
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Online question and answer sessions : How students support their own and other students' processes of inquiry in a text-based learning environment
- 2021
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Ingår i: The Internet and higher education. - : Elsevier BV. - 1096-7516 .- 1873-5525. ; 51
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Tidskriftsartikel (refereegranskat)abstract
- Online tutoring has been found to have a positive impact on student learning in STEM education. The aim of this study was to explore how and to what extent students supported their own and other students' processes of inquiry during online tutoring. More specifically, question and answer sessions (Q&As) were studied, and online tutoring transcripts were analyzed using the Relationship of Inquiry coding scheme adapted from the Community of Inquiry framework. The students interacted voluntarily with each other and with the teachers. The results show that the students supported both their own process of inquiry as well as other students' process of inquiry. Furthermore, the results indicate that students acquired metacognitive development through self- and coregulation when they expressed teaching presence. Overall, we conclude that Q&As have the potential to support student learning when working on assignments in STEM education.
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