| 1. |
- Lind, Ann-Kristina, et al.
(författare)
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Smart övervakning av nötkreatur på bete
- 2023
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Smart monitoring of cattle on pasture According to the Swedish Board of Agriculture, meadows and pastures have decreased by hundreds of thousands of hectares in Sweden over the past hundred years. Valuable pastures can be located far from the farm, which means that the farmer chooses not to use it as it means long transport distances for daily supervision and monitoring of the animals. The problem has become more common with the structural change towards fewer and larger farms that has taken place in agriculture in recent decades. Farmers can, when the pasture is far from the farm, hire people who live closer to the pasture for the day-to-day care of the animals. However, counting the animals can be a task that is difficult to maintain, as it can be difficult even for an experienced zookeeper, especially if it is a larger group of animals and hilly terrain. If this step is handled automatically, it will be easier for the farmer to hire another person for the daily care of the animals and thus the possibility of using hard-to-reach pasture is increased. The project focused on finding low-cost and smart technical solutions to facilitate the tracking of animals, with the aim of developing a monitoring system for cattle on pasture to ensure that the animals are counted as part of a farmer’s daily supervision. The monitoring system that has been developed uses satellite communication to send the position of the animals up to four times a day to a mobile app, which gives the farmers an indication that all the animals have moved. In addition, the farmer receives alarms via email if the animals have too little activity or have moved outside of their designated pasture. Based on the experience from the field trials that were carried out, and from feedback from the farmers who participated in the project, it is concluded that the monitoring system can facilitate the monitoring of animals on pasture and at the same time be economically viable for a farmer. However, there is an opportunity to further develop the monitoring system to add functions such as water and electrical fence monitoring, which would make it possible to handle even more of the daily supervision digitally and only have manual supervision a few times a week.
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| 2. |
- Nordström, Marcus, et al.
(författare)
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On image segmentation with noisy labels : characterization and volume properties of the optimal solutions to accuracy and dice.
- 2022
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Ingår i: Advances in Neural Information Processing Systems 35 - 36th Conference on Neural Information Processing Systems, NeurIPS 2022. - : Neural information processing systems foundation.
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Konferensbidrag (refereegranskat)abstract
- We study two of the most popular performance metrics in medical image segmentation, Accuracy and Dice, when the target labels are noisy. For both metrics,several statements related to characterization and volume properties of the set ofoptimal segmentations are proved, and associated experiments are provided. Ourmain insights are: (i) the volume of the solutions to both metrics may deviatesignificantly from the expected volume of the target, (ii) the volume of a solutionto Accuracy is always less than or equal to the volume of a solution to Dice and(iii) the optimal solutions to both of these metrics coincide when the set of feasiblesegmentations is constrained to the set of segmentations with the volume equal tothe expected volume of the target.
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| 3. |
- Söderberg, Jonas, et al.
(författare)
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The Genome of Setaria digitata: A Cattle Nematode Closely Related to Human Filarial Parasites
- 2020
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 12, s. 3971-3976
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Tidskriftsartikel (refereegranskat)abstract
- Here we present the draft genome sequence of Setaria digitata, a parasitic nematode affecting cattle. Due to its similarity to Wuchereria bancrofti, the parasitic nematode that causes lymphatic filariasis in humans, S. digitata has been used as a model organism at the genomic level to find drug targets which can be used for the development of novel drugs and/or vaccines for human filariasis. Setaria digitata causes cerebrospinal nematodiasis in goats, sheep, and horses posing a serious threat to livestock in developing countries. The genome sequence of S. digitata will assist in finding candidate genes to use as drug targets in both S. digitata and W. bancrofti. The assembled draft genome is similar to 90 Mb long and contains 8,974 genomicscaffolds with a G+C content of 31.73%.
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| 4. |
- Unkelbach, Jan, et al.
(författare)
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The role of computational methods for automating and improving clinical target volume definition
- 2020
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Ingår i: Radiotherapy and Oncology. - : Elsevier BV. - 0167-8140 .- 1879-0887. ; 153, s. 15-25
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Tidskriftsartikel (refereegranskat)abstract
- Treatment planning in radiotherapy distinguishes three target volume concepts: the gross tumor volume(GTV), the clinical target volume (CTV), and the planning target volume (PTV). Over time, GTV definitionand PTV margins have improved through the development of novel imaging techniques and better imageguidance, respectively. CTV definition is sometimes considered the weakest element in the planning pro-cess. CTV definition is particularly complex since the extension of microscopic disease cannot be seenusing currently available in-vivo imaging techniques. Instead, CTV definition has to incorporate knowl-edge of the patterns of tumor progression. While CTV delineation has largely been considered the domainof radiation oncologists, this paper, arising from a 2019 ESTRO Physics research workshop, discusses thecontributions that medical physics and computer science can make by developing computational meth-ods to support CTV definition. First, we overview the role of image segmentation algorithms, which mayin part automate CTV delineation through segmentation of lymph node stations or normal tissues repre-senting anatomical boundaries of microscopic tumor progression. The recent success of deep convolu-tional neural networks has also enabled learning entire CTV delineations from examples. Second, wediscuss the use of mathematical models of tumor progression for CTV definition, using as example theapplication of glioma growth models to facilitate GTV-to-CTV expansion for glioblastoma that is consis-tent with neuroanatomy. We further consider statistical machine learning models to quantify lymphaticmetastatic progression of tumors, which may eventually improve elective CTV definition. Lastly, we dis-cuss approaches to incorporate uncertainty in CTV definition into treatment plan optimization as well asgeneral limitations of the CTV concept in the case of infiltrating tumors without natural boundaries.
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| 5. |
- Tiukova, Ievgeniia, 1987, et al.
(författare)
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Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis
- 2019
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 14:5
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Tidskriftsartikel (refereegranskat)abstract
- Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.
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| 6. |
- Eriksson, Yvonne, 1957-, et al.
(författare)
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Using VR to improve the design of assembly tasks and increase task efficiency
- 2018
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Ingår i: Proceedings of NordDesign. - : The Design Society. - 9789176851852
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Konferensbidrag (refereegranskat)abstract
- In this paper we discuss how theories of vision, touch, sound, and learning behavior can form a basis for the development of a testbed through which real-life task performance can be compared with task performance in a Virtual Reality (VR) environment. By taking a multisensory approach, it will be possible to simulate the functionalities of a real training setting in a VR environment. Approaching this problem from a theoretical perspective, we will view it from a new angle and discuss whether we can enhance and nuance feedback in the virtual experience through the use of ambient media like sound, scent, heat, and wind. Sound may hold a great potential here. For visual perception, it is not only crucial that we can see relationships but that we are also able to search for patterns that we recognize. If an object is taken outside its context, its meaning can easily shift. To see is to search for patterns, but vision is also dependent on our experience of other senses. We can imagine how a given surface might feel by looking at a representation of the object, and this is because of previous tactile experiences with similar objects. From a technical perspective, integrating sound in a virtual environment is a straightforward process. Research shows that the process of learning a series of physical actions can be enhanced when it occurs in parallel with verbal or written information. In the literature, this phenomenon is described in terms of enactment or subject-performed tasks. Based on theories regarding vision, touch, sound and learning behavior, we suggest the design of a testbed that can be used in a pilot study aimed at increasing knowledge on how VR and AR can support learning in an assembly or installation context in order to produce guidelines for such an environment.
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| 7. |
- Klingström, Tomas, et al.
(författare)
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Supporting the Development of Biobanks in Low and Medium Income Countries
- 2016
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Ingår i: 2016 IST-AFRICA WEEK CONFERENCE. - 9781905824557
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Konferensbidrag (refereegranskat)abstract
- Biobanks are an organized collection of biological material and associated data. They are a fundamental resource for life science research and contribute to the development of pharmaceutical drugs, diagnostic markers and to a deeper understanding of the genetics that regulate the development of all life on earth. Biobanks are well established in High Income Countries (HIC) and are rapidly emerging in Low and Middle Income Countries (LMIC). Surveys among biobanks operating in a LMIC setting indicate that limited resources and short term funding tied to specific projects threaten the sustainability of the biobanks. Fit-for-purpose biobanks targeting major societal challenges such as HIV and Malaria provide an excellent basis for integrating biobanks with the available research communities in LMIC regions. But to become sustainable for the future it is important that biobanks become an integrated part of local research communities. To achieve this, the cost of operating biobanks must be lowered, templates must be developed to support local ethics committees and researchers must be given the opportunity to build experience in successfully operating biobank based research projects. The B3Africa consortium is based on these conclusions and set up to support biobank based research by creating a cost efficient Laboratory Information Management System (LIMS) for developing biobanks and also contribute to the training and capacity building in the local research community. The technical platform called the eB3Kit is open source and consists of a LIMS and a bioinformatics module based on the eBiokit that allow researchers to take control over the analysis of their own data. Along with the technical platform the consortium will also contribute training and support for the associated infrastructures necessary to regulate the ethical and legal implications of biobank based research.
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| 8. |
- Söderberg, Jonas
(författare)
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On Zanello's lower bound for generic quotients of level algebras
- 2014
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Ingår i: Proceedings of the American Mathematical Society. - 0002-9939 .- 1088-6826. ; 142:12, s. 4025-4028
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Tidskriftsartikel (refereegranskat)abstract
- We give a shorter and more straightforward proof of a theorem of Zanello on lower bounds for Hilbert functions of generic level quotients of artinian level algebras.
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| 9. |
- Boij, Mats, et al.
(författare)
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Betti numbers of graded modules and the multiplicity conjecture in the non-Cohen-Macaulay case
- 2012
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Ingår i: Algebra & Number Theory. - : Mathematical Sciences Publishers. - 1937-0652 .- 1944-7833. ; 6:3, s. 437-454
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Tidskriftsartikel (refereegranskat)abstract
- We use results of Eisenbud and Schreyer to prove that any Betti diagram of a graded module over a standard graded polynomial ring is a positive linear combination of Betti diagrams of modules with a pure resolution. This implies the multiplicity conjecture of Herzog, Huneke, and Srinivasan for modules that are not necessarily Cohen-Macaulay and also implies a generalized version of these inequalities. We also give a combinatorial proof of the convexity of the simplicial fan spanned by pure diagrams.
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| 10. |
- Söderberg, Jonas, 1977-
(författare)
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Surviving the ratchet : Modelling deleterious mutations in asexual populations
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- One of the most unforgiving processes in nature is that of Muller's ratchet, a seemingly irreversible accumulation of deleterious mutations that all organisms have to deal with or face extinction. The most obvious way to avoid fitness collapse is recombination, though asexual populations usually do not have the luxury of recombining freely. With the aid of computational and mathematical models, we have studied other situations where this threat is averted and the organism can survive the ratchet. The results show that a ratchet where all mutations have the same deleterious fitness effect is very effectively stalled for large effects. However, if mutations are allowed to have a broad range of effects, the fitness-loss rate can be substantial even with the same mean effect as the one-type ratchet, but we have identified parameter regions where even the broad-range effects are effectively stopped. The fitness-loss from a ratchet is very sensitive to the mutation rate and a mutation that increases the mutation rate (mutator) can easily start an otherwise stalled ratchet. Large effect mutators are heavily counter-selected, but smaller mutators can spread in the population. They can be stopped by reversals (antimutators), but even if the mutation rate is equilibrated in this way, there will be large fluctuations in mutation rate and even larger in the fitness-loss rate due to the feedback amplification in their coupling. Another way of preventing the ratchet is by reversal of the deleterious mutations themselves through back-mutations or compensatory mutations. The rate required to stop the ratchet using only back-mutations before the fitness collapses is very large. A detailed comparison between the deleterious mutations in the ratchet and in a sexual population was made and the difference was found to be greatest for large populations with large genomes. There are obviously many ways to survive the ratchet, but even more ways to drive a species to extinction by enhancing and speeding up the ratchet. By modelling and testing the ratchet for numerous different situations, we show the effects of some of these threats and benefits.
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