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Sökning: LAR1:his > Naturvetenskap

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1.
  • Ekelund Ugge, Gustaf Magnus Oskar, 1990- (författare)
  • Transcriptional biomarkers of toxicity – powerful tools or random noise? : An applied perspective from studies on bivalves
  • 2023
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Aquatic organisms are constantly at risk of being exposed to potentially harmful chemical compounds of natural or anthropogenic origin. Biological life can for instance respond to chemical stressors by changes in gene expression, and thus, certain gene transcripts can potentially function as biomarkers, i.e. early warnings, of toxicity and chemical stress. A major challenge for biomarker application is the extrapolation of transcriptional data to potential effects at the organism level or above. Importantly, successful biomarker use also requires basal understanding of how to distinguish actual responses from background noise. The aim of this thesis is, based on response magnitude and variation, to evaluate the biomarker potential in a set of putative transcriptional biomarkers of general toxicity and chemical stress.Specifically, I addressed a selection of six transcripts involved in cytoprotection and oxidative stress: catalase (cat), glutathione-S-transferase (gst), heat shock proteins 70 and 90 (hsp70, hsp90), metallothionein (mt) and superoxide dismutase (sod). Moreover, I used metal exposures to serve as a proxy for general chemical stress, and due to their ecological relevance and nature as sedentary filter-feeders, I used bivalves as study organisms.In a series of experiments, I tested transcriptional responses in the freshwater duck mussel, Anodonta anatina, exposed to copper or an industrial wastewater effluent, to address response robustness and sensitivity, and potential controlled (e.g. exposure concentration) and random (e.g. gravidness) sources of variation. In addition, I performed a systematic review and meta-analysis on transcriptional responses in metal exposed bivalves to (1) evaluate what responses to expect from arbitrary metal exposures, (2) assess the influence from metal concentration (expressed as toxic unit), exposure time and analyzed tissue, and (3) address potential impacts from publication bias in the scientific literature.Response magnitudes were generally small in relationship to the observed variation, both for A. anatina and bivalves in general. The expected response to an arbitrary metal exposure would generally be close to zero, based on both experimental observations and on the estimated impact from publication bias. Although many of the transcripts demonstrated concentration-response relationships, large background noise might in practice obscure the small responses even at relatively high exposures. As demonstrated in A. anatina under copper exposure, this can be the case already for single species under high resolution exposures to single pollutants. As demonstrated by the meta-regression, this problem can only be expected to increase further upon extrapolation between different species and exposure scenarios, due to increasing heterogeneity and random variation. Similar patterns can also be expected for time-dependent response variation, although the meta-regression revealed a general trend of slightly increasing response magnitude with increasing exposure times.In A. anatina, gravidness was identified as a source of random variability that can potentially affect the baseline of most assessed biomarkers, particularly when quantified in gills. Response magnitudes and variability in this species were generally similar for selected transcripts as for two biochemical biomarkers included for comparison (AChE, GST), suggesting that the transcripts might not capture early warnings more efficiently than other molecular endpoints that are more toxicologically relevant. Overall, high concentrations and long exposure durations presumably increase the likelihood of a detectable transcriptional response, but not to an extent that justifies universal application as biomarkers of general toxicity and chemical stress. Consequently, without a strictly defined and validated application, this approach on its own appears unlikely to be successful for future environmental risk assessment and monitoring. Ultimately, efficient use of transcriptional biomarkers might require additional implementation of complementary approaches offered by current molecular techniques.
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2.
  • Vos, M., et al. (författare)
  • Determination of the energy-momentum densities of aluminium by electron momentum spectroscopy
  • 1999
  • Ingår i: Journal of Physics. - : Institute of Physics Publishing (IOPP). - 0953-8984 .- 1361-648X. ; 11:18, s. 3645-3661
  • Tidskriftsartikel (refereegranskat)abstract
    • The energy-resolved momentum densities of thin polycrystalline aluminium films have been measured using electron momentum spectroscopy (EMS), for both the valence band and the outer core levels. The spectrometer used for these measurements has energy and momentum resolutions of around 1.0 eV and 0.15 atomic units, respectively. These measurements should, in principle, describe the electronic structure of the film very quantitatively, i.e. the dispersion and the intensity can be compared directly with theoretical spectral momentum densities for both the valence band and the outer core levels. Multiple scattering is found to hamper the interpretation somewhat. The core-level intensity distribution was studied with the main purpose of setting upper bounds on these multiple-scattering effects. Using this information we wish to obtain a full understanding of the valence band spectra using different theoretical models of the spectral function. These theoretical models differ significantly and only the cumulant expansion calculation that takes the crystal lattice into account seems to describe the data reasonably well.
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3.
  • Boström, Henrik (författare)
  • Maximizing the Area under the ROC Curve with Decision Lists and Rule Sets
  • 2007
  • Ingår i: Proceedings of the 7th SIAM International Conference on Data Mining. - : Society for Industrial and Applied Mathematics. - 9780898716306 ; , s. 27-34
  • Konferensbidrag (refereegranskat)abstract
    • Decision lists (or ordered rule sets) have two attractive properties compared to unordered rule sets: they require a simpler classi¯cation procedure and they allow for a more compact representation. However, it is an open question what effect these properties have on the area under the ROC curve (AUC). Two ways of forming decision lists are considered in this study: by generating a sequence of rules, with a default rule for one of the classes, and by imposing an order upon rules that have been generated for all classes. An empirical investigation shows that the latter method gives a significantly higher AUC than the former, demonstrating that the compactness obtained by using one of the classes as a default is indeed associated with a cost. Furthermore, by using all applicable rules rather than the first in an ordered set, an even further significant improvement in AUC is obtained, demonstrating that the simple classification procedure is also associated with a cost. The observed gains in AUC for unordered rule sets compared to decision lists can be explained by that learning rules for all classes as well as combining multiple rules allow for examples to be ranked according to a more fine-grained scale compared to when applying rules in a fixed order and providing a default rule for one of the classes.
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4.
  • Huhnstock, Nikolas Alexander, 1988-, et al. (författare)
  • An Infinite Replicated Softmax Model for Topic Modeling
  • 2019
  • Ingår i: Modeling Decisions for Artificial Intelligence. - Cham : Springer. - 9783030267728 - 9783030267735 ; , s. 307-318
  • Konferensbidrag (refereegranskat)abstract
    • In this paper, we describe the infinite replicated Softmax model (iRSM) as an adaptive topic model, utilizing the combination of the infinite restricted Boltzmann machine (iRBM) and the replicated Softmax model (RSM). In our approach, the iRBM extends the RBM by enabling its hidden layer to adapt to the data at hand, while the RSM allows for modeling low-dimensional latent semantic representation from a corpus. The combination of the two results is a method that is able to self-adapt to the number of topics within the document corpus and hence, renders manual identification of the correct number of topics superfluous. We propose a hybrid training approach to effectively improve the performance of the iRSM. An empirical evaluation is performed on a standard data set and the results are compared to the results of a baseline topic model. The results show that the iRSM adapts its hidden layer size to the data and when trained in the proposed hybrid manner outperforms the base RSM model.
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6.
  • Rexhepi, Hanife, 1984-, et al. (författare)
  • Cancer patients’ information seeking behavior related to online electronic healthcare records
  • 2021
  • Ingår i: Health Informatics Journal. - : Sage Publications. - 1460-4582 .- 1741-2811. ; 27:3, s. 1-12
  • Tidskriftsartikel (refereegranskat)abstract
    • Patients’ online access to their EHR together with the rapid proliferation of medical information on the Internet has changed how patients use information to learn about their health. Patients’ tendency to turn to the Internet to find information about their health and care is well-documented. However, little is known about patients’ information seeking behavior when using online EHRs. By using information horizons as an analytical tool this paper aims to investigate the information behavior of cancer patients who have chosen to view their EHRs (readers) and to those who have not made that option (non-readers). Thirty interviews were conducted with patients. Based on information horizons, it seems that non-reading is associated with living in a narrower information world in comparison to readers. The findings do not suggest that the smallness would be a result of active avoidance of information, or that it would be counterproductive for the patients. The findings suggest, however, that EHRs would benefit from comprehensive linking to authoritative health information sources to help users to understand their contents. In parallel, healthcare professionals should be more aware of their personal role as a key source of health information to those who choose not to read their EHRs. 
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7.
  • Shi, Lei, 1981, et al. (författare)
  • Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation
  • 2020
  • Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 37:6, s. 1667-1678
  • Tidskriftsartikel (refereegranskat)abstract
    • Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of presently uncharacterized genes (y-genes). We individually inactivated a representative sample of uncharacterized genes that arose during the same evolutionary periods as the known sporulation genes and tested the resulting strains for sporulation phenotypes. Sporulation was significantly affected in 16 out of 37 (43%) tested strains. In addition to expanding the knowledge base on B. subtilis sporulation, our findings suggest that evolutionary age could be used to help with genome mining.
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8.
  • Sweidan, Dirar, et al. (författare)
  • Predicting Customer Churn in Retailing
  • 2022
  • Ingår i: Proceedings 21st IEEE International Conference on Machine Learning and Applications ICMLA 2022. - : IEEE. - 9781665462839 - 9781665462846 ; , s. 635-640
  • Konferensbidrag (refereegranskat)abstract
    • Customer churn is one of the most challenging problems for digital retailers. With significantly higher costs for acquiring new customers than retaining existing ones, knowledge about which customers are likely to churn becomes essential. This paper reports a case study where a data-driven approach to churn prediction is used for predicting churners and gaining insights about the problem domain. The real-world data set used contains approximately 200 000 customers, describing each customer using more than 50 features. In the pre-processing, exploration, modeling and analysis, attributes related to recency, frequency, and monetary concepts are identified and utilized. In addition, correlations and feature importance are used to discover and understand churn indicators. One important finding is that the churn rate highly depends on the number of previous purchases. In the segment consisting of customers with only one previous purchase, more than 75% will churn, i.e., not make another purchase in the coming year. For customers with at least four previous purchases, the corresponding churn rate is around 25%. Further analysis shows that churning customers in general, and as expected, make smaller purchases and visit the online store less often. In the experimentation, three modeling techniques are evaluated, and the results show that, in particular, Gradient Boosting models can predict churners with relatively high accuracy while obtaining a good balance between precision and recall. 
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9.
  • Izquierdo, Milagros, 1963-, et al. (författare)
  • Isometric Point-Circle Configurations on Surfaces from Uniform Maps
  • 2016
  • Ingår i: Springer Proceedings in Mathematics and Statistics. - Cham : Springer-Verlag New York. - 2194-1009. ; 159, s. 201-212, s. 201-212
  • Tidskriftsartikel (refereegranskat)abstract
    • We embed neighborhood geometries of graphs on surfaces as point-circle configurations. We give examples coming from regular maps on surfaces with a maximum number of automorphisms for their genus, and survey geometric realization of pentagonal geometries coming from Moore graphs. An infinite family of point-circle v4'>v4v4 configurations on p-gonal surfaces with two p-gonal morphisms is given. The image of these configurations on the sphere under the two p-gonal morphisms is also described.
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10.
  • Jirstrand, Mats, 1968, et al. (författare)
  • Biochemical Modeling with Systems Biology Graphical Notation
  • 2010
  • Ingår i: Drug Discovery Today. - : Elsevier BV. - 1878-5832 .- 1359-6446. ; 15:9-10, s. 365-370
  • Tidskriftsartikel (refereegranskat)abstract
    • The Systems Biology Graphical Notation (SBGN) is an emerging standard for graphical notation developed by an international systems biology community. Standardized graphical notation is crucial for efficient and accurate communication of biological knowledge between researchers with various backgrounds in the expanding field of systems biology. Here, we highlight SBGN from a practical point of view and describe how the user can build and simulate SBGN models from a simple drag-and-drop graphical user interface in PathwayLab.
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