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  • 1. Aaghabali, M.
    et al.
    Akbari, S.
    Friedland, S.
    Markström, Klas
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Tajfirouz, Z.
    Upper bounds on the number of perfect matchings and directed 2-factors in graphs with given number of vertices and edges2015In: European journal of combinatorics (Print), ISSN 0195-6698, E-ISSN 1095-9971, Vol. 45, p. 132-144Article in journal (Refereed)
    Abstract [en]

    We give an upper bound on the number of perfect matchings in simple graphs with a given number of vertices and edges. We apply this result to give an upper bound on the number of 2-factors in a directed complete bipartite balanced graph on 2n vertices. The upper bound is sharp for even n. For odd n we state a conjecture on a sharp upper bound.

  • 2.
    Aalto, Anders
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Biodiversity and habitat conditions in reaches with high flow velocity along gradients in hydrological and geomorphological alteration: A study of six rivers in Sweden2021Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The vast majority of rivers in the developed world are affected by human alteration, which in turn negatively affects the species that rely on these highly diverse and species rich areas to survive. Homogenization of previously heterogenic areas due to a change in water discharge and the substrate availability in the rivers is often regarded as the main reason for the loss of species richness in rivers and the riparian zone. Because of this, there are a lot of restoration projects which main goal is to increase heterogeneity. The goal of this thesis is to compare hydrology and geomorphology variables between four types of reaches with high flow velocity (rapids in free-flowing reaches, rapids with regulated flow, impounded reaches and reaches in outlet channels below hydropower plants). In this thesis I wanted to find out how changes in geomorphology and hydrology affect fish species richness, riparian vegetation richness and aquatic vascular plants species richness. The result show that both fish species richness and riparian vegetation species richness are negatively affected by the changes in geomorphology and hydrology. There was no significant difference for aquatic vascular plants when comparing the regulation types. The most altered reach type, outlet channels, had significantly fewer fish species compared to the less altered reach type, impounded reaches. Outlet channels also had less riparian vegetation cover compared to all other regulation types, and fewer riparian vegetation species compared to both free-flowing reaches and impounded reaches. In conclusion, hydropower plants and timber floating have both negatively impacted the riverine ecosystem, and in turn caused a decrease in species richness for fish and riparian plants. The reaches studied in this thesis will continue to be altered and the species richness and species composition will change from an ecosystem that relied on the natural flow regime to an ecosystem more used to the flow regime created by the hydropower plants. 

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  • 3.
    Aalto, Anders
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Kanalisering och restaurering av vattendrag påverkar mossamhällen i strandzonen: -En studie av Vindelälvens biflöden2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This study compared three different types of reaches at streams and how bryophyte species richness, diversity and abundance in the riparian zone differ between them. The different types of reaches are those that have been treated by two types of restoration techniques (best practise and advanced) and streams that have still not been restored (channelized). The bryophytes were gathered from 15 tributaries to Vindelälven, which is in northern Sweden. Bryophyte species richness and diversity was highest at the streams that were still not restored, and I found numerous factors that could explain why this was the case. Fourteen environmental variables were tested against the three bryophyte factors to try to explain the variation found in the study. Time since restoration and the amount of tree biomass in the area could explain the species richness found at the different river types. The study shows that short-term effects of restoration on the riparian zone is a decrease in bryophyte species richness and diversity. However, given enough time the bryophytes are expected to recover in regards to species richness and diversity.

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  • 4. Abafe, Ovokeroye A.
    et al.
    Späth, Jana
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jansson, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Buckley, Chris
    Stark, Annegret
    Pietruschka, Bjoern
    Martincigh, Bice S.
    LC-MS/MS determination of antiretroviral drugs in influents and effluents from wastewater treatment plants in KwaZulu-Natal, South Africa2018In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 200, p. 660-670Article in journal (Refereed)
    Abstract [en]

    South Africa has the largest occurrence of the human immune deficiency virus (HIV) in the world but has also implemented the largest antiretroviral (ARV) treatment programme. It was therefore of interest to determine the presence and concentrations of commonly used antiretroviral drugs (ARVDs) and, also, to determine the capabilities of wastewater treatment plants (WWTPs) for removing ARVDs. To this end, a surrogate standard based LC-MS/MS method was optimized and applied for the detection of thirteen ARVDs used in the treatment and management of HIV/acquired immune deficiency syndrome (HIV/AIDS) in two major and one modular WWTP in the eThekwini Municipality in KwaZulu-Natal, South Africa. The method was validated and the detection limits fell within the range of 2–20 ng L−1. The analytical recoveries for the ARVDs were mainly greater than 50% with acceptable relative standard deviations. The concentration values ranged from <LOD – 53000 ng L−1 (influent), <LOD – 34000 ng L−1 (effluent) in a decentralized wastewater treatment facility (DEWATS); <LOD – 24000 ng L−1 (influent), <LOD – 33000 ng L−1 (effluent) in Northern WWTP and 61–34000 ng L−1 (influent), <LOD – 20000 ng L−1 (effluent) in Phoenix WWTP. Whilst abacavir, lamivudine and zidovudine were almost completely removed from the effluents, atazanavir, efavirenz, lopinavir and nevirapine persisted in the effluents from all three WWTPs. To estimate the ecotoxicological risks associated with the discharge of ARVDs, a countrywide survey focussing on the occurrence of ARVDs in WWTPs, surface and fresh water bodies, and aquatic organisms, is necessary.

  • 5. Abalaka, J. L.
    et al.
    Ottosson, Ulf
    Tende, Talatu
    Larson, Keith W.
    Rock Firefinch Lagonosticta sanguinodorsalis in the Mandara Mountains, north-east Nigeria: a new subspecies?2010In: African Bird Club Bulletin, ISSN 1352-481X, Vol. 17, no 2, p. 210-211Article in journal (Refereed)
    Abstract [fr]

    L’Amarante des rochers Lagonosticta sanguinodorsalis dans les Monts Mandara, Nigeria du sud-est: une nouvelle sous-espèce ? Nous fournissons une description d’un mâle et d’une femelle, ainsi que desphotos d’un mâle, d’un amarante capturé dans les Monts Mandara, au nord-est du Nigeria. Le plumage et le cri de cet amarante sont identiques à ceux de l’Amarante des rochers Lagonosticta sanguinodorsalis, une espèce précédemment rapportée de la zone, excepté que le mâle n’a pas la couronne grise typique de l’espèce. Des travaux supplémentaires sur le terrain sont nécessaires pour déterminer s’il agit d’un individu aberrant ou d’une population de l’Amarante des rochers morphologiquement distincte.

  • 6.
    Abbasi, Ahtisham Fazeel
    et al.
    German Research Center for Artificial Intelligence (DFKI), Kaiserslautern, Germany; University of Kaiserslautern-Landau, Kaiserslautern (RPTU), Germany.
    Asim, Muhammad Nabeel
    German Research Center for Artificial Intelligence (DFKI), Kaiserslautern, Germany.
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Sartorius Corporate Research, Sartorius Stedim Data Analytics, Umeå, Sweden.
    Dengel, Andreas
    German Research Center for Artificial Intelligence (DFKI), Kaiserslautern, Germany; University of Kaiserslautern-Landau, Kaiserslautern (RPTU), Germany.
    Ahmed, Sheraz
    German Research Center for Artificial Intelligence (DFKI), Kaiserslautern, Germany.
    Deep learning architectures for the prediction of YY1-mediated chromatin loops2023In: Bioinformatics research and applications: 19th international symposium, ISBRA 2023, Wrocław, Poland, October 9–12, 2023, proceedings / [ed] Xuan Guo; Serghei Mangul; Murray Patterson; Alexander Zelikovsky, Springer, 2023, p. 72-84Conference paper (Refereed)
    Abstract [en]

    YY1-mediated chromatin loops play substantial roles in basic biological processes like gene regulation, cell differentiation, and DNA replication. YY1-mediated chromatin loop prediction is important to understand diverse types of biological processes which may lead to the development of new therapeutics for neurological disorders and cancers. Existing deep learning predictors are capable to predict YY1-mediated chromatin loops in two different cell lines however, they showed limited performance for the prediction of YY1-mediated loops in the same cell lines and suffer significant performance deterioration in cross cell line setting. To provide computational predictors capable of performing large-scale analyses of YY1-mediated loop prediction across multiple cell lines, this paper presents two novel deep learning predictors. The two proposed predictors make use of Word2vec, one hot encoding for sequence representation and long short-term memory, and a convolution neural network along with a gradient flow strategy similar to DenseNet architectures. Both of the predictors are evaluated on two different benchmark datasets of two cell lines HCT116 and K562. Overall the proposed predictors outperform existing DEEPYY1 predictor with an average maximum margin of 4.65%, 7.45% in terms of AUROC, and accuracy, across both of the datases over the independent test sets and 5.1%, 3.2% over 5-fold validation. In terms of cross-cell evaluation, the proposed predictors boast maximum performance enhancements of up to 9.5% and 27.1% in terms of AUROC over HCT116 and K562 datasets.

  • 7. Abbasi, Arshad Mehmood
    et al.
    Khan, Mir Ajab
    Khan, Nadeem
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Shah, Munir H
    Ethnobotanical survey of medicinally important wild edible fruits species used by tribal communities of Lesser Himalayas-Pakistan2013In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 148, no 2, p. 528-536Article in journal (Refereed)
    Abstract [en]

    Ethnopharmacological relevance: Present survey was conducted to explore ethnomedicinal uses and cultural importance of wild edible fruits species by the inhabitants of Lesser Himalayas-Pakistan. Materials and methods: Information was obtained through informed consent semi-structured interviews, questionnaires, market survey, focus group conversation, unceremonious dialogue and village walks with key informants. Cultural significance of each species was calculated based on use report by participants at each study site. Results: A total of 35 wild edible fruits belonging to 21 genera and 17 families were used for the treatment of various ailments and consumed. Rosaceae was found dominating family with (8 spp.), followed by Moraceae (6 spp.), Rhamnaceae (5 spp.), Palmae and Vitaceae (2 spp. each) and remaining families were represented by one species each. Fruits (48%) were found highly utilized plant parts, followed by leaves (34%), bark, flowers and seeds (4% each), branches, latex and roots (2% each). Water was used as a medium for preparation while milk, ghee, oil, egg and butter are used for application. Modes of preparation were fall into seven categories like fresh parts eaten raw (38%), powder (24%), decoction (20%), extract (12 %), paste (4%), juice and latex (2% each). Based on cultural important index (CI) Morus nigra was found most significant species within top ten fruit plants followed by Morus alba, Olea ferruginea, Berberis lycium, Pyrus pashia, Ficus carica, Ficus palmata, Ziziphus mauritiana, Diospyros lotus and Ziziphus nummularia. Conclusions: Traditional uses of wild edible plant depend mainly on socio-economic factors rather than climatic conditions or wealth of flora. Use reports and citation demonstrated that there is a common cultural heritage regarding the gathered food plants. Further investigation is required for Antioxidant study, essential and toxic components, pharmacological applications; dietary requirements and biotechnological techniques to improve yields.

    (C) 2013 Elsevier Ireland Ltd. All rights reserved.

  • 8. Abbott, Benjamin W.
    et al.
    Jones, Jeremy B.
    Schuur, Edward A. G.
    Chapin, F. Stuart, III
    Bowden, William B.
    Bret-Harte, M. Syndonia
    Epstein, Howard E.
    Flannigan, Michael D.
    Harms, Tamara K.
    Hollingsworth, Teresa N.
    Mack, Michelle C.
    McGuire, A. David
    Natali, Susan M.
    Rocha, Adrian V.
    Tank, Suzanne E.
    Turetsky, Merritt R.
    Vonk, Jorien E.
    Wickland, Kimberly P.
    Aiken, George R.
    Alexander, Heather D.
    Amon, Rainer M. W.
    Benscoter, Brian W.
    Bergeron, Yves
    Bishop, Kevin
    Blarquez, Olivier
    Bond-Lamberty, Ben
    Breen, Amy L.
    Buffam, Ishi
    Cai, Yihua
    Carcaillet, Christopher
    Carey, Sean K.
    Chen, Jing M.
    Chen, Han Y. H.
    Christensen, Torben R.
    Cooper, Lee W.
    Cornelissen, J. Hans C.
    de Groot, William J.
    DeLuca, Thomas H.
    Dorrepaal, Ellen
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Fetcher, Ned
    Finlay, Jacques C.
    Forbes, Bruce C.
    French, Nancy H. F.
    Gauthier, Sylvie
    Girardin, Martin P.
    Goetz, Scott J.
    Goldammer, Johann G.
    Gough, Laura
    Grogan, Paul
    Guo, Laodong
    Higuera, Philip E.
    Hinzman, Larry
    Hu, Feng Sheng
    Hugelius, Gustaf
    Jafarov, Elchin E.
    Jandt, Randi
    Johnstone, Jill F.
    Karlsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Kasischke, Eric S.
    Kattner, Gerhard
    Kelly, Ryan
    Keuper, Frida
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Kling, George W.
    Kortelainen, Pirkko
    Kouki, Jari
    Kuhry, Peter
    Laudon, Hjalmar
    Laurion, Isabelle
    Macdonald, Robie W.
    Mann, Paul J.
    Martikainen, Pertti J.
    McClelland, James W.
    Molau, Ulf
    Oberbauer, Steven F.
    Olefeldt, David
    Pare, David
    Parisien, Marc-Andre
    Payette, Serge
    Peng, Changhui
    Pokrovsky, Oleg S.
    Rastetter, Edward B.
    Raymond, Peter A.
    Raynolds, Martha K.
    Rein, Guillermo
    Reynolds, James F.
    Robards, Martin
    Rogers, Brendan M.
    Schaedel, Christina
    Schaefer, Kevin
    Schmidt, Inger K.
    Shvidenko, Anatoly
    Sky, Jasper
    Spencer, Robert G. M.
    Starr, Gregory
    Striegl, Robert G.
    Teisserenc, Roman
    Tranvik, Lars J.
    Virtanen, Tarmo
    Welker, Jeffrey M.
    Zimov, Sergei
    Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire: an expert assessment2016In: Environmental Research Letters, E-ISSN 1748-9326, Vol. 11, no 3, article id 034014Article in journal (Refereed)
    Abstract [en]

    As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export. Models predict that some portion of this release will be offset by increased production of Arctic and boreal biomass; however, the lack of robust estimates of net carbon balance increases the risk of further overshooting international emissions targets. Precise empirical or model-based assessments of the critical factors driving carbon balance are unlikely in the near future, so to address this gap, we present estimates from 98 permafrost-region experts of the response of biomass, wildfire, and hydrologic carbon flux to climate change. Results suggest that contrary to model projections, total permafrost-region biomass could decrease due to water stress and disturbance, factors that are not adequately incorporated in current models. Assessments indicate that end-of-the-century organic carbon release from Arctic rivers and collapsing coastlines could increase by 75% while carbon loss via burning could increase four-fold. Experts identified water balance, shifts in vegetation community, and permafrost degradation as the key sources of uncertainty in predicting future system response. In combination with previous findings, results suggest the permafrost region will become a carbon source to the atmosphere by 2100 regardless of warming scenario but that 65%-85% of permafrost carbon release can still be avoided if human emissions are actively reduced.

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  • 9.
    Abd Alrahman, Chadi
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Khodabakhsh, Amir
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Schmidt, Florian M.
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Qu, Zhechao
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Foltynowicz, Aleksandra
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Cavity-enhanced optical frequency comb spectroscopy of high-temperature H2O in a flame2014In: Optics Express, E-ISSN 1094-4087, Vol. 22, no 11, p. 13889-13895Article in journal (Refereed)
    Abstract [en]

    We demonstrate near-infrared cavity-enhanced optical frequency comb spectroscopy of water in a premixed methane/air flat flame. The detection system is based on an Er:fiber femtosecond laser, a high finesse optical cavity containing the flame, and a fast-scanning Fourier transform spectrometer (FTS). High absorption sensitivity is obtained by the combination of a high-bandwidth two-point comb-cavity lock and auto-balanced detection in the FTS. The system allows recording high-temperature water absorption spectra with a resolution of 1 GHz and a bandwidth of 50 nm in an acquisition time of 0.4 s, with absorption sensitivity of 4.2 x 10 (9) cm(-1) Hz(-1/2) per spectral element.

  • 10.
    Abdel-Fattah, Wael R.
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Carlsson, Mattias
    Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden.
    Hu, Guo-Zhen
    Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden.
    Singh, Ajeet
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Vergara, Alexander
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Aslam, Rameen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Ronne, Hans
    Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden.
    Björklund, Stefan
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes2024In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 52, no 11, p. 6220-6233Article in journal (Refereed)
    Abstract [en]

    Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2–8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3́-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3́-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron–exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.

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  • 11.
    Abdelrahman, Kholoud N.
    et al.
    Faculty of Development and Technology, Zagazig University, Zagazig, Egypt.
    Abdel Ghany, Abdel Ghany A.
    Faculty of Development and Technology, Zagazig University, Zagazig, Egypt.
    Saber, Refaat A.
    Faculty of Development and Technology, Zagazig University, Zagazig, Egypt.
    Osman, Ali
    Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
    Sitohy, Basel
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology. Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Immunology.
    Sitohy, Mahmoud
    Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
    Anthocyanins from pomegranate peel (Punica granatum), chili pepper fruit (Capsicum annuum), and bougainvillea flowers (Bougainvillea spectabilis) with multiple biofunctions: antibacterial, antioxidant, and anticancer2024In: Heliyon, E-ISSN 2405-8440, Vol. 10, no 11, article id e32222Article in journal (Refereed)
    Abstract [en]

    Background: Natural colorants, including natural pigments, e.g., anthocyanins, carotenoids, and chlorophylls, in novel and attractive food matrixes have become a popular trend. They impart favorite colors to food products and provide significant therapeutic effects. This study is aimed at extracting and identifying some natural pigments from different plant sources and evaluating their ability as antibacterial, antioxidant, and anticancer activities.

    Methods: The anthocyanin-rich extract (ARE) is derived from three natural plant sources: pomegranate peel (Punica granatum), chili pepper fruit (Capsicum annuum), and Bougainvillea flowers. Bougainvillea spectabilis are analyzed for biochemical composition, as well as antioxidant, antibacterial, and anticancer activity, HPLC, DPPH, FRAP, disc diffusion assay, MIC, MTT, VEGFR‐2, and caspase-9 assays.

    Results: All three extracts had varying total phenolic contents, ranging from 14 to 466 mg GAE/g extract, where Punica granatum was the highest (466 mg GAE/g extract), followed by Bougainvillea spectabilis (180 mg GAE/g extract), and then Capsicum annuum (14 mg GAE/g extract). The antioxidant activity rose steadily with raising concentration. The ARE of pomegranate peels recorded highest value, followed by Bougainvillea flowers and chili pepper fruit. The MTT assay revealed an inhibitory action of the tested extracts on the proliferation of HCT-116, MCF-7, and HepG2 in a concentration-based manner. Gene expression of caspase-9 transcripts was considerably multiplied by the application of ARE of pomegranate peels. All the tested extracts inhibited VEGFR-2, and the inhibition (%) expanded gradually with increasing concentrations, achieving the highest value (80 %) at 10 μg/mL. The ARE of pomegranate peels scored highest antibacterial activity, followed by ARE of chili pepper fruit and Bougainvillea flowers. The inhibition zone diameter escalated gradually with rising concentrations of the tested samples.

    Conclusion: The AREs of the three studied plant sources can be used as multifunctional products with antioxidant, anticancer, and antibacterial activities that are natural, safe, and cheap.

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  • 12.
    Abdelraouf, Hussein
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    LARGE LANGUAGE MODELS ADAPTED TO SWEDISH OF THE 1920S2023Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Large Language Models typically perform best when there is a lot of data to train on. An interesting question is how such models perform in less dominant languages (e.g., Swedish) and over domains of historical interest where less modern words and phrasings are used. Specifically, how can existing language models for current usage be adapted to get the best question-answering results when applied over such historical domains? In this Master's thesis, we will use domain adaption on three different pre-trained Swedish NLP language models: BERT base Swedish Cased SQuAD Experimental, GPT-SW3, and IBM Watson. We will fine-tune these models on the specific domain of Vasaloppet's 100-year-old articles to evaluate if the models will have difficulties predicting results from a Swedish source that is a century old. We will evaluate how well these models perform on question answering and report results and lessons learned. 

  • 13. Abdelsalam, UM
    et al.
    Moslem, WM
    Shukla, Padma Kant
    Umeå University, Faculty of Science and Technology, Department of Physics. Institut für Theoretische Physik IV, Fakultät für Physik und Astronomie, Ruhr-Universität Bochum, D-44780 Bochum, Germany; Nonlinear Physics Centre & Center for Plasma Science and Astrophysics, Ruhr-Universität Bochum, D-44780 Bochum, Germany; Max-Planck-Institut für extraterrestrische Physik, D-85741 Garching, Germany; GoLP/Instituto Superior Técnico, 1049-001 Lisbon, Portugal; CCLRC Centre for Fundamental Physics, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon 0X11 0QX, UK; SUPA Department of Physics, University of Strathclyde, Glasgow G 40NG, UK; School of Physics, Faculty of Science & Agriculture, University of Kwazulu-Natal, Durban 4000, South Africa; Department of Physics, CITT, Islamabad, Pakistan.
    Ion-acoustic solitary waves in a dense pair-ion plasma containing degenerate electrons and positrons2008In: Physics Letters A, ISSN 0375-9601, E-ISSN 1873-2429, Vol. 372, no 22, p. 4057-4061Article in journal (Refereed)
    Abstract [en]

    Fully nonlinear propagation of ion-acoustic solitary waves in a collisionless dense/quantum electron-positron-ion plasma is investigated. The electrons and positrons are assumed to follow the Thomas-Fermi density distribution and the ions are described by the hydrodynamic equations. An energy balance-like equation involving a Sagdeev-type pseudo-potential is derived. Finite amplitude solutions are obtained numerically and their characteristics are discussed. The small-but finite-amplitude limit is also considered and an exact analytical solution is obtained. The present studies might be helpful to understand the excitation of nonlinear ion-acoustic solitary waves in a degenerate plasma such as in superdense white dwarfs.

  • 14. Abdelsalam, UM
    et al.
    Moslem, WM
    Shukla, Padma Kant
    Umeå University, Faculty of Science and Technology, Department of Physics. Institut für Theoretische Physik IV, Fakultät für Physik und Astronomie, Ruhr-Universität Bochum, D-44780 Bochum, Germany; Nonlinear Physics Centre & Center for Plasma Science and Astrophysics, Ruhr-Universität Bochum, D-44780 Bochum, Germany; Max-Planck-Institut für Extraterrestrische Physik, D-85741 Garching, Germany; GoLP/Instituto Superior Técnico, 1049-001 Lisbon, Portugal; CCLRC Centre for Fundamental Physics, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon 0X11 0QX, UK; SUPA Department of Physics, University of Strathclyde, Glasgow G 40NG, UK; School of Physics, Faculty of Science & Agriculture, University of Kwazulu-Natal, Durban 4000, South Africa; Department of Physics, CITT, Islamabad, Pakistan.
    Localized electrostatic excitations in a Thomas-Fermi plasma containing degenerate electrons2008In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 15, no 5, article id 052303Article in journal (Refereed)
    Abstract [en]

    By using the Thomas-Fermi electron density distribution for quantum degenerate electrons, the hydrodynamic equations for ions, and the Poisson equation, planar and nonplanar ion-acoustic solitary waves in an unmagnetized collisionless plasma are investigated. The reductive perturbation method is used to derive cylindrical and spherical Korteweg-de Vries equations. Numerical solutions of the latter are presented. The present results can be useful in understanding the features of small but finite amplitude localized ion-acoustic solitary pulses in a degenerate plasma.

  • 15.
    Abdel-Shafi, Seham
    et al.
    Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
    El-Nemr, Mona
    Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
    Enan, Gamal
    Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
    Osman, Ali
    Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
    Sitohy, Basel
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.
    Sitohy, Mahmoud
    Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
    Isolation and characterization of antibacterial conglutinins from Lupine seeds2023In: Molecules, ISSN 1431-5157, E-ISSN 1420-3049, Vol. 28, no 1, article id 35Article in journal (Refereed)
    Abstract [en]

    The main target of this work is to discover new protein fractions from natural resources with high antibacterial action. The 7S and 11S globulin fractions, as well as the basic subunit (BS), were isolated from lupine seeds (Lupinus termis), chemically characterized, and screened for antibacterial activity against seven pathogenic bacteria. SDS-PAGE revealed molecular weights ranging from 55 to 75 kDa for 7S globulin, 20–37 kD for 11S globulin, and 20 kD for the BS. 11S globulin and the BS migrated faster on Urea-PAGE toward the cathode compared to 7S globulin. FTIR and NMR showed different spectral patterns between the 7S and 11S globulins but similar ones between 11S globulin and the BS. The MICs of the BS were in the range of 0.05–2 μg/mL against Listeria monocytogenes, Klebsiella oxytoca, Proteus mirabilis, Staphylococcus aureus, Listeria ivanovii, Salmonella typhimurium, and Pseudomonas aeruginosa compared to higher values for 11S globulin. The BS surpassed 11S globulin in antibacterial action, while 7S globulin showed no effect. The MICs of 11S globulin and the BS represented only 5% and 2.5% of the specific antibiotic against L. monocytogenes, respectively. Scanning electron microscopy (SEM) demonstrated different signs of cellular deformation and decay in the protein-treated bacteria, probably due to interaction with the bacterial cell wall and membranes. 11S globulin and the BS can be nominated as effective food biopreservatives.

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  • 16.
    Abderhalden, Bigna Lu
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Seasonal Reindeer Grazing Effects on Mountain Birch Forests: A 3D Perspective using Drones2024Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Reindeer are important drivers of ecosystem processes in arctic and subarctic ecosystems, changing nutrient conditions and influencing vegetation by grazing and trampling. Mountain birch forests are one of the ecosystems impacted by reindeer grazing, but the effect on the 3D structure of these forests is not well understood. Drones are revolutionising ecological studies, allowing to create high-resolution 3D point clouds at low costs. I investigated the effect of year-round and autumn reindeer grazing on mountain birch forest vegetation in historically separated grazing areas at the Finnish-Norwegian border, using a combination of field data and drone data. The two sampling techniques were further compared to evaluate the possibility to use photogrammetric point clouds to characterise mountain birch forests. I found lower productivity in the year-round grazing regime, coinciding with generally higher vegetation density. Vertically, higher densities were found above browsing height, while the understory showed lower densities compared to autumn grazed areas. These results suggest that mountain birches allocate more biomass to the canopy area, which can be direct or indirect grazing effects. Nevertheless, overall productivity is lowered by grazing indicating changes in vegetation biomass and composition. The point clouds generally matched field data, but the understory vegetation tended to be underrepresented, arising the question if found effects are ecological or technical. As this could not be disentangled, cautious interpretation of my results is required. I conclude that using photogrammetric point clouds is a promising technique for ecological studies, but needs further development to improve accuracy and reliability of results.

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    Thesis_Ecology_VT24
  • 17.
    Abdollahi, Elham
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Development of breath sampling system for detection of exhaled nitric oxide by Faraday modulation spectroscopy2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Technological developments over the years have resulted in many different techniques for detection of nitric oxide (NO) in both the atmosphere and from biological sources. One such technique is Faraday Modulation Spectroscopy (FAMOS), which is a laser-based spectroscopic technique for detection of paramagnetic molecules in gas phase. The technique uses a modulated magnetic field that introduce rotation of the polarization plane of linearly polarized laser light, which can be related to the concentration of the molecules. This enables sensitive and selective detection of paramagnetic gaseous compounds and the technique is thus well suited for detection of NO for biomedical applications in low concentrations which is essential for breath analysis.

    In this thesis, a system for breath analysis is developed and coupled to a Faraday modulation spectrometer for sensitive detection of NO at 5.33 μm based on a room temperature continuous wave distributed feedback (DFB) QCL. It also provides a theoretical model of FAMOS utilizing the most sensitive Q3/2 (3/2 ) transition in NO. The results from this study indicate that the mid-infrared FAMOS system, which was built around a continuous wave (cw) quantum cascade laser (QCL) emitting light with an output power of approximately 70 mW, is fully capable of detection of ppb levels of NO in exhaled human breath.

  • 18.
    Abdollahi, Elham
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Realization of an instrumentation for detection of acetylene in breath by the NICE-OHMS technique2014Independent thesis Advanced level (degree of Master (Two Years)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Measurement is an important activity in nearly all branches of science and technology. A measurement technique provides an observer with a numerical value corresponding to the variable being measured. Researchers envision that laser spectroscopy will serve as a functional tool for measurement to detect molecules in gas phase. One such a laser spectroscopic technique for measurement is noise-immune cavity enhanced optical heterodyne molecular spectroscopy (NICE-OHMS), which is a highly sensitive laser-based spectroscopic technique for detection of molecules in gas phase. The technique was developed in the mid-1990s at the Joint Institute for Laboratory Astrophysics (JILA).

    In this thesis, a realization of instrumentation for detection of acetylene in breath by a fiber laser-based NICE-OHMS instrumentation working in the near-infrared wavelength region is obtained. The results of this study show that the NICE-OHMS system is fully capable of detection of parts-per-billion (ppb) levels of acetylene in exhaled human breath.

  • 19.
    Abdollahian, Josef
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Kanwar, Anna
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Optimering av kortaste vägen vid hantering och avledning av skadligt dagvatten: Lösning med A-stjärna algoritm samt en guide med ekonomiska styrmedel för beslutsfattande aktörer2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The earth's population is growing and increasingly more people move into urban areas. This means that as cities grow, new buildings are being built and infrastructures are expanding. This rapid growth is directly related to increased floods as a result of man-made changes in nature.

    The already overloaded storm water systems for rain-, melt-, rinsing and other surplus water cannot often handle the existing demand. Therefore, floods arise at greater rain intensity and pose significant costs to society. Due to an unclear division of responsibility within the municipality's organizations there is a failure to handle the existing storm water problem. In order to be able to plan for sustainable cities in the future, it is important to find a viable solution regarding the responsibility issue and how to best handle the storm water to achieve cost advantage.

    This study presents a guide for municipalities on how to allocate the responsibility between the municipality and the exploiter. The guide is based on simulations and theories in optimization to propose effective solutions for harmful surplus storm water. Through simulations of the storm water system, the amount of surplus water that does not fit the storm water system capacity has been quantified. In addition, to find a reasonable alternative run-off path for the surplus water, different methods of the shortest path problem have been investigated.

    The results show that a classical shortest path algorithm with a heuristic function is not the most appropriate alternative. This because the heuristic function in the algorithm prevents the selection of a more natural pathway upstream even though it could be a more optimal solution.

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    Optimering av kortaste vägen vid hantering och avledning av skadligt dagvatten
  • 20. Abdoullaye, Doukary
    et al.
    Acevedo, I
    Adebayo, Abisola A
    Behrmann-Godel, Jasminca
    Benjamin, RC
    Bock, Dan G
    Born, Celine
    Brouat, Carine
    Caccone, Adalgisa
    Cao, Ling-Zhen
    Casadoamezua, P
    Cataneo, J
    Correa-Ramirez, MM
    Cristescu, Melania E
    Dobigny, Gauthier
    Egbosimba, Emmanuel E
    Etchberger, Lianna K
    Fan, Bin
    Fields, Peter D
    Forcioli, D
    Furla, P
    de Leon, FJ Garcia
    Garcia-Jimenez, R
    Gauthier, Philippe
    Gergs, Rene
    Gonzalez, Clementina
    Granjon, Laurent
    Gutierrez-Rodriguez, Carla
    Havill, Nathan P
    Helsen, P
    Hether, Tyler D
    Hoffman, Eric A
    Hu, Xiangyang
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ishizaki, S
    Ji, Heyi
    Ji, XS
    Jimenez, ML
    Kapil, R
    Karban, R
    Keller, Stephen R
    Kubota, S
    Li, Shuzhen
    Li, Wansha
    Lim, Douglas D
    Lin, Haoran
    Liu, Xiaochun
    Luo, Yayan
    Machordom, A
    Martin, Andrew P
    Matthysen, E
    Mazzella, Maxwell N
    McGeoch, Melodie A
    Meng, Zining
    Nishizawa, M
    O'Brien, Patricia
    Ohara, M
    Ornelas, Juan Francisco
    Ortu, MF
    Pedersen, Amy B
    Preston, L
    Ren, Qin
    Rothhaupt, Karl-Otto
    Sackett, Loren C
    Sang, Qing
    Sawyer, GM
    Shiojiri, K
    Taylor, Douglas R
    van Dongen, S
    van Vuuren, Bettine Jansen
    Vandewoestijne, S
    Wang, H
    Wang, JT
    Wang, Le
    Xu, Xiang-Li
    Yang, Guang
    Yang, Yongping
    Zeng, YQ
    Zhang, Qing-Wen
    Zhang, Yongping
    Zhao, Y
    Zhou, Yan
    Permanent genetic resources added to molecular ecology resources database 1 August 2009 - 30 September 20092010In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 10, no 1, p. 232-236Article in journal (Refereed)
    Abstract [en]

    This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.

  • 21. Abdullah, Muhammad Imran
    et al.
    Janjua, Muhammad Ramzan Saeed Ashraf
    Mahmood, Asif
    Ali, Sajid
    Ali, Muhammad
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Quantum Chemical Designing of Efficient Sensitizers for Dye Sensitized Solar Cells2013In: Bulletin of the Korean Chemical Society (Print), ISSN 0253-2964, E-ISSN 1229-5949, Vol. 34, no 7, p. 2093-2098Article in journal (Refereed)
    Abstract [en]

    Density functional theory (DFT) was used to determine the ground state geometries of indigo and new design dyes (IM-Dye-1 IM-Dye-2 and IM-Dye-3). The time dependant density functional theory (TDDFT) was used to calculate the excitation energies. All the calculations were performed in both gas and solvent phase. The LUMO energies of all the dyes were above the conduction band of TiO2, while the HOMOs were below the redox couple (except IM-Dye-3). The HOMO-LUMO energy gaps of new design dyes were smaller as compared to indigo. All new design dyes were strongly red shifted as compared to indigo. The improved light harvesting efficiency (LHE) and free energy change of electron injection Delta G(inject) of new designed sensitizers revealed that these materials would be excellent sensitizers. The broken coplanarity between the benzene near anchoring group having LUMO and the last benzene attached to TPA unit in all new design dyes consequently would hamper the recombination reaction. This theoretical designing will the pave way for experimentalists to synthesize the efficient sensitizers for solar cells.

  • 22.
    Abdullah, Sarwin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Low-energy radar for handheld IR-cameras: Using mmWave radar as a complement for Multi Spectral Dynamic Imaging in handheld cameras2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The aim of this project is to assess whether a low energy radar, more specifically the mmWave radar from Acconer could be used as a complement to the handheld cameras from FLIR, in order to improve its performance, in particular the alignment of visual and infra-red image. The specific camera used for this project is a FLIR C5 IR-camera. It was found that if the distance is known, then one could align the images more easily and by the help of the radar this could occur automatically instead of doing it manually as it is implemented today. 

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  • 23.
    Abdulle, Assyr
    et al.
    ANMC, EPFL.
    Cohen, David
    Institut für Angewandte und Numerische Mathematik, KIT.
    Vilmart, Gilles
    ANMC, EPFL.
    Konstantinos, Zygalakis
    ANMC, EPFL.
    High weak order methods for stochastic differential equations based on modified equations2012In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 34, no 3, p. A1800-A1823Article in journal (Refereed)
    Abstract [en]

    Inspired by recent advances in the theory of modified differential equations, we propose a new methodology for constructing numerical integrators with high weak order for the time integration of stochastic differential equations. This approach is illustrated with the constructions of new methods of weak order two, in particular, semi-implicit integrators well suited for stiff (mean-square stable) stochastic problems, and implicit integrators that exactly conserve all quadratic firstintegrals of a stochastic dynamical system. Numerical examples confirm the theoretical results and show the versatility of our methodology.

  • 24.
    Abedan Kondori, Farid
    et al.
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Yousefi, Shahrouz
    KTH Royal Institute of Technology, Department of Media Technology and Interaction Design.
    Liu, Li
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Li, Haibo
    KTH Royal Institute of Technology, Department of Media Technology and Interaction Design.
    Head operated electric wheelchair2014In: IEEE Southwest Symposium on Image Analysis and Interpretation (SSIAI 2014), IEEE , 2014, p. 53-56Conference paper (Refereed)
    Abstract [en]

    Currently, the most common way to control an electric wheelchair is to use joystick. However, there are some individuals unable to operate joystick-driven electric wheelchairs due to sever physical disabilities, like quadriplegia patients. This paper proposes a novel head pose estimation method to assist such patients. Head motion parameters are employed to control and drive an electric wheelchair. We introduce a direct method for estimating user head motion, based on a sequence of range images captured by Kinect. In this work, we derive new version of the optical flow constraint equation for range images. We show how the new equation can be used to estimate head motion directly. Experimental results reveal that the proposed system works with high accuracy in real-time. We also show simulation results for navigating the electric wheelchair by recovering user head motion.

  • 25.
    Abedin, Md Reaz Ashraful
    et al.
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Bensch, Suna
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Hellström, Thomas
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Self-supervised language grounding by active sensing combined with Internet acquired images and text2017In: Proceedings of the Fourth International Workshop on Recognition and Action for Scene Understanding (REACTS2017) / [ed] Jorge Dias George Azzopardi, Rebeca Marf, Málaga: REACTS , 2017, p. 71-83Conference paper (Refereed)
    Abstract [en]

    For natural and efficient verbal communication between a robot and humans, the robot should be able to learn names and appearances of new objects it encounters. In this paper we present a solution combining active sensing of images with text based and image based search on the Internet. The approach allows the robot to learn both object name and how to recognise similar objects in the future, all self-supervised without human assistance. One part of the solution is a novel iterative method to determine the object name using image classi- fication, acquisition of images from additional viewpoints, and Internet search. In this paper, the algorithmic part of the proposed solution is presented together with evaluations using manually acquired camera images, while Internet data was acquired through direct and reverse image search with Google, Bing, and Yandex. Classification with multi-classSVM and with five different features settings were evaluated. With five object classes, the best performing classifier used a combination of Pyramid of Histogram of Visual Words (PHOW) and Pyramid of Histogram of Oriented Gradient (PHOG) features, and reached a precision of 80% and a recall of 78%.

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  • 26. Abegg, Bruno
    et al.
    Morin, Samuel
    Demiroglu, O. Cenk
    Umeå University, Arctic Research Centre at Umeå University. Umeå University, Faculty of Social Sciences, Department of Geography.
    François, H.
    Rothleitner, M.
    Strasser, U.
    Overloaded!: Critical revision and a new conceptual approach for snow indicators in ski tourism2021In: International journal of biometeorology, ISSN 0020-7128, E-ISSN 1432-1254, Vol. 65, no 5, p. 691-701Article in journal (Refereed)
    Abstract [en]

    Indicators are widely used in climate variability and climate change assessments to simplify the tracking of complex processes and phenomena in the state of the environment. Apart from the climatic criteria, the snow indicators in ski tourism have been increasingly extended with elements that relate to the technical, operational, and commercial aspects of ski tourism. These non-natural influencing factors have gained in importance in comparison with the natural environmental conditions but are more difficult to comprehend in time and space, resulting in limited explanatory power of the related indicators when applied for larger/longer scale assessments. We review the existing indicator approaches to derive quantitative measures for the snow conditions in ski areas, to formulate the criteria that the indicators should fulfill, and to provide a list of indicators with their technical specifications which can be used in snow condition assessments for ski tourism. For the use of these indicators, a three-step procedure consisting of definition, application, and interpretation is suggested. We also provide recommendations for the design of indicator-based assessments of climate change effects on ski tourism. Thereby, we highlight the importance of extensive stakeholder involvement to allow for real-world relevance of the achieved results.

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  • 27. Abeli, Thomas
    et al.
    Orsenigo, Simone
    Guzzon, Filippo
    Fae, Matteo
    Balestrazzi, Alma
    Carlsson-Graner, Ulla
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mueller, Jonas V.
    Mondoni, Andrea
    Geographical pattern in the response of the arctic-alpine Silene suecica (Cariophyllaceae) to the interaction between water availability and photoperiod2015In: Ecological research, ISSN 0912-3814, E-ISSN 1440-1703, Vol. 30, no 2, p. 327-335Article in journal (Refereed)
    Abstract [en]

    We hypothesized a geographical pattern of the plant performance (seedling development, biomass production, relative water content and chlorophyll content) as a result of response to the interaction between photoperiod and water availability in populations of the arctic-alpine Silene suecica from different latitudes, thus experiencing different photoperiods during the growing season. Particularly, we expected a lower drought sensitivity in northern compared to southern populations as a consequence of harsher conditions experienced by the northern populations in terms of water availability. The experiment was carried out under common garden conditions, manipulating the water availability (wet and dry) and the photoperiod (21 and 16 h). We found an interaction between photoperiod and water availability on plant height, leaves, growth, biomass and total chlorophyll. However, the photoperiod neither counteracted nor intensified the effect of drought. Plants exposed to drought compensated for decreasing water availability by reducing their shoot growth. Changes in the chlorophyll content and chlorophyll a/b ratio were observed. Northern populations showed a higher basal growth performance and a greater response to the changed water regime (from wet to dry) than the southern populations. Southern populations showed a reduced ability to respond to drought, but their low basal performance may be advantageous under low water availability, avoiding water loss. In contrast, northern populations showed a stronger plastic response that limited the negative effects of reduced water availability. This study highlights the possibility that the plant response to environmental constraints (specifically water availability) may follow a geographical pattern.

  • 28.
    Abidine, Yara
    et al.
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Wallenberg Centre for Molecular Medicine at Umeå University (WCMM).
    Liu, Lifeng
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Wallenberg Centre for Molecular Medicine at Umeå University (WCMM).
    Wallén, Oskar
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Trybala, Edward
    Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
    Olofsson, Sigvard
    Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
    Bergström, Tomas
    Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
    Bally, Marta
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Wallenberg Centre for Molecular Medicine at Umeå University (WCMM).
    Cellular Chondroitin Sulfate and the Mucin-like Domain of Viral Glycoprotein C Promote Diffusion of Herpes Simplex Virus 1 While Heparan Sulfate Restricts Mobility2022In: Viruses, E-ISSN 1999-4915, Vol. 14, no 8, article id 1836Article in journal (Refereed)
    Abstract [en]

    The diffusion of viruses at the cell membrane is essential to reach a suitable entry site and initiate subsequent internalization. Although many viruses take advantage of glycosaminoglycans (GAG) to bind to the cell surface, little is known about the dynamics of the virus–GAG interactions. Here, single-particle tracking of the initial interaction of individual herpes simplex virus 1 (HSV-1) virions reveals a heterogeneous diffusive behavior, regulated by cell-surface GAGs with two main diffusion types: confined and normal free. This study reports that different GAGs can have competing influences in mediating diffusion on the cells used here: chondroitin sulfate (CS) enhances free diffusion but hinders virus attachment to cell surfaces, while heparan sulfate (HS) promotes virus confinement and increases entry efficiency. In addition, the role that the viral mucin-like domains (MLD) of the HSV-1 glycoprotein C plays in facilitating the diffusion of the virus and accelerating virus penetration into cells is demonstrated. Together, our results shed new light on the mechanisms of GAG-regulated virus diffusion at the cell surface for optimal internalization. These findings may be extendable to other GAG-binding viruses.

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  • 29.
    Abiodun Daramola, Olamide
    et al.
    Centre for Chemico- and Biomedicinal Research (CCBR), Department of Chemistry, Faculty of Science, Rhodes University, Grahamstown, South Africa; Department of Chemical and Physical Sciences, Faculty of Natural Science, Walter Sisulu University, Private Bag XI, Mthatha, South Africa.
    Bazibuhe Safari, Justin
    Centre for Chemico- and Biomedicinal Research (CCBR), Department of Chemistry, Faculty of Science, Rhodes University, Grahamstown, South Africa; Department of Pharmacy, Faculty of Pharmaceutical Sciences and Public Health, Official University of Bukavu, Bukavu, Democratic Republic Congo.
    Adeniyi, Kayode Omotayo
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Siwe-Noundou, Xavier
    Department of Pharmaceutical Sciences, School of Pharmacy, Sefako Makgatho Health Sciences University, Gauteng, Pretoria, South Africa.
    Margaret Kirkpatrick Dingle, Laura
    Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Faculty of Science, Rhodes University, Grahamstown, South Africa.
    Lesley Edkins, Adrienne
    Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Faculty of Science, Rhodes University, Grahamstown, South Africa.
    Foster Tseki, Potlaki
    Department of Chemical and Physical Sciences, Faculty of Natural Science, Walter Sisulu University, Private Bag XI, Mthatha, South Africa.
    Werner Maçedo Krause, Rui
    Centre for Chemico- and Biomedicinal Research (CCBR), Department of Chemistry, Faculty of Science, Rhodes University, Grahamstown, South Africa.
    Biocompatible liposome and chitosan-coated CdTe/CdSe/ZnSe multi-core-multi-shell fluorescent nanoprobe for biomedical applications2024In: Journal of Photochemistry and Photobiology A: Chemistry, ISSN 1010-6030, E-ISSN 1873-2666, Vol. 454, article id 115714Article in journal (Refereed)
    Abstract [en]

    Cadmium telluride (CdTe) semiconductor quantum dots (QDs) are brightly luminescent nanocrystals that have emerged as a new class of fluorescent probes for in vivo bioimaging and theranostic applications. CdTe QDs toxicity to normal human cells is minimized by coating with a less toxic ZnS and ZnSe shell forming a core–shell nanostructure. However, coating with ZnS or ZnSe shell is insufficient to prevent the leaching of toxic Cd metal ions. To further minimize toxicity, thiol dual capped CdTe/CdSe/ZnSe multi-core-multi-shell quantum dots were coated with nanoliposome or liposome vesicles (CdTe/CdSe/ZnSe@liposome) and chitosan nanoparticles (CdTe/CdSe/ZnSe@ChitNPs) and their biocompatibility on HeLa and Vero cells were investigated. Different spectroscopic and microscopic techniques were used to elucidate nanocomposites' optical, morphological, and physicochemical properties. The coating of CdTe/CdSe/ZnSe multi-core-multi-shell quantum dots were conducted at different formulations (F1, F2 and F3) and results from the fluorescence studies show that F3 demonstrated the best interaction for both liposome and ChitNPs composite. Exposure to 12 h UV illumination studies also reveals that CdTe/CdSe/ZnSe@liposome shows an enhancement in fluorescence compared to CdTe/CdSe/ZnSe@ChitNPs. The cytotoxicity of the formulations towards HeLa and Vero cells also depicted minimal toxicity compared to CdTe/CdSe/ZnSe QDs that shows much higher toxicity (IC50 = 0.09381 mg/ml). It was further observed that liposome coated multi-core-multi-shell QDs@F2 demonstrated lower toxicity (IC50 = 0.4364 mg/ml) compared to ChitNPs coated multi-core-multi-shell QDs@F2 (IC50 = 0.1618 mg/ml). Results from the florescence imaging studies reveal that CdTe/CdSe/ZnSe-multi-core-multi-shell QDs liposomes and ChitNPs composite retained most of their fluorescence and properties and could easily be tracked in cells and visualized around the nucleus. This indicates the successful internalization of the QDs in the cytosol. Therefore, these results shows that coating CdTe multi-core-mutli-shell QDs with liposomes and ChitNPs produce better biocompatibility compared to uncoated multi-core–shell QDs. However, liposome coated CdTe/CdSe/ZnSe multi-core-multi-shell quantum dots show better optical properties, photostability and biocompatibility compared to CdTe/CdSe/ZnSe multi-core-multi-shell quantum dots with ChitNPs coating. These particles therefore show good promise in cell-labelling and drug delivery studies.

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  • 30. Abou-Hamad, E.
    et al.
    Babaa, M. -R
    Bouhrara, M.
    Kim, Y.
    Saih, Y.
    Dennler, S.
    Mauri, F.
    Basset, J. -M
    Goze-Bac, C.
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Structural properties of carbon nanotubes derived from (13)C NMR2011In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 84, no 16, p. 165417-Article in journal (Refereed)
    Abstract [en]

    We present a detailed experimental and theoretical study on how structural properties of carbon nanotubes can be derived from 13C NMR investigations. Magic angle spinning solid state NMR experiments have been performed on single-and multiwalled carbon nanotubes with diameters in the range from 0.7 to 100 nm and with number of walls from 1 to 90. We provide models on how diameter and the number of nanotube walls influence NMR linewidth and line position. Both models are supported by theoretical calculations. Increasing the diameter D, from the smallest investigated nanotube, which in our study corresponds to the inner nanotube of a double-walled tube to the largest studied diameter, corresponding to large multiwalled nanotubes, leads to a 23.5 ppm diamagnetic shift of the isotropic NMR line position d. We show that the isotropic line follows the relation d = 18.3/D + 102.5 ppm, where D is the diameter of the tube and NMR line position d is relative to tetramethylsilane. The relation asymptotically tends to approach the line position expected in graphene. A characteristic broadening of the line shape is observed with the increasing number of walls. This feature can be rationalized by an isotropic shift distribution originating from different diamagnetic shielding of the encapsulated nanotubes together with a heterogeneity of the samples. Based on our results, NMR is shown to be a nondestructive spectroscopic method that can be used as a complementary method to, for example, transmission electron microscopy to obtain structural information for carbon nanotubes, especially bulk samples.

  • 31. Abou-Hamad, E.
    et al.
    Kim, Y.
    Bouhrara, M.
    Saih, Y.
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Luzzi, D. E.
    Goze-Bac, C.
    NMR strategies to study the local magnetic properties of carbon nanotubes2012In: Physica. B, Condensed matter, ISSN 0921-4526, E-ISSN 1873-2135, Vol. 407, no 4, p. 740-742Article in journal (Refereed)
    Abstract [en]

    The local magnetic properties of the one dimensional inner space of the nanotubes are investigated using C-13 nuclear magnetic resonance spectroscopy of encapsulated fullerene molecules inside single walled carbon nanotubes. Isotope engineering and magnetically purified nanotubes have been advantageously used on our study to discriminate between the different diamagnetic and paramagnetic shifts of the resonances. Ring currents originating from the pi electrons circulating on the nanotube, are found to actively screen the applied magnetic field by -36.9 ppm. Defects and holes in the nanotube walls cancel this screening locally. What is interesting, that at high magnetic fields, the modifications of the NMR resonances of the molecules from free to encapsulated can be exploited to determine some structural characteristics of the surrounding nanotubes, never observed experimentally. (C) 2011 Elsevier B.V. All rights reserved.

  • 32.
    Abou-Hamad, Edy
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Goze-Bac, Christophe
    Université Montpellier II, France.
    Nitze, Florian
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Schmid, Michael
    Physikalisches Institut, Universität Stuttgart, Germany.
    Aznar, Robert
    Université Montpellier II, France.
    Mehring, Michael
    Physikalisches Institut, Universität Stuttgart, Germany.
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Electronic properties of Cs-intercalated single-walled carbon nanotubes derived from nuclear magnetic resonance2011In: New Journal of Physics, E-ISSN 1367-2630, Vol. 13, p. 053045 (1)-(9)Article in journal (Refereed)
    Abstract [en]

    We report on the electronic properties of Cs-intercalated singlewalled carbon nanotubes (SWNTs). A detailed analysis of the 13C and133Cs nuclear magnetic resonance (NMR) spectra reveals an increased metallization of the pristine SWNTs under Cs intercalation. The ‘metallization’ of CsxC materials where x =0–0.144 is evidenced from the increased local electronic density of states (DOS) n(EF)at the Fermi level of the SWNTs as determined from spin–lattice relaxation measurements. In particular, there are two distinct electronic phases called α and β and the transition between these occurs around x = 0.05. The electronic DOS at the Fermi level increases monotonically at low intercalation levels x <0.05 (α-phase), whereas it reaches a plateau in the range 0.05 < x < 0.143 at high intercalation levels (β-phase). The new β-phase is accompanied by a hybridization of Cs(6s) orbitals with C(sp2)orbitals of the SWNTs. In both phases, two types of metallic nanotubes are found with a low and a high local n(EF), corresponding to different local electronic band structures of the SWNTs.

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  • 33.
    Abou-Hamad, Edy
    et al.
    Universite Montpellier II.
    Kim, Y
    University of Pennsylvania.
    Talyzin, Alexandr
    Umeå University, Faculty of Science and Technology, Physics.
    Goze-Bac, Christophe
    Universite Montpellier II.
    Luzzi, David
    University of Pennsylvania.
    Rubio, Angelo
    University of Basque Country.
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Physics.
    Hydrogenation of C-60 in Peapods: Physical Chemistry in Nano Vessels2009In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 113, no 20, p. 8583-8587Article in journal (Refereed)
    Abstract [en]

    Hydrogenation of C-60 molecules inside SWNT was achieved by direct reaction with hydrogen gas at elevated pressure and temperature. Evidence for the C-60 hydrogenation in peapods is provided by isotopic engineering with specific enrichment of encapsulated species and high resolution C-13 and H-1 NMR spectroscopy with the observation of characteristic diamagnetic and paramagnetic shifts of the NMR lines and the appearance of sp(3) carbon resonances. We estimate that approximately 78% of the C-60 molecules inside SWNTs are hydrogenated to an average degree of 14 hydrogen atoms per C-60 molecule. As a consequence, the rotational dynamics of the encapsulated C60Hx molecules is clearly hindered. Our successful hydrogenation experiments open completely new roads to understand and control confined chemical reactions at the nano scale

  • 34.
    Abou-Hamad, Edy
    et al.
    Universite Montpellier 2, France.
    Kim, Y.
    University of Pennsylvania, Philadelphia.
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Boesch, D.
    University of California at Berkeley, and Materials Sciences Division, Lawrence Berkeley National Laboratory.
    Aloni, S.
    University of California at Berkeley, and Materials Sciences Division, Lawrence Berkeley National Laboratory.
    Zettl, Alex
    University of California at Berkeley, and Materials Sciences Division, Lawrence Berkeley National Laboratory.
    Rubio, Angelo
    Universidad del Pas Vasco UPV/EHU.
    Luzzi, David E.
    University of Pennsylvania, Philadelphia.
    Goze-Bac, Christophe
    CNRS Universit Montpellier 2.
    Molecular dynamics and phase transition in one-dimensional crystal of C60 encapsulated inside single wall carbon nanotubes2009In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 3, no 12, p. 3878-3883Article in journal (Refereed)
    Abstract [en]

    One-dimensional crystals of 25% 13C-enriched C60 encapsulated inside highly magnetically purified SWNTs were investigated by following the temperature dependence of the 13C NMR line shapes and the relaxation rates from 300 K down to 5 K. High-resolution MAS techniques reveal that 32% of the encapsulated molecules, so-called the C60α, are blocked at room temperature and 68%, labeled C60β, are shown to reversly undergo molecular reorientational dynamics. Contrary to previous NMR studies, spin−lattice relaxation time reveals a phase transition at 100 K associated with the changes in the nature of the C60β dynamics. Above the transition, the C60β exhibits continuous rotational diffusion; below the transition, C60β executes uniaxial hindered rotations most likely along the nanotubes axis and freeze out below 25 K. The associated activation energies of these two dynamical regimes are measured to be 6 times lower than in fcc-C60, suggesting a quiet smooth orientational dependence of the interaction between C60β molecules and the inner surface of the nanotubes.

  • 35. Abraham, Edit
    et al.
    Miskolczi, Pal
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ayaydin, Ferhan
    Yu, Ping
    Kotogany, Edit
    Bako, Laszlo
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Oetvoes, Krisztina
    Horvath, Gabor V.
    Dudits, Denes
    Immunodetection of retinoblastoma-related protein and its phosphorylated form in interphase and mitotic alfalfa cells2011In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 62, no 6, p. 2155-2168Article in journal (Refereed)
    Abstract [en]

    Plant retinoblastoma-related (RBR) proteins are primarily considered as key regulators of G(1)/S phase transition, with functional roles in a variety of cellular events during plant growth and organ development. Polyclonal antibody against the C-terminal region of the Arabidopsis RBR1 protein also specifically recognizes the alfalfa 115 kDa MsRBR protein, as shown by the antigen competition assay. The MsRBR protein was detected in all cell cycle phases, with a moderate increase in samples representing G(2)/M cells. Antibody against the human phospho-pRb peptide (Ser807/811) cross-reacted with the same 115 kDa MsRBR protein and with the in vitro phosphorylated MsRBR protein C-terminal fragment. Phospho-MsRBR protein was low in G(1) cells. Its amount increased upon entry into the S phase and remained high during the G(2)/M phases. Roscovitine treatment abolished the activity of alfalfa MsCDKA1;1 and MsCDKB2;1, and the phospho-MsRBR protein level was significantly decreased in the treated cells. Colchicine block increased the detected levels of both forms of MsRBR protein. Reduced levels of the MsRBR protein in cells at stationary phase or grown in hormone-free medium can be a sign of the division-dependent presence of plant RBR proteins. Immunolocalization of the phospho-MsRBR protein indicated spots of variable number and size in the labelled interphase nuclei and high signal intensity of nuclear granules in prophase. Structures similar to phospho-MsRBR proteins cannot be recognized in later mitotic phases. Based on the presented western blot and immunolocalization data, the possible involvement of RBR proteins in G(2)/M phase regulation in plant cells is discussed.

  • 36.
    Abrahamsson, Anton
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Three dimensional tracking of multiple objects using digital holographic microscopy2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
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  • 37.
    Abrahamsson, Johan
    et al.
    Umeå University, Faculty of Social Sciences, Department of Informatics.
    Sjöberg, Robin
    Umeå University, Faculty of Social Sciences, Department of Informatics.
    E-tjänstutveckling ur ett medborgarperspektiv: Att skapa beslutsunderlag baserat på medborgarärendens lämplighet för olika kommunikationskanaler2009Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Citizens’ interaction with governments is an area with unique implications for channel management. Governments need to take the citizens perspective into further consideration in order to be successful in delivering high-quality e-services. This paper aims to determine if a categorization of citizen-initiated contacts from a citizen-centric perspective can be a valuable basis for decisions regarding e-service development. The study consisted of three steps. The first step was an examination of the existing related literature, which resulted in the uncovering of the most important aspects of citizens channel choice. The second step consisted of an elaboration of a classification based on perceived task characteristics and a subsequent matching of the categories to desirable channel characteristics. The third and final step consisted of an application of the proposed categorization on a content management system containing all citizen-initiated contacts in a Swedish municipality. The application indicated that the proposed categorization could possibly be used to guide investments in e-services towards a channel-appropriate direction.

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  • 38.
    Abramowicz, Konrad
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Numerical analysis for random processes and fields and related design problems2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, we study numerical analysis for random processes and fields. We investigate the behavior of the approximation accuracy for specific linear methods based on a finite number of observations. Furthermore, we propose techniques for optimizing performance of the methods for particular classes of random functions. The thesis consists of an introductory survey of the subject and related theory and four papers (A-D).

    In paper A, we study a Hermite spline approximation of quadratic mean continuous and differentiable random processes with an isolated point singularity. We consider a piecewise polynomial approximation combining two different Hermite interpolation splines for the interval adjacent to the singularity point and for the remaining part. For locally stationary random processes, sequences of sampling designs eliminating asymptotically the effect of the singularity are constructed.

    In Paper B, we focus on approximation of quadratic mean continuous real-valued random fields by a multivariate piecewise linear interpolator based on a finite number of observations placed on a hyperrectangular grid. We extend the concept of local stationarity to random fields and for the fields from this class, we provide an exact asymptotics for the approximation accuracy. Some asymptotic optimization results are also provided.

    In Paper C, we investigate numerical approximation of integrals (quadrature) of random functions over the unit hypercube. We study the asymptotics of a stratified Monte Carlo quadrature based on a finite number of randomly chosen observations in strata generated by a hyperrectangular grid. For the locally stationary random fields (introduced in Paper B), we derive exact asymptotic results together with some optimization methods. Moreover, for a certain class of random functions with an isolated singularity, we construct a sequence of designs eliminating the effect of the singularity.

    In Paper D, we consider a Monte Carlo pricing method for arithmetic Asian options. An estimator is constructed using a piecewise constant approximation of an underlying asset price process. For a wide class of Lévy market models, we provide upper bounds for the discretization error and the variance of the estimator. We construct an algorithm for accurate simulations with controlled discretization and Monte Carlo errors, andobtain the estimates of the option price with a predetermined accuracy at a given confidence level. Additionally, for the Black-Scholes model, we optimize the performance of the estimator by using a suitable variance reduction technique.

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  • 39.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Arnqvist, Per
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Sjöstedt de Luna, Sara
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Secchi, Piercesare
    Vantini, Simone
    Vitelli, Valeria
    Was it snowing on lake Kassjön in January 4486 BC? Functional data analysis of sediment data2014Conference paper (Other academic)
  • 40.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Häger, Charlotte
    Umeå University, Faculty of Medicine, Department of Community Medicine and Rehabilitation, Physiotherapy.
    Hérbert-Losier, Kim
    Swedish Winter Sports Research Centre Mid Sweden; University Department of Health Sciences, Östersund, Sweden.
    Pini, Alessia
    MOX – Department of Mathematics, Politecnico di Milano.
    Schelin, Lina
    Umeå University, Faculty of Social Sciences, Umeå School of Business and Economics (USBE), Statistics. Umeå University, Faculty of Medicine, Department of Community Medicine and Rehabilitation, Physiotherapy.
    Strandberg, Johan
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Vantini, Simone
    MOX – Department of Mathematics, Politecnico di Milano.
    An inferential framework for domain selection in functional anova2014In: Contributions in infinite-dimensional statistics and related topics / [ed] Bongiorno, E.G., Salinelli, E., Goia, A., Vieu, P, Esculapio , 2014Conference paper (Refereed)
    Abstract [en]

    We present a procedure for performing an ANOVA test on functional data, including pairwise group comparisons. in a Scheff´e-like perspective. The test is based on the Interval Testing Procedure, and it selects intervals where the groups significantly differ. The procedure is applied on the 3D kinematic motion of the knee joint collected during a functional task (one leg hop) performed by three groups of individuals.

  • 41.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Häger, Charlotte
    Umeå University, Faculty of Medicine, Department of Community Medicine and Rehabilitation, Physiotherapy.
    Pini, Alessia
    Umeå University, Faculty of Social Sciences, Umeå School of Business and Economics (USBE), Statistics. Department of Statistical Sciences, Università Cattolica del Sacro Cuore, Milan, Italy.
    Schelin, Lina
    Umeå University, Faculty of Medicine, Department of Community Medicine and Rehabilitation. Umeå University, Faculty of Social Sciences, Umeå School of Business and Economics (USBE), Statistics.
    Sjöstedt de Luna, Sara
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Vantini, Simone
    Nonparametric inference for functional-on-scalar linear models applied to knee kinematic hop data after injury of the anterior cruciate ligament2018In: Scandinavian Journal of Statistics, ISSN 0303-6898, E-ISSN 1467-9469, Vol. 45, no 4, p. 1036-1061Article in journal (Refereed)
    Abstract [en]

    Motivated by the analysis of the dependence of knee movement patterns during functional tasks on subject-specific covariates, we introduce a distribution-free procedure for testing a functional-on-scalar linear model with fixed effects. The procedure does not only test the global hypothesis on the entire domain but also selects the intervals where statistically significant effects are detected. We prove that the proposed tests are provided with an asymptotic control of the intervalwise error rate, that is, the probability of falsely rejecting any interval of true null hypotheses. The procedure is applied to one-leg hop data from a study on anterior cruciate ligament injury. We compare knee kinematics of three groups of individuals (two injured groups with different treatments and one group of healthy controls), taking individual-specific covariates into account.

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  • 42.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Pini, Alessia
    Department of Statistical Sciences, Università Cattolica del Sacro Cuore, Milan, Italy.
    Schelin, Lina
    Umeå University, Faculty of Social Sciences, Umeå School of Business and Economics (USBE), Statistics.
    Sjöstedt de Luna, Sara
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Stamm, Aymeric
    Department of Mathematics Jean Leray, UMR CNRS 6629, Nantes University, Nantes, France.
    Vantini, Simone
    MOX – Modelling and Scientific Computing Laboratory, Department of Mathematics, Politecnico di Milano, Milan, Italy.
    Domain selection and family-wise error rate for functional data: a unified framework2023In: Biometrics, ISSN 0006-341X, E-ISSN 1541-0420, Vol. 79, no 2, p. 1119-1132Article in journal (Refereed)
    Abstract [en]

    Functional data are smooth, often continuous, random curves, which can be seen as an extreme case of multivariate data with infinite dimensionality. Just as component-wise inference for multivariate data naturally performs feature selection, subset-wise inference for functional data performs domain selection. In this paper, we present a unified testing framework for domain selection on populations of functional data. In detail, p-values of hypothesis tests performed on point-wise evaluations of functional data are suitably adjusted for providing a control of the family-wise error rate (FWER) over a family of subsets of the domain. We show that several state-of-the-art domain selection methods fit within this framework and differ from each other by the choice of the family over which the control of the FWER is provided. In the existing literature, these families are always defined a priori. In this work, we also propose a novel approach, coined threshold-wise testing, in which the family of subsets is instead built in a data-driven fashion. The method seamlessly generalizes to multidimensional domains in contrast to methods based on a-priori defined families. We provide theoretical results with respect to consistency and control of the FWER for the methods within the unified framework. We illustrate the performance of the methods within the unified framework on simulated and real data examples, and compare their performance with other existing methods.

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  • 43.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Schelin, Lina
    Umeå University, Faculty of Social Sciences, Umeå School of Business and Economics (USBE), Statistics.
    Sjöstedt de Luna, Sara
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Strandberg, Johan
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Multiresolution clustering of dependent functional data with application to climate reconstruction2019In: Stat, E-ISSN 2049-1573, Vol. 8, no 1, article id e240Article in journal (Refereed)
    Abstract [en]

    We propose a new nonparametric clustering method for dependent functional data, the double clustering bagging Voronoi method. It consists of two levels of clustering. Given a spatial lattice of points, a function is observed at each grid point. In the first‐level clustering, features of the functional data are clustered. The second‐level clustering takes dependence into account, by grouping local representatives, built from the resulting first‐level clusters, using a bagging Voronoi strategy. Depending on the distance measure used, features of the functions may be included in the second‐step clustering, making the method flexible and general. Combined with the clustering method, a multiresolution approach is proposed that searches for stable clusters at different spatial scales, aiming to capture latent structures. This provides a powerful and computationally efficient tool to cluster dependent functional data at different spatial scales, here illustrated by a simulation study. The introduced methodology is applied to varved lake sediment data, aiming to reconstruct winter climate regimes in northern Sweden at different time resolutions over the past 6,000 years.

  • 44.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Seleznjev, Oleg
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Multivariate piecewise linear interpolation of a random field2011Manuscript (preprint) (Other academic)
    Abstract [en]

    We consider a multivariate piecewise linear interpolation of a continuous random field on a-dimensional cube. The approximation performance is measured by the integrated mean square error. Multivariate piecewise linear interpolator is defined by N field observations on a locations grid (or design). We investigate the class of locally stationary random fields whose local behavior is like a fractional Brownian field in mean square sense and find the asymptotic approximation accuracy for a sequence of designs for large N. Moreover, for certain classes of continuous and continuously differentiable fields we provide the upper bound for the approximation accuracy in the uniform mean square norm.

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  • 45.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Seleznjev, Oleg
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    On the error of the Monte Carlo pricing method for Asian option2008In: Journal of Numerical and Applied Mathematics, ISSN 0868-6912, Vol. 96, no 1, p. 1-10Article in journal (Refereed)
    Abstract [en]

    We consider a Monte Carlo method to price a continuous arithmetic Asian option with a given precision. Piecewise constant approximation and plain simulation are used for a wide class of models based on L\'{e}vy processes. We give bounds of the possible discretization and simulation errors. The sufficient numbers of discretization points and simulations to obtain requested accuracy are derived. To demonstrate the general approach, the Black-Scholes model is studied in more detail. We undertake the case of continuous averaging and starting time zero,  but the obtained results can be applied to the discrete case  and generalized for any time before an execution date. Some numerical experiments and comparison to the PDE based method are also presented.

  • 46.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Seleznjev, Oleg
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Piecewise multilinear interpolation of a random field2013In: Advances in Applied Probability, ISSN 0001-8678, E-ISSN 1475-6064, Vol. 45, no 4, p. 945-959Article in journal (Refereed)
    Abstract [en]

    We consider a piecewise-multilinear interpolation of a continuous random field on a d-dimensional cube. The approximation performance is measured using the integrated mean square error. Piecewise-multilinear interpolator is defined by N-field observations on a locations grid (or design). We investigate the class of locally stationary random fields whose local behavior is like a fractional Brownian field, in the mean square sense, and find the asymptotic approximation accuracy for a sequence of designs for large N. Moreover, for certain classes of continuous and continuously differentiable fields, we provide the upper bound for the approximation accuracy in the uniform mean square norm.

  • 47.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Seleznjev, Oleg
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Stratified Monte Carlo quadrature for continuous random fields2015In: Methodology and Computing in Applied Probability, ISSN 1387-5841, E-ISSN 1573-7713, Vol. 17, no 1, p. 59-72Article in journal (Refereed)
    Abstract [en]

    We consider the problem of numerical approximation of integrals of random fields over a unit hypercube. We use a stratified Monte Carlo quadrature and measure the approximation performance by the mean squared error. The quadrature is defined by a finite number of stratified randomly chosen observations with the partition generated by a rectangular grid (or design). We study the class of locally stationary random fields whose local behavior is like a fractional Brownian field in the mean square sense and find the asymptotic approximation accuracy for a sequence of designs for large number of the observations. For the H¨older class of random functions, we provide an upper bound for the approximation error. Additionally, for a certain class of isotropic random functions with an isolated singularity at the origin, we construct a sequence of designs eliminating the effect of the singularity point.

  • 48.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Sjöstedt de Luna, Sara
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Strandberg, Johan
    Umeå University, Faculty of Social Sciences, Umeå School of Business and Economics (USBE), Statistics.
    Nonparametric bagging clustering methods to identify latent structures from a sequence of dependent categorical data2022In: Computational Statistics & Data Analysis, ISSN 0167-9473, E-ISSN 1872-7352, Vol. 177, article id 107583Article in journal (Refereed)
    Abstract [en]

    Nonparametric bagging clustering methods are studied and compared to identify latent structures from a sequence of dependent categorical data observed along a one-dimensional (discrete) time domain. The frequency of the observed categories is assumed to be generated by a (slowly varying) latent signal, according to latent state-specific probability distributions. The bagging clustering methods use random tessellations (partitions) of the time domain and clustering of the category frequencies of the observed data in the tessellation cells to recover the latent signal, within a bagging framework. New and existing ways of generating the tessellations and clustering are discussed and combined into different bagging clustering methods. Edge tessellations and adaptive tessellations are the new proposed ways of forming partitions. Composite methods are also introduced, that are using (automated) decision rules based on entropy measures to choose among the proposed bagging clustering methods. The performance of all the methods is compared in a simulation study. From the simulation study it can be concluded that local and global entropy measures are powerful tools in improving the recovery of the latent signal, both via the adaptive tessellation strategies (local entropy) and in designing composite methods (global entropy). The composite methods are robust and overall improve performance, in particular the composite method using adaptive (edge) tessellations.

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  • 49.
    Abramowicz, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Sjöstedt de Luna, Sara
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Strandberg, Johan
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Nonparametric clustering methods to identify latent structures from a sequence of dependent categorical dataManuscript (preprint) (Other academic)
  • 50.
    Abramowizc, Konrad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Arnqvist, Per
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Secchi, Piercesare
    Politecnico di Milano, Italy.
    Sjöstedt de Luna, Sara
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Vantini, Simone
    Politecnico di Milano, Italy.
    Vitelli, Valeria
    Oslo University, Norway.
    Clustering misaligned dependent curves applied to varved lake sediment for climate reconstruction2017In: Stochastic environmental research and risk assessment (Print), ISSN 1436-3240, E-ISSN 1436-3259, Vol. 31, no 1, p. 71-85Article in journal (Refereed)
    Abstract [en]

    In this paper we introduce a novel functional clustering method, the Bagging Voronoi K-Medoid Aligment (BVKMA) algorithm, which simultaneously clusters and aligns spatially dependent curves. It is a nonparametric statistical method that does not rely on distributional or dependency structure assumptions. The method is motivated by and applied to varved (annually laminated) sediment data from lake Kassjön in northern Sweden, aiming to infer on past environmental and climate changes. The resulting clusters and their time dynamics show great potential for seasonal climate interpretation, in particular for winter climate changes.

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