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  • 1.
    Malakuti, Iman
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Odontology & Maxillofacial Surgery.
    Thor, Andreas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Oral and Maxillofacial Surgery.
    Bilateral TMJ Ankylosis: Total Joint Reconstruction in a Patient With Zero Mouth Opening: A Case Report2032In: Craniomaxillofacial research & Innovation, Vol. 8, no 1-6Article in journal (Refereed)
    Abstract [en]

    Present a case of a young patient with bilateral bony ankylosis of the TMJ with zero mouth opening treated with TMJ prosthesis.

    Methods

    The ankylosis was studied in detail with computed tomography (CT) and we used virtual surgical planning in the pre-operative phase to provide splints and cutting guides. The patient was treated with bilateral custom-made alloplastic TMJ prosthesis.

    Results

    Optimal functional improvement at the 5.5 year follow up after total joint reconstruction without any adverse effects. Mouth opening was 35 mm and the patient was free from pain. CT-images showed no signs of pathology or increased remodeling and bone formation.

    Conclusion

    Ankylosis of the TMJ in young and adult population presents unique challenges given the need to account for growth of the mandible and anatomical variations. This report supports the use of total joint reconstruction for end-stage TMJ disease.

  • 2.
    Nourzaei, Maryam
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Linguistics and Philology.
    Kholosi: A Corpus-based Grammatical Description2026Book (Refereed)
  • 3.
    Vinogradova, Olena
    et al.
    Södertörns Univ, Sch Nat Sci Technol & Environm Studies, Alfred Nobels Alle 7, S-14189 Flemingsberg, Huddinge, Sweden..
    Gaillard, Marie-José
    Linnaeus Univ, Dept Biol & Environm Sci, Stuvaregatan 4, S-39231 Kalmar, Sweden..
    Andrén, Elinor
    Södertörns Univ, Sch Nat Sci Technol & Environm Studies, Alfred Nobels Alle 7, S-14189 Flemingsberg, Huddinge, Sweden..
    Palm, Veronica
    Vasterviks Museum, Vastervik, Sweden.;Södertörn Univ, Sch Hist & Contemporary Studies, Flemingsberg, Huddinge, Sweden..
    Rönnby, Johan
    Södertörn Univ, Sch Hist & Contemporary Studies, Flemingsberg, Huddinge, Sweden..
    Dahl, Martin
    Södertörns Univ, Sch Nat Sci Technol & Environm Studies, Alfred Nobels Alle 7, S-14189 Flemingsberg, Huddinge, Sweden..
    Almgren, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Karlsson, Jon
    Umeå Univ, Dept Ecol & Environm Sci, Umeå, Sweden..
    Nielsen, Anne Birgitte
    Lund Univ, Dept Geol, Lund, Sweden..
    Akesson, Christine
    Lund Univ, Dept Geol, Lund, Sweden.;Univ St Andrews, Sch Geog & Sustainable Dev, St Andrews, Scotland..
    Andrén, Thomas
    Södertörns Univ, Sch Nat Sci Technol & Environm Studies, Alfred Nobels Alle 7, S-14189 Flemingsberg, Huddinge, Sweden..
    3000 Years of past regional and local land-use and land-cover change in the southeastern Swedish coastal area: Early human-induced increases in landscape openness as a potential nutrient source to the Baltic Sea coastal waters2024In: The Holocene, ISSN 0959-6836, E-ISSN 1477-0911, Vol. 34, no 1, p. 56-73Article in journal (Refereed)
    Abstract [en]

    Reconstructions of past land use and related land-cover changes at local and regional scales are needed to evaluate the potential long-term impacts of land use on the coastal waters of the Baltic Sea. In this purpose, we selected the Gamleby area at the Swedish Baltic Sea coast for a case study. We use a new, high resolution pollen record from a small lake (Lillsjön) located 3.6 km NNW of the bay Gamlebyviken and detailed analysis of the available archeological data to reconstruct local land-use changes over the last 3000 years. To estimate land-cover change at local (2–3 km radius area) and regional (50 km radius area) scales we use four additional, published pollen records from two small and two large lakes (25–70 km S of Lillsjön) and the Landscape Reconstruction Algorithm, a pollen-vegetation modeling scheme. Results show that regional and local (small lakes Lillsjön and Hyttegöl) land-cover changes are comparable over the last 1500 years (Late Iron Age to present), and that landscape openness was much larger locally than regionally (difference of 20–40% cover over the last 500 years). The periods of largest potential impacts on the Gamlebyviken Bay from regional and local land use are 200–950 CE (Late Iron Age) and 1450 CE to present, and of lowest potential impacts 950–1450 CE. The question on whether the large landscape openness 1150–50 BCE and significant afforestation 50 BCE–200 CE reconstructed for Lillsjön’s area are characteristic of the Gamlebyviken region will require additional pollen records in the catchment area.

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  • 4.
    Rangaiah, Pramod
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Electrical Engineering, Solid-State Electronics.
    Engstrand, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Electrical Engineering, Solid-State Electronics.
    Johansson, Ted
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Electrical Engineering, Solid-State Electronics.
    Perez, Mauricio D.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Electrical Engineering, Solid-State Electronics.
    Augustine, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Electrical Engineering, Solid-State Electronics.
    92 Mb/s Fat-Intrabody Communication (Fat-IBC) With Low-Cost WLAN Hardware2024In: IEEE Transactions on Biomedical Engineering, ISSN 0018-9294, E-ISSN 1558-2531, Vol. 71, no 1, p. 89-96Article in journal (Refereed)
    Abstract [en]

    The human subcutaneous fat layer, skin and muscle together act as a waveguide for microwave transmissions and provide a low-loss communication medium for implantable and wearable body area networks (BAN). In this work, fat-intrabody communication (Fat-IBC) as a human body-centric wireless communication link is explored. To reach a target 64 Mb/s inbody communication, wireless LAN in the 2.4 GHz band was tested using low-cost Raspberry Pi single-board computers. The link was characterized using scattering parameters, bit error rate (BER) for different modulation schemes, and IEEE 802.11n wireless communication using inbody (implanted) and onbody (on the skin) antenna combinations. The human body was emulated by phantoms of different lengths. All measurements were done in a shielded chamber to isolate the phantoms from external interference and to suppress unwanted transmission paths. The BER measurements show that, except when using dual on-body antennas with longer phantoms, the Fat-IBC link is very linear and can handle modulations as complex as 512-QAM without any significant degradation of the BER. For all antenna combinations and phantoms lengths, link speeds of 92 Mb/s were achieved using 40 MHz bandwidth provided by the IEEE 802.11n standard in the 2.4 GHz band. This speed is most likely limited by the used radio circuits, not the Fat-IBC link. The results show that Fat-IBC, using low-cost off-the-shelf hardware and established IEEE 802.11 wireless communication, can achieve high-speed data communication within the body. The obtained data rate is among the fastest measured with intrabody communication.

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  • 5.
    Pihl, Christopher
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of History.
    A bank in a monarchy: an early modern anomaly? The Swedish Bank of the Estates of the Realm2024In: Scandinavian Journal of History, ISSN 0346-8755, E-ISSN 1502-7716, Vol. 49, no 1, p. 1-23Article in journal (Refereed)
    Abstract [en]

    This article aims to analyse credit as a core element in the political changes and processes of state formation that took place in Sweden in the second half of the seventeenth-century. The study focuses on discussions within the Council of the Realm and at the Diets about how to use the two Swedish seventeenth-century banks as creditors to the state. The two banks were essential parts of an elaborate attempt to shift public debt regime from one based on private creditors and the personal credit of the king and the men in the government to a regime based on institutional creditors and the credit of the Estates of the Realm. The outcome of the procesess was contingent upon some of the core topics of early modern Europe's political and financial discourses: the nature of the sovereign, the relationship between private interests and the public good, and the role and functioning of representative assemblies. This process was the beginning of a development in which sovereign borrowing became a public concern, which eventually strengthened the Estate's position vis-a-vis the government, and is a significant example of the interconnectedness of politics and credit.

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  • 6.
    Grad, Philipp
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Edwards, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Gedda, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Agmo Hernández, Víctor
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    A closer look at calcium-induced interactions between phosphatidylserine-(PS) doped liposomes and the structural effects caused by inclusion of gangliosides or polyethylene glycol- (PEG) modified lipids2024In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1866, no 2, article id 184253Article in journal (Refereed)
    Abstract [en]

    The effects of polyethylene glycol- (PEG) modified lipids and gangliosides on the Ca2+ induced interaction between liposomes composed of palmitoyl-oleoyl phosphatidylethanolamine (POPE) and palmitoyl-oleoyl phosphatidylserine (POPS) was investigated at physiological ionic strength. Förster resonance energy transfer (FRET) studies complemented with dynamic light scattering (DLS) and cryo-transmission electron microscopy (Cryo-EM) show that naked liposomes tend to adhere, rupture, and collapse on each other's surfaces upon addition of Ca2+, eventually resulting in the formation of large multilamellar aggregates and bilayer sheets. Noteworthy, the presence of gangliosides or PEGylated lipids does not prevent the adhesion-rupture process, but leads to the formation of small, long-lived bilayer fragments/disks. PEGylated lipids seem to be more effective than gangliosides at stabilizing these structures. Attractive interactions arising from ion correlation are proposed to be a driving force for the liposome-liposome adhesion and rupture processes. The results suggest that, in contrast with the conclusions drawn from previous solely FRET-based studies, direct liposome-liposome fusion is not the dominating process triggered by Ca2+ in the systems studied.

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  • 7. Li, Guoqiang
    et al.
    Yan, Zhongfeng
    Song, Yougui
    Fitzsimmons, Kathryn E.
    Yi, Shuangwen
    Kang, Shugang
    E, Chongyi
    Stevens, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. Department of Geosciences and Geography, University of Helsinki, P.O. Box 64, 00014, Helsinki, Finland.
    Lai, Zhongping
    Dave, Aditi K.
    Chen, Chunzhu
    Deng, Yanqing
    Yang, He
    Wang, Leibin
    Zhang, Xiaojian
    Qin, Caixin
    Zhao, Qiuyue
    Buylaert, Jan-Pieter
    Lu, Tao
    Wang, Yixuan
    Liu, Xiangjun
    Ling, Zhiyong
    Chang, Qiufang
    Wei, Haitao
    Wang, Xiaoyan
    Chen, Fahu
    A comprehensive dataset of luminescence chronologies and environmental proxy indices of loess-paleosol deposits across Asia2024In: npj Climate and Atmospheric Science, E-ISSN 2397-3722, Vol. 7, no 1, article id 7Article in journal (Refereed)
    Abstract [en]

    Loess-paleosol sequences have been used in Asia to study climate and environmental changes during the Quaternary. The scarcity of age control datasets and proxy indices analysis data for Asian loess has limited our understanding of loess depositional processes and the reconstruction of paleoclimatic changes from loess-paleosol records. In this study, we present a dataset that includes 1785 quartz optically stimulated luminescence ages and 1038 K-feldspar post-infrared infrared stimulated luminescence ages from 128 loess-paleosol sequences located in different regions of Asia. We generate 38 high-resolution age-depth models of loess records based on the provided datasets. We provide data on 12,365 grain size records, 14,964 magnetic susceptibility records, 2204 CaCO3 content records, and 3326 color reflection records. This dataset contains the most detailed and accurate chronologies and proxy index data for loess records in Asia yet published. It provides fundamental data for understanding the spatial-temporal variations in loess depositional processes and climatic changes across the continent during the mid-late Quaternary.

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  • 8.
    Clouard, Camille
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing.
    A computational and statistical framework for cost-effective genotyping combining pooling and imputation2024Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The information conveyed by genetic markers, such as single nucleotide polymorphisms (SNPs), has been widely used in biomedical research to study human diseases and is increasingly valued in agriculture for genomic selection purposes. Specific markers can be identified as a genetic signature that correlates with certain characteristics in a living organism, e.g. a susceptibility to disease or high-yield traits. Capturing these signatures with sufficient statistical power often requires large volumes of data, with thousands of samples to be analysed and potentially millions of genetic markers to be screened. Relevant effects are particularly delicate to detect when the genetic variations involved occur at low frequencies.

    The cost of producing such marker genotype data is therefore a critical part of the analysis. Despite recent technological advances, production costs can still be prohibitive on a large scale and genotype imputation strategies have been developed to address this issue. Genotype imputation methods have been extensively studied in human data and, to a lesser extent, in crop and animal species. A recognised weakness of imputation methods is their lower accuracy in predicting the genotypes for rare variants, whereas those can be highly informative in association studies and improve the accuracy of genomic selection. In this respect, pooling strategies can be well suited to complement imputation, as pooling is efficient at capturing the low-frequency items in a population. Pooling also reduces the number of genotyping tests required, making its use in combination with imputation a cost-effective compromise between accurate but expensive high-density genotyping of each sample individually and stand-alone imputation. However, due to the nature of genotype data and the limitations of genotype testing techniques, decoding pooled genotypes into unique data resolutions is challenging. 

    In this work, we study the characteristics of decoded genotype data from pooled observations with a specific pooling scheme using the examples of a human cohort and a population of inbred wheat lines. We propose different inference strategies to reconstruct the genotypes before devising them as input to imputation, and we reflect on how the reconstructed distributions affect the results of imputation methods such as tree-based haplotype clustering or coalescent models.

    List of papers
    1. A joint use of pooling and imputation for genotyping SNPs
    Open this publication in new window or tab >>A joint use of pooling and imputation for genotyping SNPs
    2022 (English)In: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 23, article id 421Article in journal (Refereed) Published
    Abstract [en]

    Background

    Despite continuing technological advances, the cost for large-scale genotyping of a high number of samples can be prohibitive. The purpose of this study is to design a cost-saving strategy for SNP genotyping. We suggest making use of pooling, a group testing technique, to drop the amount of SNP arrays needed. We believe that this will be of the greatest importance for non-model organisms with more limited resources in terms of cost-efficient large-scale chips and high-quality reference genomes, such as application in wildlife monitoring, plant and animal breeding, but it is in essence species-agnostic. The proposed approach consists in grouping and mixing individual DNA samples into pools before testing these pools on bead-chips, such that the number of pools is less than the number of individual samples. We present a statistical estimation algorithm, based on the pooling outcomes, for inferring marker-wise the most likely genotype of every sample in each pool. Finally, we input these estimated genotypes into existing imputation algorithms. We compare the imputation performance from pooled data with the Beagle algorithm, and a local likelihood-aware phasing algorithm closely modeled on MaCH that we implemented.

    Results

    We conduct simulations based on human data from the 1000 Genomes Project, to aid comparison with other imputation studies. Based on the simulated data, we find that pooling impacts the genotype frequencies of the directly identifiable markers, without imputation. We also demonstrate how a combinatorial estimation of the genotype probabilities from the pooling design can improve the prediction performance of imputation models. Our algorithm achieves 93% concordance in predicting unassayed markers from pooled data, thus it outperforms the Beagle imputation model which reaches 80% concordance. We observe that the pooling design gives higher concordance for the rare variants than traditional low-density to high-density imputation commonly used for cost-effective genotyping of large cohorts.

    Conclusions

    We present promising results for combining a pooling scheme for SNP genotyping with computational genotype imputation on human data. These results could find potential applications in any context where the genotyping costs form a limiting factor on the study size, such as in marker-assisted selection in plant breeding.

    Place, publisher, year, edition, pages
    Springer Nature, 2022
    Keywords
    Pooling, Imputation, Genotyping
    National Category
    Bioinformatics (Computational Biology)
    Research subject
    Scientific Computing
    Identifiers
    urn:nbn:se:uu:diva-486864 (URN)10.1186/s12859-022-04974-7 (DOI)000867656900001 ()36229780 (PubMedID)
    Projects
    eSSENCE - An eScience Collaboration
    Funder
    Swedish Research Council Formas, 2017-00453Swedish National Infrastructure for Computing (SNIC), 2019/8-216Swedish National Infrastructure for Computing (SNIC), 2020/5-455Uppsala University
    Available from: 2022-10-18 Created: 2022-10-18 Last updated: 2024-01-17Bibliographically approved
    2. Consistency Study of a Reconstructed Genotype Probability Distribution via Clustered Bootstrapping in NORB Pooling Blocks
    Open this publication in new window or tab >>Consistency Study of a Reconstructed Genotype Probability Distribution via Clustered Bootstrapping in NORB Pooling Blocks
    2022 (English)Report (Other academic)
    Abstract [en]

    For applications with biallelic genetic markers, group testing techniques, synonymous to pooling techniques, are usually applied for decreasing the cost of large-scale testing as e.g. when detecting carriers of rare genetic variants. In some configurations, the results of the grouped tests cannot be decoded and the pooled items are missing. Inference of these missing items can be performed with specific statistical methods that are for example related to the Expectation-Maximization algorithm. Pooling has also been applied for determining the genotype of markers in large populations. The particularity of full genotype data for diploid organisms in the context of group testing are the ternary outcomes (two homozygous genotypes and one heterozygous), as well as the distribution of these three outcomes in a population, which is often ruled by the Hardy-Weinberg Equilibrium and depends on the allele frequency in such situation. When using a nonoverlapping repeated block pooling design, the missing items are only observed in particular arrangements. Overall, a data set of pooled genotypes can be described as an inference problem in Missing Not At Random data with nonmonotone missingness patterns. This study presents a preliminary investigation of the consistency of various iterative methods estimating the most likely genotype probabilities of the missing items in pooled data. We use the Kullback-Leibler divergence and the L2 distance between the genotype distribution computed from our estimates and a simulated empirical distribution as a measure of the distributional consistency.

    Place, publisher, year, edition, pages
    Uppsala: Uppsala University, 2022. p. 13
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2022-005
    National Category
    Probability Theory and Statistics
    Identifiers
    urn:nbn:se:uu:diva-487718 (URN)
    Available from: 2022-10-31 Created: 2022-10-31 Last updated: 2024-01-10Bibliographically approved
    3. Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation
    Open this publication in new window or tab >>Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation
    2024 (English)In: Theoretical and Applied Genetics, ISSN 0040-5752, E-ISSN 1432-2242, Vol. 137, no 1, article id 26Article in journal (Refereed) Published
    Abstract [en]

    The plant breeding industry has shown growing interest in using the genotype data of relevant markers for performing selection of new competitive varieties. The selection usually benefits from large amounts of marker data and it is therefore crucial to dispose of data collection methods that are both cost-effective and reliable. Computational methods such as genotype imputation have been proposed earlier in several plant science studies for addressing the cost challenge. Genotype imputation methods have though been used more frequently and investigated more extensively in human genetics research. The various algorithms that exist have shown lower accuracy at inferring the genotype of genetic variants occurring at low frequency, while these rare variants can have great significance and impact in the genetic studies that underlie selection. In contrast, pooling is a technique that can efficiently identify low-frequency items in a population and it has been successfully used for detecting the samples that carry rare variants in a population. In this study, we propose to combine pooling and imputation, and demonstrate this by simulating a hypothetical microarray for genotyping a population of recombinant inbred lines in a cost-effective and accurate manner, even for rare variants. We show that with an adequate imputation model, it is feasible to accurately predictthe individual genotypes at lower cost than sample-wise genotyping and time-effectively. Moreover, we provide code resources for reproducing the results presented in this study in the form of a containerized workflow.

    Place, publisher, year, edition, pages
    Springer Nature, 2024
    Keywords
    genotyping, imputation, MAGIC population, pooling, wheat
    National Category
    Bioinformatics (Computational Biology)
    Research subject
    Scientific Computing
    Identifiers
    urn:nbn:se:uu:diva-518436 (URN)10.1007/s00122-023-04533-5 (DOI)001145311600001 ()38243086 (PubMedID)
    Projects
    eSSENCE - An eScience Collaboration
    Funder
    Swedish Research Council Formas, 2017-00453
    Available from: 2024-01-10 Created: 2024-01-10 Last updated: 2024-02-05Bibliographically approved
    4. Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost
    Open this publication in new window or tab >>Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Conducting genomic selection in plant breeding programs can substantially speed up the development of new varieties. Genomic selection provides more reliable insights when it is based on dense marker data, in which the rare variants can be particularly informative while they are delicate to capture with sufficient statistical power. Despite the release of new performing technologies, the cost of large-scale genotyping remains a major limitation to the implementation of genomic selection. We suggest to combine pooled genotyping with population-based imputation as a cost-effective computational strategy for genotyping SNPs. Pooling saves genotyping tests and has proven to accurately capture the rare variants that are usually missed by imputation. In this study, we investigate an extension to our joint model of pooling and imputation via iterative coupling. In each iteration, the imputed genotype probabilities serve as feedback input for rectifying the decoded data, before running a new imputation in these adjusted data. Such flexible set up indirectly imposes consistency between the imputed genotypes and the pooled observations. We demonstrate that repeated cycles of feedback can take full advantage of the strengths in both pooling and imputation. The iterations improve greatly upon the initial genotype predictions, achieving very high genotype accuracy for both low and high frequency variants. We enhance the average concordance from 94.5% to 98.4% at a very limited computational cost and without requiring any additional genotype testing. We believe that these results could be of interest for plant breeders and crop scientists.

    Keywords
    SNP array, pooling, imputation, iterative refinement
    National Category
    Bioinformatics (Computational Biology)
    Research subject
    Scientific Computing
    Identifiers
    urn:nbn:se:uu:diva-518429 (URN)
    Funder
    Swedish Research Council Formas, 2017-00453
    Available from: 2023-12-19 Created: 2023-12-19 Last updated: 2024-01-10Bibliographically approved
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  • 9.
    Rerkasem, Amaraporn
    et al.
    Chiang Mai Univ, Res Inst Hlth Sci, Environm Occupat Hlth Sci & Noncommunicable Dis Re, Chiang Mai 50200, Thailand.;Chiang Mai Univ, Res Inst Hlth Sci, Res Ctr Infect Dis & Subst Use, Chiang Mai 50200, Thailand..
    Thaichana, Pak
    Chiang Mai Univ, Res Inst Hlth Sci, Environm Occupat Hlth Sci & Noncommunicable Dis Re, Chiang Mai 50200, Thailand..
    Bunsermvicha, Nuttida
    Chiang Mai Univ, Fac Med, Clin Surg Res Ctr, Dept Surg, Chiang Mai 50200, Thailand..
    Nopparatkailas, Rawee
    Chiang Mai Univ, Fac Med, Dept Family Med, Chiang Mai 50200, Thailand..
    Arwon, Supapong
    Chiang Mai Univ, Fac Med, Clin Surg Res Ctr, Dept Surg, Chiang Mai 50200, Thailand..
    Orrapin, Saranat
    Chiang Mai Univ, Fac Med, Clin Surg Res Ctr, Dept Surg, Chiang Mai 50200, Thailand..
    Reanpang, Termpong
    Chiang Mai Univ, Fac Med, Clin Surg Res Ctr, Dept Surg, Chiang Mai 50200, Thailand..
    Apichartpiyakul, Poon
    Chiang Mai Univ, Fac Med, Clin Surg Res Ctr, Dept Surg, Chiang Mai 50200, Thailand..
    Orrapin, Saritphat
    Thammasat Univ, Fac Med, Dept Surg, Rangsit Campus, Pathum Thani 12120, Thailand..
    Siribumrungwong, Boonying
    Thammasat Univ, Fac Med, Dept Surg, Rangsit Campus, Pathum Thani 12120, Thailand..
    Lumjuan, Nongkran
    Chiang Mai Univ, Res Inst Hlth Sci, Res Ctr Mol & Cell Biol, Chiang Mai 50200, Thailand..
    Rerkasem, Kittipan
    Chiang Mai Univ, Res Inst Hlth Sci, Environm Occupat Hlth Sci & Noncommunicable Dis Re, Chiang Mai 50200, Thailand.;Chiang Mai Univ, Fac Med, Clin Surg Res Ctr, Dept Surg, Chiang Mai 50200, Thailand..
    Derraik, José G. B.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Perinatal, Neonatal and Pediatric Cardiology Research. Chiang Mai Univ, Res Inst Hlth Sci, Environm Occupat Hlth Sci & Noncommunicable Dis Re, Chiang Mai 50200, Thailand; Univ Auckland, Fac Med & Hlth Sci, Dept Pediat Child & Youth Hlth, Auckland 1142, New Zealand.
    A COVID-19 Silver Lining — Decline in Antibiotic Resistance in Ischemic Leg Ulcers during the Pandemic: A 6-Year Retrospective Study from a Regional Tertiary Hospital (2017-2022)2024In: Antibiotics, E-ISSN 2079-6382, Vol. 13, no 1, article id 35Article in journal (Refereed)
    Abstract [en]

    Antibiotic resistance (AR) associated with chronic limb-threatening ischemia (CLTI) poses additional challenges for the management of ischemic leg ulcers, increasing the likelihood of severe outcomes. This study assessed AR prevalence in bacteria isolated from CLTI-associated leg ulcers before (1 January 2017–10 March 2020; n = 69) and during (11 March 2020–31 December 2022; n = 59) the COVID-19 pandemic from patients admitted with positive wound cultures to a regional hospital in Chiang Mai (Thailand). There was a marked reduction in AR rates from 78% pre-pandemic to 42% during the pandemic (p < 0.0001), with rates of polymicrobial infections 22 percentage points lower (from 61% to 39%, respectively; p = 0.014). There were reduced AR rates to amoxicillin/clavulanate (from 42% to 4%; p < 0.0001) and ampicillin (from 16% to 2%; p = 0.017), as well as multidrug resistance (19% to 8%; p = 0.026). Factors associated with increased AR odds were polymicrobial infections (adjusted odds ratio (aOR) 5.6 (95% CI 2.1, 15.0); p = 0.001), gram-negative bacteria (aOR 7.0 (95% CI 2.4, 20.5); p < 0.001), and prior use of antibiotics (aOR 11.9 (95% CI 1.1, 128.2); p = 0.041). Improvements in infection control measures and hygiene practices in the community during the pandemic were likely key factors contributing to lower AR rates. Thus, strategic public health interventions, including community education on hygiene and the informed use of antibiotics, may be crucial in mitigating the challenges posed by AR in CLTI. Further, advocating for more judicious use of empirical antibiotics in clinical settings can balance effective treatment against AR development, thereby improving patient outcomes.

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  • 10.
    Järleblad, H.
    et al.
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark..
    Stagner, L.
    Gen Atom, POB 85608, San Diego, CA 92186 USA..
    Salewski, M.
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark..
    Eriksson, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Applied Nuclear Physics.
    Nocente, M.
    Univ Milano Bicocca, Dept Phys, I-20126 Milan, Italy..
    Schmidt, B. S.
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark..
    Larsen, M. Rud
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark..
    A framework for synthetic diagnostics using energetic-particle orbits in tokamaks2024In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 294, article id 108930Article in journal (Refereed)
    Abstract [en]

    In fusion plasma physics, the large-scale trajectories of energetic particles in magnetic confinement devices are known as orbits. To effectively and efficiently be able to work with orbits, the Orbit Weight Computational Framework (OWCF) was developed. The OWCF constitutes a set of scripts, functions and applications capable of computing, visualizing and working with quantities related to fast-ion (FI) orbits in toroidally symmetric fusion devices. The current version is highly integrated with the DRESS code, which enables the OWCF to compute and analyze the orbit sensitivity for arbitrary neutron- and gammadiagnostics. However, the framework is modular in the sense that any future codes (e.g. FIDASIM) can be easily integrated. The OWCF can also compute projected velocity spectra for FI orbits, which play a key role in many FI diagnostics. Via interactive applications, the OWCF can function both as a tool for investigative research but also for teaching. The OWCF will be used to analyze and simulate the diagnostic results of current and future fusion experiments such as ITER. The orbit weight functions computed with the OWCF can be used to reconstruct the FI distribution in terms of FI orbits from experimental measurements using tomographic inversion.

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  • 11.
    Lundgren, Lukas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nazarov, Murtazo
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A high-order residual-based viscosity finite element method for incompressible variable density flow2024In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 497, article id 112608Article in journal (Refereed)
    Abstract [en]

    In this paper, we introduce a high-order accurate finite element method for incompressible variable density flow. The method uses high-order Taylor-Hood velocity-pressure elements in space and backward differentiation formula (BDF) time stepping in time. This way of discretization leads to two main issues: (i) a saddle point system that needs to be solved at each time step; a stability issue when the viscosity of the flow goes to zero or if the density profile has a discontinuity. We address the first issue by using Schur complement preconditioning and artificial compressibility approaches. We observed similar performance between these two approaches. To address the second issue, we introduce a modified artificial Guermond-Popov viscous flux where the viscosity coefficients are constructed using a newly developed residual-based shock-capturing method. Numerical validations confirm high-order accuracy for smooth problems and accurately resolved discontinuities for problems in 2D and 3D with varying density ratios.

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  • 12.
    Lei, Qinghua
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Sornette, Didier
    Institute of Risk Analysis, Prediction and Management, Southern University of Science and Technology, Shenzhen, China.
    Yang, Haonan
    Department of Earth Sciences, ETH Zurich, Zurich, Switzerland.
    Loew, Simon
    Department of Earth Sciences, ETH Zurich, Zurich, Switzerland.
    A novel dragon-king approach to forecasting catastrophic rock slope failures at Preonzo (Switzerland) and Veslemannen (Norway)2024Conference paper (Other academic)
  • 13. Sandén, Ulrika
    et al.
    Nilsson, Fredrik
    Thulesius, Hans
    Hägglund, Maria
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Participatory eHealth and Health Data Research Group.
    Scandurra, Isabella
    Harrysson, Lars
    A perspective-taking university course for cancer survivors, loved ones and healthcare professionals2024In: Social Sciences & Humanities Open, ISSN 2590-2911, Vol. 9Article in journal (Refereed)
    Abstract [en]

    This study reports the results of a university course aimed at exploring and improving cooperation in healthcare with both cancer survivors, loved ones and healthcare professionals as students. Central to the course was the understanding of and moving between each other's perspectives. Operating within a framework inspired by problem-based learning (PBL), small groups consisting of at least one cancer survivor, one loved one and one healthcare professional, collaboratively created scenarios based on their personal experiences. The students developed, elaborated, and identified problems and potential solutions. The pedagogical framing illustrated an empowering process of defining and elaborating a problem of their combined concerns, using their different knowledge. Although cooperation presented challenges, most students were able to explore and appreciate each other's perspectives when provided with a safe environment. Our experiences highlight the importance of both contextual safety and personal development as key factors in addressing power imbalances in healthcare.

  • 14.
    Olivetti, Leonardo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. Uppsala Univ, Ctr Nat Hazards & Disaster Sci, Uppsala, Sweden..
    Messori, Gabriele
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. Uppsala Univ, Ctr Nat Hazards & Disaster Sci, Uppsala, Sweden.;Stockholm Univ, Dept Meteorol, Stockholm, Sweden.;Stockholm Univ, Bolin Ctr Climate Res, Stockholm, Sweden..
    Jin, Shaobo
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Statistics. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Statistics, AI and Data Science.
    A Quantile Generalized Additive Approach for Compound Climate Extremes: Pan-Atlantic Extremes as a Case Study2024In: Journal of Advances in Modeling Earth Systems, ISSN 1942-2466, Vol. 16, no 1, article id e2023MS003753Article in journal (Refereed)
    Abstract [en]

    We present an application of quantile generalized additive models (QGAMs) to study spatially compounding climate extremes, namely extremes that occur (near-) simultaneously in geographically remote regions. We take as an example wintertime cold spells in North America and co-occurring wet or windy extremes in Western Europe, which we collectively term Pan-Atlantic compound extremes. QGAMS are largely novel in climate science applications and present a number of key advantages over conventional statistical models of weather extremes. Specifically, they remove the need for a direct identification and parametrization of the extremes themselves, since they model all quantiles of the distributions of interest. They thus make use of all information available, and not only of a small number of extreme values. Moreover, they do not require any a priori knowledge of the functional relationship between the predictors and the dependent variable. Here, we use QGAMs to both characterize the co-occurrence statistics and investigate the role of possible dynamical drivers of the Pan-Atlantic compound extremes. We find that cold spells in North America are a useful predictor of subsequent wet or windy extremes in Western Europe, and that QGAMs can predict those extremes more accurately than conventional peak-over-threshold models. In this paper we propose a new data-driven method to study climate extremes occurring simultaneously in multiple, possibly remote, locations. Such extremes can pose a greater threat to human societies than single, isolated extremes, as their effects may exacerbate each other and lead to correlated losses. The method we suggest requires fewer assumptions than conventional extreme value statistical techniques, and can help us to identify previously unknown relationships between the extremes themselves and their possible drivers. We exemplify its use by studying the co-occurrence of periods of unusually cold weather in North America and subsequent uncommonly strong wind and abundant precipitation in Western Europe. We find that the new method has better predictive power for the European extremes than conventional statistical approaches. Furthermore, we confirm the results of previous studies suggesting an association between the wintertime extremes in North America and Western Europe. Quantile general additive models (QGAMs) can model the relationship between compound climate extremes flexibly and robustlyNorth American cold spells show some predictive skill for wet or windy extremes in Western Europe, even when accounting for confoundersGiven relevant atmospheric predictors, QGAMs can predict these extremes more accurately than peak-over-threshold models in most regions

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