| 1. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
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Tidskriftsartikel (refereegranskat)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 4. |
- Aggestam, Emil, 1992, et al.
(författare)
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Numerical model reduction with error control in computational homogenization of transient heat flow
- 2017
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Ingår i: Computer Methods in Applied Mechanics and Engineering. - : Elsevier BV. - 0045-7825. ; 326, s. 193-222
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Tidskriftsartikel (refereegranskat)abstract
- Numerical Model Reduction (NMR) is exploited for solving the finite element problem on a Representative Volume Element (RVE) that arises from the computational homogenization of a model problem of transient heat flow. Since the problem is linear, an orthogonal basis is obtained via the classical method of spectral decomposition. A symmetrized version of the space–time variational format is adopted for estimating the error from the model reduction in (i) energy norm and in (ii) given Quantities of Interest. This technique, which was recently developed in the context of the (non-selfadjoint) stationary diffusion–convection problem, is novel in the present context of NMR. By considering the discrete, unreduced, model as exact, we are able to obtain guaranteed bounds on the error while using only the reduced basis and with minor computational effort. The performance of the error estimates is demonstrated via numerical results, where the subscale is modeled in both one and three spatial dimensions.
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| 5. |
- Ahlström, Tommy, et al.
(författare)
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Correlation between plasma calcium, parathyroid hormone (PTH) and the metabolic syndrome (MetS) in a community-based cohort of men and women
- 2009
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Ingår i: Clinical Endocrinology. - : Wiley. - 0300-0664 .- 1365-2265. ; 71:5, s. 673-678
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Tidskriftsartikel (refereegranskat)abstract
- CONTEXT: In recent years, an association has been noted between several abnormalities that characterize the metabolic syndrome (MetS) and primary hyperparathyroidism (pHPT). These abnormalities include dyslipidaemia, obesity, insulin resistance and hypertension. The correlations between plasma calcium, parathyroid hormone (PTH) and the variables in the MetS in a normal population are still unclear.OBJECTIVE: To describe correlations between plasma calcium and PTH and the various abnormalities present in the MetS in a healthy population.DESIGN: We studied 1016 healthy individuals from the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) population of 70 years old, by means of plasma analyses of calcium, PTH, creatinine, lipids, insulin and glucose, as well as by standardized blood pressure measurements. Further, body mass index (BMI) and waist circumference were determined.RESULTS: The more National Cholesterol Education Program (NCEP) criteria for the MetS that were met, the higher the s-PTH and albumin-corrected s-calcium. Further, positive correlations between plasma calcium and BMI (P = 0.0003), waist circumference (P = 0.0009) and insulin resistance (P = 0.079) were found. PTH and BMI (P < 0.0001), waist circumference (P < 0.0001), systolic blood pressure (P = 0.0034), diastolic blood pressure (P = 0.0008), serum triglycerides (P = 0.0003) and insulin resistance (P = 0.0003) were positively correlated, whereas serum high density lipoproteins (HDL) (P = 0.036) and PTH were negatively correlated.CONCLUSIONS: We conclude that PTH correlates with several of the metabolic factors included in the MetS within a normocalcaemic population. In addition, individuals with mild pHPT present significantly more NCEP criteria for MetS. We postulate that increased levels of PTH in pHPT may be associated with the increased cardiovascular morbidity and mortality seen in pHPT.
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| 6. |
- Akbar, Noman, et al.
(författare)
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Downlink Power Control in Massive MIMO Networks with Distributed Antenna Arrays
- 2018
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Ingår i: 2018 IEEE INTERNATIONAL CONFERENCE ON COMMUNICATIONS (ICC). - : IEEE. - 9781538631805 - 9781538631812
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Konferensbidrag (refereegranskat)abstract
- In this paper, we investigate downlink power control in massive multiple-input multiple-output (MIMO) networks with distributed antenna arrays. The base station (BS) in each cell consists of multiple antenna arrays, which are deployed in arbitrary locations within the cell. Due to the spatial separation between antenna arrays, the large-scale propagation effect is different from a user to different antenna arrays in a cell, which makes power control a challenging problem as compared to conventional massive MIMO. We assume that the BS in each cell obtains the channel estimates via uplink pilots. Based on the channel estimates, the BSs perform maximum ratio transmission for the downlink. We then derive a closed-form spectral efficiency (SE) expression, where the channels are subject to correlated fading. Utilizing the derived expression, we propose a max-min power control algorithm to ensure that each user in the network receives a uniform quality of service. Numerical results demonstrate that, for the network considered in this work, optimizing for max-min SE through the max-min power control improves the sum SE of the network as compared to the equal power allocation.
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| 7. |
- Akbar, Noman, et al.
(författare)
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Max-Min Power Control in Downlink Massive MIMO With Distributed Antenna Arrays
- 2021
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Ingår i: IEEE Transactions on Communications. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 0090-6778 .- 1558-0857. ; 69:2, s. 740-751
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we investigate optimal downlink power allocation in massive multiple-input multiple-output (MIMO) networks with distributed antenna arrays (DAAs) under correlated and uncorrelated channel fading. In DAA massive MIMO, a base station (BS) consists of multiple antenna sub-arrays. Notably, the antenna sub-arrays are deployed in arbitrary locations within a DAA massive MIMO cell. Consequently, the distance-dependent large-scale propagation coefficients are different from a user to these different antenna sub-arrays, which makes power control a challenging problem. We assume that the network operates in time-division duplex mode, where each BS obtains the channel estimates via uplink pilots. Based on the channel estimates, the BSs perform maximum-ratio transmission in the downlink. We then derive a closed-form signal-to-interference-plus-noise ratio (SINR) expression, where the channels are subject to correlated fading. Based on the SINR expression, we propose a network-wide max-min power control algorithm to ensure that each user in the network receives a uniform quality of service. Numerical results demonstrate the performance advantages offered by DAA massive MIMO. For some specific scenarios, DAA massive MIMO can improve the average per-user throughput up to 55%. Furthermore, we demonstrate that channel fading covariance is an important factor in determining the performance of DAA massive MIMO.
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| 8. |
- Almstedt, Elin, 1988-, et al.
(författare)
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Integrative discovery of treatments for high-risk neuroblastoma
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Despite advances in the molecular exploration of paediatric cancers, approximately 50% of children with high-risk neuroblastoma lack effective treatment. To identify therapeutic options for this group of high-risk patients, we combine predictive data mining with experimental evaluation in patient-derived xenograft cells. Our proposed algorithm, TargetTranslator, integrates data from tumour biobanks, pharmacological databases, and cellular networks to predict how targeted interventions affect mRNA signatures associated with high patient risk or disease processes. We find more than 80 targets to be associated with neuroblastoma risk and differentiation signatures. Selected targets are evaluated in cell lines derived from high-risk patients to demonstrate reversal of risk signatures and malignant phenotypes. Using neuroblastoma xenograft models, we establish CNR2 and MAPK8 as promising candidates for the treatment of high-risk neuroblastoma. We expect that our method, available as a public tool (targettranslator.org), will enhance and expedite the discovery of risk-associated targets for paediatric and adult cancers.
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| 10. |
- Andersson Sjöland, Annika, et al.
(författare)
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Versican in inflammation and tissue remodelling: the impact on lung disorders.
- 2015
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 1460-2423 .- 0959-6658. ; 25:3, s. 243-251
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Forskningsöversikt (refereegranskat)abstract
- Versican is a proteoglycan that has many different roles in tissue homeostasis and inflammation. The biochemical structure is comprised of four different types of the core protein with attached glycosaminoglycans that can be sulphated to various extents and has the capacity to regulate differentiation of different cell types, migration, cell adhesion, proliferation, tissue stabilization and inflammation. Versican's regulatory properties are of importance during both homeostasis and changes that lead to disease progression. The glycosaminoglycans that are attached to the core protein are of the chondroitin sulfate/dermatan sulfate type and are known to be important in inflammation through interactions with cytokines and growth factors. For a more complex understanding of versican it is of importance to study the tissue niche, where the wound healing process in both healthy and diseased conditions take place. In previous studies our group has identified changes in the amount of the multifaceted versican in chronic lung disorders such as asthma, chronic obstructive pulmonary disease and bronchiolitis obliterans syndrome, which could be a result of pathologic, transforming growth factor β driven, on-going remodelling processes. Reversely, the context of versican in its niche is of great importance since versican has been reported to have a beneficial role in other contexts e.g. emphysema. Here we explore the vast mechanisms of versican in healthy lung and in lung disorders.
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