| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
- Arnab, Anurag, et al.
(författare)
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Conditional Random Fields Meet Deep Neural Networks for Semantic Segmentation: Combining Probabilistic Graphical Models with Deep Learning for Structured Prediction
- 2018
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Ingår i: IEEE Signal Processing Magazine. - 1558-0792 .- 1053-5888. ; 35:1, s. 37-52
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Tidskriftsartikel (refereegranskat)abstract
- Semantic segmentation is the task of labeling every pixel in an image with a predefined object category. It has numerous applications in scenarios where the detailed understanding of an image is required, such as in autonomous vehicles and medical diagnosis. This problem has traditionally been solved with probabilistic models known as conditional random fields (CRFs) due to their ability to model the relationships between the pixels being predicted. However, deep neural networks (DNNs) recently have been shown to excel at a wide range of computer vision problems due to their ability to automatically learn rich feature representations from data, as opposed to traditional handcrafted features. The idea of combining CRFs and DNNs have achieved state-of-the-art results in a number of domains. We review the literature on combining the modeling power of CRFs with the representation-learning ability of DNNs, ranging from early work that combines these two techniques as independent stages of a common pipeline to recent approaches that embed inference of probabilistic models directly in the neural network itself. Finally, we summarize future research directions.
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| 3. |
- Bäckryd, Emmanuel, et al.
(författare)
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High levels of cerebrospinal fluid chemokines point to the presence of neuroinflammation in peripheral neuropathic pain : a cross-sectional study of 2 cohorts of patients compared with healthy controls
- 2017
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Ingår i: Pain. - : Ovid Technologies (Wolters Kluwer Health). - 0304-3959 .- 1872-6623. ; 158:12, s. 2487-2495
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Tidskriftsartikel (refereegranskat)abstract
- Animal models suggest that chemokines are important mediators in the pathophysiology of neuropathic pain. Indeed, these substances have been called “gliotransmitters,” a term that illustrates the close interplay between glial cells and neurons in the context of neuroinflammation and pain. However, evidence in humans is scarce. The aim of the study was to determine a comprehensive cerebrospinal fluid (CSF) inflammatory profile of patients with neuropathic pain. Our hypothesis was that we would thereby find indications of a postulated on-going process of central neuroinflammation. Samples of CSF were collected from 2 cohorts of patients with neuropathic pain (n = 11 and n = 16, respectively) and healthy control subjects (n = 11). The samples were analyzed with a multiplex proximity extension assay in which 92 inflammation-related proteins were measured simultaneously (Proseek Multiplex Inflammation I; Olink Bioscience, Uppsala, Sweden). Univariate testing with control of false discovery rate, as well as orthogonal partial least squares discriminant analysis, were used for statistical analyses. Levels of chemokines CXCL6, CXCL10, CCL8, CCL11, CCL23 in CSF, as well as protein LAPTGF-beta-1, were significantly higher in both neuropathic pain cohorts compared with healthy controls, pointing to neuroinflammation in patients. These 6 proteins were also major results in a recent similar study in patients with fibromyalgia. The findings need to be confirmed in larger cohorts, and the question of causality remains to be settled. Because it has been suggested that prevalent comorbidities to chronic pain (eg, depression, anxiety, poor sleep, and tiredness) also are associated with neuroinflammation, it will be important to determine whether neuroinflammation is a common mediator.
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| 4. |
- Ekenberg, Love, et al.
(författare)
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Deliberation, representation, equity : research approaches, tools and algorithms for participatory processes
- 2017
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- What can we learn about the development of public interaction in e-democracy from a drama delivered by mobile headphones to an audience standing around a shopping center in a Stockholm suburb? In democratic societies there is widespread acknowledgment of the need to incorporate citizens' input in decision-making processes in more or less structured ways. But participatory decision making is balancing on the borders of inclusion, structure, precision and accuracy. To simply enable more participation will not yield enhanced democracy, and there is a clear need for more elaborated elicitation and decision analytical tools. This rigorous and thought-provoking volume draws on a stimulating variety of international case studies, from flood risk management in the Red River Delta of Vietnam, to the consideration of alternatives to gold mining in Ro?ia Montana in Transylvania, to the application of multi-criteria decision analysis in evaluating the impact of e-learning opportunities at Uganda's Makerere University. Editors Love Ekenberg (senior research scholar, International Institute for Applied Systems Analysis [IIASA], Laxenburg, professor of Computer and Systems Sciences, Stockholm University), Karin Hansson (artist and research fellow, Department of Computer and Systems Sciences, Stockholm University), Mats Danielson (vice president and professor of Computer and Systems Sciences, Stockholm University, affiliate researcher, IIASA) and Göran Cars (professor of Societal Planning and Environment, Royal Institute of Technology, Stockholm) draw innovative collaborations between mathematics, social science, and the arts. They develop new problem formulations and solutions, with the aim of carrying decisions from agenda setting and problem awareness through to feasible courses of action by setting objectives, alternative generation, consequence assessments, and trade-off clarifications. As a result, this book is important new reading for decision makers in government, public administration and urban planning, as well as students and researchers in the fields of participatory democracy, urban planning, social policy, communication design, participatory art, decision theory, risk analysis and computer and systems sciences.
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| 5. |
- Fellström, Bengt, 1947-, et al.
(författare)
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Associations Between Apolipoprotein A1, High-Density Lipoprotein Cholesterol, and Urinary Cytokine Levels in Elderly Males and Females
- 2019
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Ingår i: Journal of Interferon and Cytokine Research. - : Mary Ann Liebert Inc. - 1079-9907 .- 1557-7465. ; 40:2, s. 71-74
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Tidskriftsartikel (refereegranskat)abstract
- There exists a close relationship between cardiovascular diseases and chronic kidney disease. Apolipoprotein A1 and high-density lipoprotein (HDL) cholesterol are widely used as cardiovascular risk markers but they also have anti-inflammatory properties. The aim of this study was to investigate any associations between HDL levels and cytokine levels in urine. We randomly selected 90 urine samples from the Prospective Investigation of the Vasculature in Uppsala Seniors Study (41 males and 49 females). The samples were analyzed with 2 multiplex assays, Multiplex Inflammation I and Cardiovascular II kits (Olink Bioscience, Uppsala, Sweden). We analyzed the correlations between 158 cytokines in urine with apolipoprotein A1, HDL cholesterol, apolipoprotein B, and low-density lipoprotein cholesterol. There were strong correlations for apolipoprotein A1 and HDL cholesterol with individual cytokines. After adjustment for multiplicity testing, there were 33 significant correlations between apolipoprotein A1 and cytokine levels and 14 of these were also significantly correlated with HDL cholesterol. The strongest associations were observed for IL-1α, SPON2, RAGE, PAR-1, TRAIL-R2, IL-4RA, TNFRSF11A, and SCF. A total of 28 out of 33 correlations were negative, indicating a negative relationship between apolipoprotein A1 and urinary cytokines. The study shows a negative correlation between apolipoprotein A1 and HDL cholesterol and urinary cytokine levels. The finding is in agreement with the anti-inflammatory properties of HDL.
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| 6. |
- Gómez, Etzar, et al.
(författare)
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Alluvial aquifer thickness and bedrock structure delineation by electromagnetic methods in the highlands of Bolivia
- 2019
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Ingår i: Environmental Earth Sciences. - : Springer Science and Business Media LLC. - 1866-6280 .- 1866-6299. ; 78:3
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Tidskriftsartikel (refereegranskat)abstract
- The porous aquifers in the area called Challapampa are the most important groundwater reservoirs that supply drinking water to Oruro city in the highlands of Bolivia. They consist of unconsolidated fluvial–lacustrine deposits, resting on a complex sedimentary bedrock and covered by a thin surficial clay layer. The settings of these geological units and the structures governing the flow patterns have barely been investigated, despite this reservoir having been utilized during the last 50 years. This study applied transient electromagnetic (TEM) soundings and electrical resistivity tomography (ERT) in the middle part of the alluvial fan of River Paria to investigate the thickness of the porous aquifer and detect the relief of the bedrock. Likewise, some results expressed as resistivity models indicate the possible existence of geological structures below the unconsolidated sediments. The average depth of investigation reached in this study is between 200 and 250 m below the surface, for both the applied methods. The geological structures inferred have similar directions as the major faults in the vicinity, from southeast to northwest, which in turn are assumed as part of fractured aquifers underlying the porous aquifers. The geo-electrical techniques were successfully tested in the study area and the resistivity models from TEM complement very well those obtained from ERT. Therefore, extended investigations using the same techniques would help to develop a more complete description of the hydrogeological settings of the aquifer system.
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| 7. |
- Jin, Shaobo, 1987-, et al.
(författare)
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Approximate Bayesianity of frequentist confidence intervals for a binomial proportion
- 2017
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Ingår i: American Statistician. - : Informa UK Limited. - 0003-1305 .- 1537-2731. ; 71, s. 106-111
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Tidskriftsartikel (refereegranskat)abstract
- The well-known Wilson and Agresti–Coull confidence intervals for a binomial proportion p are centered around a Bayesian estimator. Using this as a starting point, similarities between frequentist confidence intervals for proportions and Bayesian credible intervals based on low-informative priors are studied using asymptotic expansions. A Bayesian motivation for a large class of frequentist confidence intervals is provided. It is shown that the likelihood ratio interval for p approximates a Bayesian credible interval based on Kerman’s neutral noninformative conjugate prior up to O(n− 1) in the confidence bounds. For the significance level α ≲ 0.317, the Bayesian interval based on the Jeffreys’ prior is then shown to be a compromise between the likelihood ratio and Wilson intervals. Supplementary materials for this article are available online.
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| 8. |
- Larsson, Anders, et al.
(författare)
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The body mass index (BMI) is significantly correlated with levels of cytokines and chemokines in cerebrospinal fluid
- 2015
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Ingår i: Cytokine. - : Elsevier BV. - 1043-4666 .- 1096-0023. ; 76:2, s. 514-518
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Tidskriftsartikel (refereegranskat)abstract
- Cytokines and chemokines regulate many functions in the body including the brain. The interactions between adipose tissue and the central nervous system (CNS) are important for the regulation of energy balance. CNS function is also influenced by age. The aim of the present study was to investigate the effects of body mass index (BMI) and age on cytokine and chemokine levels in cerebrospinal fluid. Cerebrospinal fluid samples (n=89) were collected from patients undergoing routine surgical procedures. The samples were analyzed using the multiplex proximity extension assay (PEA) in which 92 different cytokines are measured simultaneously using minute sample volume. We found no significant correlations between age and cytokine levels for any of the studied markers. In contrast, at a false discovery rate of 10%, 19 markers were significantly associated with BMI (in decreasing significance: FGF-5, ADA, Beta-NGF, CD40, IL-10RB, CCL19, TGF-alpha, SIRT2, TWEAK, SCF, CSF-1, 4E-BP1, DNER, LIF-R, STAMPB, CXCL10, CXCL6, VEGF-A and CX3CL1). This study reveals a clear effect of BMI on cytokine and chemokine levels in cerebrospinal fluid.
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| 9. |
- Larsson, Anders, et al.
(författare)
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The effects of age and gender on plasma levels of 63 cytokines
- 2015
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Ingår i: JIM - Journal of Immunological Methods. - : Elsevier BV. - 0022-1759 .- 1872-7905. ; 425, s. 58-61
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Tidskriftsartikel (refereegranskat)abstract
- Cytokines play important roles as regulators of cell functions, and over the last decades a number of cytokine assays have been developed. The aim of the present study was to investigate the effects of age and gender on a large number of cytokines. Plasma samples were collected from 33 healthy blood donors. The samples were analyzed using the multiplex proximity extension assay (PEA) allowing simultaneous measurement of 92 cytokines and four technical controls. Biomarkers with less than 80% quantitative results were excluded leaving 63 cytokines that were analyzed for the effects of gender and age. The plasma level of three of the investigated biomarkers (DNER, MCP-4 and MMP-10) were found to be significantly different for the two genders (adjusted p-value <0.05), and 15 of the biomarkers (CCL11, CCL25, CDCP1, CSF-1, CXCL11, CXCL9, FGF-23, Flt3L, HGF, IL-10RB, MCP-3, MCP-4, MMP-10, OPG, VEGF-A) were significantly associated with age. This study reveals the effects of age and gender on a large number of cytokine assays. CXCL5 and TNFB were significantly higher in females, while the other markers with significant gender-dependent differences were higher in males. For the markers that were significantly associated with age, only CXCL6 was found to decrease with age, while the other biomarkers increased with age.
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| 10. |
- Larsson, Måns, 1989, et al.
(författare)
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A cross-season correspondence dataset for robust semantic segmentation
- 2019
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Ingår i: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. - 1063-6919. ; 2019-June, s. 9524-9534
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Konferensbidrag (refereegranskat)abstract
- In this paper, we present a method to utilize 2D-2D point matches between images taken during different image conditions to train a convolutional neural network for semantic segmentation. Enforcing label consistency across the matches makes the final segmentation algorithm robust to seasonal changes. We describe how these 2D-2D matches can be generated with little human interaction by geometrically matching points from 3D models built from images. Two cross-season correspondence datasets are created providing 2D-2D matches across seasonal changes as well as from day to night. The datasets are made publicly available to facilitate further research. We show that adding the correspondences as extra supervision during training improves the segmentation performance of the convolutional neural network, making it more robust to seasonal changes and weather conditions.
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