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  • 1.
    Butler, Simon
    et al.
    Högskolan i Skövde, Institutionen för informationsteknologi. Högskolan i Skövde, Forskningscentrum för Informationsteknologi.
    Gamalielsson, Jonas
    Högskolan i Skövde, Institutionen för informationsteknologi. Högskolan i Skövde, Forskningscentrum för Informationsteknologi. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Lundell, Björn
    Högskolan i Skövde, Institutionen för informationsteknologi. Högskolan i Skövde, Forskningscentrum för Informationsteknologi.
    Brax, Christoffer
    Combitech AB, Linköping, Sweden.
    Mattsson, Anders
    Husqvarna AB, Huskvarna, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Stockholm, Sweden.
    Feist, Jonas
    RedBridge AB, Stockholm, Sweden.
    Lönroth, Erik
    Scania IT AB, Södertälje, Sweden.
    Maintaining interoperability in open source software: A case study of the Apache PDFBox project2020Ingår i: Journal of Systems and Software, ISSN 0164-1212, E-ISSN 1873-1228, Vol. 159, artikel-id 110452Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Software interoperability is commonly achieved through the implementation of standards for communication protocols or data representation formats. Standards documents are often complex, difficult to interpret, and may contain errors and inconsistencies, which can lead to differing interpretations and implementations that inhibit interoperability. Through a case study of two years of activity in the Apache PDFBox project we examine day-to-day decisions made concerning implementation of the PDF specifications and standards in a community open source software (OSS) project. Thematic analysis is used to identify semantic themes describing the context of observed decisions concerning interoperability. Fundamental decision types are identified including emulation of the behaviour of dominant implementations and the extent to which to implement the PDF standards. Many factors influencing the decisions are related to the sustainability of the project itself, while other influences result from decisions made by external actors, including the developers of dependencies of PDFBox. This article contributes a fine grained perspective of decision-making about software interoperability by contributors to a community OSS project. The study identifies how decisions made support the continuing technical relevance of the software, and factors that motivate and constrain project activity. 

  • 2.
    Fernandes, Ricardo A.
    et al.
    Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, United Kingdom / Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, United Kingdom / Department of Molecular and Cellular Physiology, Department of Structural Biology, Stanford University, United States.
    Ganzinger, Kristina A.
    Department of Chemistry, University of Cambridge, United Kingdom / Living Matter Department, Physics of Cellular Interactions Group, AMOLF, Amsterdam, Netherlands.
    Tzou, Justin C.
    Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, United States.
    Jönsson, Peter
    Department of Chemistry, University of Cambridge, United Kingdom / Department of Chemistry, Lund University, Sweden.
    Lee, Steven F.
    Department of Chemistry, University of Cambridge, United Kingdom.
    Palayret, Matthieu
    Department of Chemistry, University of Cambridge, United Kingdom.
    Santos, Ana Mafalda
    Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, United Kingdom / Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, United Kingdom.
    Carr, Alexander R.
    Department of Chemistry, University of Cambridge, United Kingdom.
    Ponjavic, Aleks
    Department of Chemistry, University of Cambridge, United Kingdom.
    Chang, Veronica T.
    Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, United Kingdom / Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, United Kingdom / Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.
    Macleod, Charlotte
    Department of Chemistry, University of Cambridge, United Kingdom.
    Lagerholm, B. Christoffer
    Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, United Kingdom.
    Lindsay, Alan E.
    Mathematics Department, University of British Columbia, Vancouver, Canada.
    Dushek, Omer
    Sir William Dunn School of Pathology, University of Oxford, United Kingdom / Wolfson Centre for Mathematical Biology, University of Oxford, United Kingdom.
    Tilevik, Andreas
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. School of Bioscience, University of Skövde, Sweden.
    Davis, Simon J.
    Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, United Kingdom / Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, United Kingdom.
    Klenerman, David
    Department of Chemistry, University of Cambridge, United Kingdom.
    A cell topography-based mechanism for ligand discrimination by the T cell receptor2019Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, nr 28, s. 14002-14010Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The T cell receptor (TCR) initiates the elimination of pathogens and tumors by T cells. To avoid damage to the host, the receptor must be capable of discriminating between wild-type and mutated self and nonself peptide ligands presented by host cells. Exactly how the TCR does this is unknown. In resting T cells, the TCR is largely unphosphorylated due to the dominance of phosphatases over the kinases expressed at the cell surface. However, when agonist peptides are presented to the TCR by major histocompatibility complex proteins expressed by antigen-presenting cells (APCs), very fast receptor triggering, i.e., TCR phosphorylation, occurs. Recent work suggests that this depends on the local exclusion of the phosphatases from regions of contact of the T cells with the APCs. Here, we developed and tested a quantitative treatment of receptor triggering reliant only on TCR dwell time in phosphatase-depleted cell contacts constrained in area by cell topography. Using the model and experimentally derived parameters, we found that ligand discrimination likely depends crucially on individual contacts being ∼200 nm in radius, matching the dimensions of the surface protrusions used by T cells to interrogate their targets. The model not only correctly predicted the relative signaling potencies of known agonists and nonagonists but also achieved this in the absence of kinetic proofreading. Our work provides a simple, quantitative, and predictive molecular framework for understanding why TCR triggering is so selective and fast and reveals that, for some receptors, cell topography likely influences signaling outcomes. 

  • 3.
    Säterberg, Torbjörn
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Division of Theoretical Biology, Sweden / Swedish University of Agricultural Sciences, Department of Aquatic Resources, Öregrund, Sweden.
    Jonsson, Tomas
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Swedish University of Agricultural Sciences, Department of Ecology, Uppsala, Sweden.
    Yearsley, Jon
    University College Dublin, School of Biology & Environmental Science, Ireland / UCD Earth Institute, Belfield, Dublin 4, Ireland.
    Berg, Sofia
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Ebenman, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Division of Theoretical Biology, Sweden / Stockholm University, SRC, Sweden.
    A potential role for rare species in ecosystem dynamics2019Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, s. 1-12, artikel-id 11107Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The ecological importance of common species for many ecosystem processes and functions is unquestionably due to their high a bundance.Yet, the importance of rare species is much less understood. Here we take a theoretical approach, exposing dynamical models of ecological networks to small perturbations, to explore the dynamical importance of rare and common species. We find that both species types contribute to the recovery of communities following generic perturbations (i.e. perturbations affecting all species).Yet, when perturbations are selective (i.e. affects only one species), perturbations to rare species have the most pronounced effect on community stability. We show that this is due to the strong indirect effects induced by perturbations to rare species. Because indirect effects typically set in at longer timescales, our results indicate that the importance of rare species may be easily overlooked and thus underrated. Hence, our study provides a potential ecological motive for the management and protection of rare species.

  • 4.
    Jonsson, Annie
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Wennergren, Uno
    Linköping University, Linköpings Universitet.
    Approximations of population growth in a noisy environment: on the dichotomy of non-age and age structure2019Ingår i: Theoretical Ecology, ISSN 1874-1738, E-ISSN 1874-1746, Vol. 12, nr 1, s. 99-110Artikel i tidskrift (Refereegranskat)
  • 5.
    Torra, Vicenç
    et al.
    Högskolan i Skövde, Institutionen för informationsteknologi. Högskolan i Skövde, Forskningscentrum för Informationsteknologi.
    Karlsson, Alexander
    Högskolan i Skövde, Institutionen för informationsteknologi. Högskolan i Skövde, Forskningscentrum för Informationsteknologi.
    Steinhauer, H. Joe
    Högskolan i Skövde, Institutionen för informationsteknologi. Högskolan i Skövde, Forskningscentrum för Informationsteknologi.
    Berglund, Stefan
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Artificial Intelligence2019Ingår i: Data Science in Practice / [ed] Alan Said, Vicenç Torra, Springer, 2019, s. 9-26Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    This chapter gives a brief introduction to what artificial intelligence is. We begin discussing some of the alternative definitions for artificial intelligence and introduce the four major areas of the field. Then, in subsequent sections we present these areas. They are problem solving and search, knowledge representation and knowledge-based systems, machine learning, and distributed artificial intelligence. The chapter follows with a discussion on some ethical dilemma we find in relation to artificial intelligence. A summary closes this chapter.

  • 6.
    Kajonius, Petri
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Psychology, University of Gothenburg, Gothenburg, Sweden / Department of Psychology, University West, Trollhättan, Sweden.
    Johnson, John
    Department of Psychology, Pennsylvania State University, State College, USA.
    Assessing the Structure of the Five Factor Model of Personality (IPIP-NEO-120) in the Public Domain2019Ingår i: Europe's Journal of Psychology, ISSN 1841-0413, E-ISSN 1841-0413, Vol. 15, nr 2, s. 260-275Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Assessment of individual differences in personality traits is arguably one of the hallmarks of psychological research. Testing the structural validity of trait measurements is paramount in this endeavor. In the current study, we investigated 30 facet traits in one of the accessible and comprehensive public-domain Five Factor Model (FFM) personality inventories, IPIP-NEO-120 (Johnson, 2014), using one of the largest US samples to date (N = 320,128). We present structural loadings for all trait facets organized into respective FFM-trait domain (Neuroticism, Extraversion, Openness, Agreeableness, and Conscientiousness). Both hierarchical second-order and bi-factor models showed tolerable model fit indices, using confirmatory factor analysis in a structural equation modeling (SEM) framework. Some facet traits were substantially more representative than others for their respective trait domain, which facilitate further discussions on FFM-construct content. We conclude that IPIP-NEO is sufficiently structurally robust for future use, for the benefit of research and practice in personality assessment.

  • 7.
    Weishaupt, Holger
    et al.
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
    Johansson, Patrik
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
    Sundström, Anders
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
    Lubovac-Pilav, Zelmina
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Olsson, Björn
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Nelander, Sven
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
    Swartling, Fredrik J.
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
    Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes2019Ingår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35, nr 18, s. 3357-3364Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Motivation: Medulloblastoma (MB) is a brain cancer predominantly arising in children. Roughly 70% of patients are cured today, but survivors often suffer from severe sequelae. MB has been extensively studied by molecular profiling, but often in small and scattered cohorts. To improve cure rates and reduce treatment side effects, accurate integration of such data to increase analytical power will be important, if not essential.

    Results: We have integrated 23 transcription datasets, spanning 1350 MB and 291 normal brain samples. To remove batch effects, we combined the Removal of Unwanted Variation (RUV) method with a novel pipeline for determining empirical negative control genes and a panel of metrics to evaluate normalization performance. The documented approach enabled the removal of a majority of batch effects, producing a large-scale, integrative dataset of MB and cerebellar expression data. The proposed strategy will be broadly applicable for accurate integration of data and incorporation of normal reference samples for studies of various diseases. We hope that the integrated dataset will improve current research in the field of MB by allowing more large-scale gene expression analyses.

  • 8.
    Toto, Robert D.
    et al.
    University of Texas Southwestern Medical Center, Dallas, TX, USA.
    Goldenberg, Ronald
    LMC Diabetes & Endocrinology, Thornhill, ON, Canada.
    Chertow, Glenn M.
    Stanford University School of Medicine, CA, USA.
    Cain, Valerie
    Bogier Clinical and IT Solutions, Raleigh, NC, USA.
    Stefánsson, Bergur V.
    Late-stage Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
    Sjöström, Carl David
    Late-stage Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
    Sartipy, Peter
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Late-stage Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
    Correction of hypomagnesemia by dapagliflozin in patients with type 2 diabetes: A post hoc analysis of 10 randomized, placebo-controlled trials2019Ingår i: Journal of diabetes and its complications, ISSN 1056-8727, E-ISSN 1873-460X, Vol. 33, nr 10, artikel-id 107402Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Aims: Hypomagnesemia (serum magnesium [Mg] <0.74 mmol/L [<1.8 mg/dL]) is commonly observed in patients with type 2 diabetes (T2D). This study investigated the effect of treatment with dapagliflozin 10 mg on Mg concentrations in patients with T2D. Methods: In this post hoc analysis, we used pooled data from 10 placebo-controlled studies of dapagliflozin over 24 weeks of treatment in patients with T2D. We evaluated the change in Mg in patients receiving dapagliflozin vs. placebo overall, and in subgroups with baseline hypomagnesemia and normal/hypermagnesemia (≥0.74 mmol/L [≥1.8 mg/dL]). We determined the proportion of patients with baseline hypomagnesemia who achieved Mg ≥0.74 mmol/L (≥1.8 mg/dL). Results: A total of 4398 patients with T2D were included. The mean change from baseline to week 24 in Mg was significantly larger with dapagliflozin vs. placebo; difference, 0.06 mmol/L (95% confidence interval [CI]: 0.05, 0.06). The proportion of patients with Mg within the population reference range after 24 weeks of treatment was significantly higher with dapagliflozin vs. placebo; difference, 47.8% (95% CI: 41.4, 53.9). The proportion of patients displaying hypermagnesemia did not increase with dapagliflozin treatment. Conclusions: Treatment with dapagliflozin 10 mg resulted in correction of Mg concentrations in patients with T2D and hypomagnesemia. 

  • 9.
    Persson, Björn N.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Psychology, University of Turku, Finland / Blekinge Center of Competence, Region Blekinge, Karlskrona, Sweden.
    Current Directions in Psychiatric Classification: From the DSM to RDoC2019Ingår i: Personality and Brain Disorders: Associations and Interventions / [ed] Danilo Garcia, Trevor Archer, Richard M. Kostrzewa, Cham: Springer, 2019, 1, s. 253-268Kapitel i bok, del av antologi (Refereegranskat)
  • 10.
    Granéli, Cecilia
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Discovery Sciences, IMED Biotech Unit, AstraZeneca Gothenburg, Mölndal, Sweden.
    Hicks, Ryan
    Discovery Sciences, IMED Biotech Unit, AstraZeneca Gothenburg, Mölndal, Sweden.
    Brolén, Gabriella
    Discovery Sciences, IMED Biotech Unit, AstraZeneca Gothenburg, Mölndal, Sweden.
    Synnergren, Jane
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Sartipy, Peter
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Global Medicines Development, CVRM, AstraZeneca Gothenburg, Mölndal, Sweden.
    Diabetic Cardiomyopathy Modelling Using Induced Pluripotent Stem Cell Derived Cardiomyocytes: Recent Advances and Emerging Models2019Ingår i: Stem Cell Reviews, ISSN 1550-8943, E-ISSN 1558-6804, Vol. 15, nr 1, s. 13-22Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The global burden of diabetes has drastically increased over the past decades and in 2017 approximately 4 million deaths were caused by diabetes and cardiovascular complications. Diabetic cardiomyopathy is a common complication of diabetes with early manifestations of diastolic dysfunction and left ventricular hypertrophy with subsequent progression to systolic dysfunction and ultimately heart failure. An in vitro model accurately recapitulating key processes of diabetic cardiomyopathy would provide a useful tool for investigations of underlying disease mechanisms to further our understanding of the disease and thereby potentially advance treatment strategies for patients. With their proliferative capacity and differentiation potential, human induced pluripotent stem cells (iPSCs) represent an appealing cell source for such a model system and cardiomyocytes derived from induced pluripotent stem cells have been used to establish other cardiovascular related disease models. Here we review recently made advances and discuss challenges still to be overcome with regard to diabetic cardiomyopathy models, with a special focus on iPSC-based systems. Recent publications as well as preliminary data presented here demonstrate the feasibility of generating cardiomyocytes with a diabetic phenotype, displaying insulin resistance, impaired calcium handling and hypertrophy. However, capturing the full metabolic- and functional phenotype of the diabetic cardiomyocyte remains to be accomplished. 

  • 11.
    Salminen-Vaparanta, Niina
    et al.
    University of Turku, Finland.
    Koivisto, Mika
    University of Turku, Finland.
    Vorobyev, Victor
    University of Turku, Finland.
    Alakurtti, Kati
    University of Turku, Turku, Finland.
    Revonsuo, Antti
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. University of Turku, Finland.
    Does TMS on V3 block conscious visual perception?2019Ingår i: Neuropsychologia, ISSN 0028-3932, E-ISSN 1873-3514, Vol. 128, s. 223-231Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Primary visual cortex (V1) and extrastriate V2 are necessary for the emergence of visual consciousness, but the effects of involvement of extrastriate V3 on visual consciousness is unclear. The objective of this study was to examine the causal role of V3 in visual consciousness in humans. We combined neuronavigated transcranial magnetic stimulation (TMS) with a computational model of the TMS-induced electric field to test whether or not the intact processing of visual input in V3, like in V1 and V2, is necessary for conscious visual perception. We targeted the stimulation both to V2 and to V3. If TMS of V3 blocks conscious visual perception of stimuli, then activation in V3 is a causally necessary prerequisite for conscious perception of stimuli. According to the alternative hypothesis, TMS of V3 will not block the conscious visual perception of stimuli, because the pathways from V1 to the higher cortical areas that go around V3 provide sufficient visual input for the emergence of conscious visual perception. The results showed that TMS interfered with conscious perception of features, detection of stimulus presence and the ability to discriminate the letter stimuli both when TMS was targeted either to V3 or to V2. For the conscious detection of stimulus presence, the effect was significantly stronger when V2 was stimulated than when V3 was stimulated. The results of the present study suggest that in addition to the primary visual cortex and V2, also V3 causally contributes to the generation of the most basic form of visual consciousness. Importantly, the results also indicate that V3 is necessary for visual perception in general, not only for visual consciousness.

  • 12.
    Curtsdotter, Alva
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden / Department of Environmental Sciences, Emory University, Atlanta, GA, Georgia, United States.
    Banks, H. Thomas
    Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, United States.
    Banks, John E.
    Undergraduate Research Opportunities Center (UROC), California State University, Monterey Bay, Seaside, CA, United States.
    Jonsson, Mattias
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Jonsson, Tomas
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Laubmeier, Amanda N.
    Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, United States.
    Traugott, Michael
    Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria.
    Bommarco, Riccardo
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Ecosystem function in predator-prey food webs: confronting dynamic models with empirical data2019Ingår i: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 88, nr 2, s. 196-210Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Most ecosystem functions and related services involve species interactions across trophic levels, for example, pollination and biological pest control. Despite this, our understanding of ecosystem function in multitrophic communities is poor, and research has been limited to either manipulation in small communities or statistical descriptions in larger ones. Recent advances in food web ecology may allow us to overcome the trade-off between mechanistic insight and ecological realism. Molecular tools now simplify the detection of feeding interactions, and trait-based approaches allow the application of dynamic food web models to real ecosystems. We performed the first test of an allometric food web model's ability to replicate temporally nonaggregated abundance data from the field and to provide mechanistic insight into the function of predation. We aimed to reproduce and explore the drivers of the population dynamics of the aphid herbivore Rhopalosiphum padi observed in ten Swedish barley fields. We used a dynamic food web model, taking observed interactions and abundances of predators and alternative prey as input data, allowing us to examine the role of predation in aphid population control. The inverse problem methods were used for simultaneous model fit optimization and model parameterization. The model captured >70% of the variation in aphid abundance in five of ten fields, supporting the model-embodied hypothesis that body size can be an important determinant of predation in the arthropod community. We further demonstrate how in-depth model analysis can disentangle the likely drivers of function, such as the community's abundance and trait composition. Analysing the variability in model performance revealed knowledge gaps, such as the source of episodic aphid mortality, and general method development needs that, if addressed, would further increase model success and enable stronger inference about ecosystem function. The results demonstrate that confronting dynamic food web models with abundance data from the field is a viable approach to evaluate ecological theory and to aid our understanding of function in real ecosystems. However, to realize the full potential of food web models, in ecosystem function research and beyond, trait-based parameterization must be refined and extended to include more traits than body size. © 2018 The Authors. Journal of Animal Ecology © 2018 British Ecological Society

  • 13.
    Sikka, Pilleriin
    et al.
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för biovetenskap. Department of Psychology, University of Turku, Finland.
    Revonsuo, Antti
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Psychology, University of Turku, Finland.
    Noreika, Valdas
    Department of Psychology, University of Cambridge, UK.
    Valli, Katja
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Psychology, University of Turku, Finland.
    EEG Frontal Alpha Asymmetry and Dream Affect: Alpha Oscillations Over the Right Frontal Cortex During REM Sleep and Pre-Sleep Wakefulness Predict Anger in REM Sleep Dreams2019Ingår i: Journal of Neuroscience, ISSN 0270-6474, E-ISSN 1529-2401, Vol. 39, nr 24, s. 4775-4784, artikel-id 2884-18Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Affective experiences are central not only to our waking life but also to rapid eye movement(REM) sleep dreams. Despite our increasing understanding of the neural correlates of dreaming, we know little about the neural correlates of dream affect. Frontal alpha asymmetry (FAA) is considered a marker of affective states and traits as well as affect regulation in the waking state. Here, we explored whether FAA during REM sleep and during evening resting wakefulness is related to affective experiences in REM sleep dreams. EEG recordings were obtained from 17humanparticipants (7men)whospent 2 nights in the sleep laboratory. Participants were awakened 5minafter the onset of everyREMstage after which they provided a dream report and rated their dream affect. Two-minute preawakening EEG segments were analyzed. Additionally, 8 min of evening presleep and morning postsleep EEG were recorded during resting wakefulness. Mean spectral power in the alpha band (8 –13 Hz and correspondingFAAwere calculated over the frontal (F4-F3) sites. Results showed that FAA during REM sleep, and during evening resting wakefulness, predicted ratings of dream anger. This suggests that individuals with greater alpha power in the right frontal hemisphere may be less able to regulate (i.e., inhibit) strong affective states, such as anger, in dreams. Additionally, FAA was positively correlated across wakefulness and REM sleep. Together, these findings imply that FAA may serve as a neural correlate of affect regulation not only in the waking but also in the dreaming state.

    Publikationen är tillgänglig i fulltext från 2019-12-13 00:01
  • 14.
    Walleczek, Jan
    et al.
    Phenoscience Laboratories, Berlin, Germany.
    Grössing, Gerhard
    Austrian Institute for Nonlinear Studies, Akademiehof, Austria.
    Pylkkänen, Paavo
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Philosophy, History, and Art Studies, University of Helsinki, Helsinki, Finland.
    Hiley, Basil
    Department of Physics and Astronomy, University College London, London, United Kingdom.
    Emergent quantum mechanics: David Bohm Centennial perspectives2019Ingår i: Entropy, ISSN 1099-4300, E-ISSN 1099-4300, Vol. 21, nr 2, artikel-id 113Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Emergent quantum mechanics (EmQM) explores the possibility of an ontology for quantum mechanics. The resurgence of interest in realist approaches to quantum mechanics challenges the standard textbook view, which represents an operationalist approach. The possibility of an ontological, i.e., realist, quantum mechanics was first introduced with the original de Broglie-Bohm theory, which has also been developed in another context as Bohmian mechanics. This Editorial introduces a Special Issue featuring contributions which were invited as part of the David Bohm Centennial symposium of the EmQM conference series (www.emqm17.org). Questions directing the EmQM research agenda are: Is reality intrinsically random or fundamentally interconnected? Is the universe local or nonlocal? Might a radically new conception of reality include a form of quantum causality or quantum ontology? What is the role of the experimenter agent in ontological quantum mechanics? The Special Issue also includes research examining ontological propositions that are not based on the Bohm-type nonlocality. These include, for example, local, yet time-symmetric, ontologies, such as quantum models based upon retrocausality. This Editorial provides topical overviews of thirty-one contributions which are organized into seven categories to provide orientation. 

  • 15.
    Walleczek, Jan
    et al.
    Phenoscience Laboratories, Berlin, Germany.
    Grössing, GerhardAustrian Institute for Nonlinear Studies, Vienna, Austria.Pylkkänen, PaavoHögskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Philosophy, History, and Art Studies, University of Helsinki, Helsinki, Finland.Hiley, BasilUniversity College of London, UK.
    Emergent Quantum Mechanics: David Bohm Centennial Perspectives2019Samlingsverk (redaktörskap) (Refereegranskat)
  • 16.
    Delsing, Louise
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Sweden / Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Mölndal, Sweden.
    Kallur, Therese
    BioLamina, Sundbyberg, Sweden.
    Zetterberg, Henrik
    Department of Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Sweden / Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden / Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK / UK Dementia Research Institute at UCL, London, UK.
    Hicks, Ryan
    Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Mölndal, Sweden.
    Synnergren, Jane
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Enhanced xeno-free differentiation of hiPSC-derived astroglia applied in a blood-brain barrier model2019Ingår i: Fluids and Barriers of the CNS, ISSN 2045-8118, E-ISSN 2045-8118, Vol. 16, nr 1, artikel-id 27Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background Human induced pluripotent stem cells (hiPSC) hold great promise for use in cell therapy applications and for improved in vitro models of human disease. So far, most hiPSC differentiation protocols to astroglia use undefined, animal-containing culture matrices. Laminins, which play an essential role in the regulation of cell behavior, offer a source of defined, animal-free culture matrix. Methods In order to understand how laminins affect astroglia differentiation, recombinant human laminin-521 (LN521), was compared to a murine Engelbreth-Holm-Swarm sarcoma derived laminin (L2020). Astroglia expression of protein and mRNA together with glutamate uptake and protein secretion function, were evaluated. Finally, these astroglia were evaluated in a coculture model of the blood-brain barrier (BBB). Results Astroglia of good quality were generated from hiPSC on both LN521 and L2020. However, astroglia differentiated on human LN521 showed higher expression of several astroglia specific mRNAs and proteins such as GFAP, S100B, Angiopoietin-1, and EAAT1, compared to astroglia differentiated on murine L2020. In addition, glutamate uptake and ability to induce expression of junction proteins in endothelial cells were affected by the culture matrix for differentiation. Conclusion Our results suggest that astroglia differentiated on LN521 display an improved phenotype and are suitable for coculture in a hiPSC-derived BBB model. This provides a starting point for a more defined and robust derivation of astroglia for use in BBB coculture models.

  • 17.
    Enroth, Helena
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Retz, Karolina
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Andersson, Sofie
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Andersson, Carl
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Svensson, Kristina
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Ljungström, Lars
    Department of Infectious Diseases, Skaraborg Hospital, Skövde, Sweden.
    Tilevik, Diana
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Evaluation of QuickFISH and maldi Sepsityper for identification of bacteria in bloodstream infection2019Ingår i: Infectious Diseases, ISSN 2374-4235, E-ISSN 2374-4243, Vol. 51, nr 4, s. 249-258Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Early detection of bacteria and their antibiotic susceptibility patterns are critical to guide therapeutic decision-making for optimal care of septic patients. The current gold standard, blood culturing followed by subculture on agar plates for subsequent identification, is too slow leading to excessive use of broad-spectrum antibiotic with harmful consequences for the patient and, in the long run, the public health. The aim of the present study was to assess the performance of two commercial assays, QuickFISH® (OpGen) and Maldi Sepsityper™ (Bruker Daltonics) for early and accurate identification of microorganisms directly from positive blood cultures.

    Materials and methods: During two substudies of positive blood cultures, the two commercial assays were assessed against the routine method used at the clinical microbiology laboratory, Unilabs AB, at Skaraborg Hospital, Sweden.

    Results: The Maldi Sepsityper™ assay enabled earlier microorganism identification. Using the cut-off for definite species identification according to the reference method (>2.0), sufficiently accurate species identification was achieved, but only among Gram-negative bacteria. The QuickFISH®assay was time-saving and showed high concordance with the reference method, 94.8% (95% CI 88.4–98.3), when the causative agent was covered by the QuickFISH® assay.

    Conclusions: The use of the commercial assays may shorten the time to identification of causative agents in bloodstream infections and can be a good complement to the current clinical routine diagnostics. Nevertheless, the performance of the commercial assays is considerably affected by the characteristics of the causative agents.

  • 18.
    Pylkkänen, Paavo
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. University of Helsinki, Finland.
    Henry Stapp Vs. David Bohm on Mind, Matter, and Quantum Mechanics2019Ingår i: Activitas Nervosa Superior: Journal for Neuroscience and Cognitive Research, ISSN 1802-9698, Vol. 61, nr 1-2, s. 48-50Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This paper briefly discusses some of David Bohm’s views on mind and matter and suggests that they allow for a stronger possibility for conscious free will to influence quantum dynamics than Henry Stapp’s approach.

  • 19.
    Sikka, Pilleriin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Centre for Cognitive Neuroscience, Department of Psychology, University of Turku, Finland.
    How to Study Dream Experiences2019Ingår i: Dreams: Understanding Biology, Psychology, and Culture Volume 1 / [ed] Robert J. Hoss, Katja Valli, Robert P. Gongloff, Santa Barbara, CA: Greenwood, an Imprint of ABC-CLIO, LLC , 2019, 1, s. 153-166Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    In the scientific study of dreams, as in the scientific study of any other topic, it is important to first clearly define the phenomenon one is investigating. The definition determines what exactly is being studied. Then, the methods for collecting and analyzing data regarding this phenomenon need to be chosen. These methods determine what kind of results are obtained, to what extent the results reflect the phenomenon of interest, and whether the results can be trusted. This chapter gives an overview of how dream experiences are scientifically studied: how dreams and dreaming are defined, what kinds of methods are used to collect and analyze dream data, and what aspects need to be considered when conducting and reading studies that investigate dream experiences (see also Kahan & Horton, 2012, and Zadra & Domhoff, 2017).

    Publikationen är tillgänglig i fulltext från 2020-02-01 00:01
  • 20.
    Kotta, Jonne
    et al.
    Estonian Marine Institute, University of Tartu, Tallinn, Estonia.
    Vanhatalo, Jarno
    Department of Mathematics and Statistics and Organismal and Evolutionary Biology Research Program, University of Helsinki, Helsinki, Finland.
    Jänes, Holger
    Estonian Marine Institute, University of Tartu, Tallinn, Estonia / Centre for Integrative Ecology, Deakin University, Melbourne, Victoria, Australia.
    Orav-Kotta, Helen
    Estonian Marine Institute, University of Tartu, Tallinn, Estonia.
    Rugiu, Luca
    Department of Biology, University of Turku, Turku, Finland.
    Jormalainen, Veijo
    Department of Biology, University of Turku, Turku, Finland.
    Bobsien, Ivo
    GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
    Viitasalo, Markku
    Finnish Environment Institute, Helsinki, Finland.
    Virtanen, Elina
    Finnish Environment Institute, Helsinki, Finland.
    Nyström Sandman, Antonia
    AquaBiota Water Research, Stockholm, Sweden.
    Isaeus, Martin
    AquaBiota Water Research, Stockholm, Sweden.
    Leidenberger, Sonja
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Jonsson, Per R.
    Department of Marine Sciences – Tjärnö, University of Gothenburg, Tjärnö, Strömstad, Sweden.
    Johannesson, Kerstin
    Department of Marine Sciences – Tjärnö, University of Gothenburg, Tjärnö, Strömstad, Sweden.
    Integrating experimental and distribution data to predict future species patterns2019Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, artikel-id 1821Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Predictive species distribution models are mostly based on statistical dependence between environmental and distributional data and therefore may fail to account for physiological limits and biological interactions that are fundamental when modelling species distributions under future climate conditions. Here, we developed a state-of-the-art method integrating biological theory with survey and experimental data in a way that allows us to explicitly model both physical tolerance limits of species and inherent natural variability in regional conditions and thereby improve the reliability of species distribution predictions under future climate conditions. By using a macroalga-herbivore association (Fucus vesiculosus - Idotea balthica) as a case study, we illustrated how salinity reduction and temperature increase under future climate conditions may significantly reduce the occurrence and biomass of these important coastal species. Moreover, we showed that the reduction of herbivore occurrence is linked to reduction of their host macroalgae. Spatial predictive modelling and experimental biology have been traditionally seen as separate fields but stronger interlinkages between these disciplines can improve species distribution projections under climate change. Experiments enable qualitative prior knowledge to be defined and identify cause-effect relationships, and thereby better foresee alterations in ecosystem structure and functioning under future climate conditions that are not necessarily seen in projections based on non-causal statistical relationships alone.

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