| 1. |
- Andersson, Claes, 1987, et al.
(författare)
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A Bayesian hierarchical point process model for epidermal nerve fiber patterns
- 2019
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Ingår i: Mathematical Biosciences. - : Elsevier BV. - 1879-3134 .- 0025-5564. ; 313, s. 48-60
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Tidskriftsartikel (refereegranskat)abstract
- We introduce the Thomas process in a Bayesian hierarchical setting as a model for point pattern data with a nested structure. This model is applied to a nerve fiber data set which consists of several point patterns of nerve entry points from 47 subjects divided into 3 groups, where the grouping is based on the diagnosed severity of a certain nerve disorder. The modeling assumption is that each point pattern is a realization of a Thomas process, with parameter values specific to the subject. These parameter values are in turn assumed to come from distributions that depend on which group the subject belongs to. To fit the model, we construct an MCMC algorithm, which is evaluated in a simulation study. The results of the simulation study indicate that the group level mean of each parameter is well estimated, but that the estimation of the between subject variance is more challenging. When fitting the model to the nerve fiber data, we find that the structure within clusters appears to be the same in all groups, but that the number of clusters decreases with the progression of the nerve disorder.
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| 2. |
- Andersson, Claes, 1973, et al.
(författare)
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An evolutionary developmental approach to cultural evolution
- 2014
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Ingår i: Current Anthropology. - : University of Chicago Press. - 0011-3204 .- 1537-5382. ; 55:2, s. 154-174
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Tidskriftsartikel (refereegranskat)abstract
- Evolutionary developmental theories in biology see the processes and organization of organisms as crucial for understanding the dynamic behavior of organic evolution. Darwinian forces are seen as necessary but not sufficient for explaining observed evolutionary patterns. We here propose that the same arguments apply with even greater force to culture vis-à-vis cultural evolution. In order not to argue entirely in the abstract, we demonstrate the proposed approach by combining a set of different models into a provisional synthetic theory, and by applying this theory to a number of short case studies. What emerges is a set of concepts and models that allow us to consider entirely new types of explanations for the evolution of cultures. For example we see how feedback relations - both within societies and between societies and their ecological environment - have the power to shape evolutionary history in profound ways. The ambition here is not to produce a definite statement on what such a theory should look like but rather to propose a starting point along with an argumentation and demonstration of its potential.
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| 3. |
- Andersson, Claes, 1973, et al.
(författare)
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Developing of the future: scaffolded Darwinism in societal evolution
- 2014
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Ingår i: Behavioral and Brain Sciences. - 0140-525X .- 1469-1825. ; 37:4, s. 417-418
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Tidskriftsartikel (refereegranskat)abstract
- We sympathize with the project of a synthetic approach for devising a "theory of intentional change" and agree that Darwinism should be central in such a theory. But Darwinism is not the only process of evolution that needs to be included. Evolutionary biology itself has taken such a turn recently, with the emergence of developmental evolutionary approaches.
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| 4. |
- Andersson, Claes, 1987, et al.
(författare)
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Discovering early diabetic neuropathy from epidermal nerve fiber patterns
- 2016
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Ingår i: Statistics in Medicine. - : Wiley. - 0277-6715 .- 1097-0258. ; 35:24, s. 4427-4442
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Tidskriftsartikel (refereegranskat)abstract
- Epidermal nerve fibre (ENF) density and morphology are used to study small fibre involvement in diabetic, HIV, chemotherapy induced and other neuropathies. ENF density and summed length of ENFs per epidermal surface area are reduced, and ENFs may appear more clustered within the epidermis in subjects with small fibre neuropathy than in healthy subjects. Therefore, it is important to understand the spatial structure of ENFs. In this paper, we compare the ENF patterns between healthy subjects and subjects suffering from mild diabetic neuropathy. The study is based on suction skin blister specimens from the right foot of 32 healthy subjects and eight subjects with mild diabetic neuropathy. We regard the ENF entry point (location where the trunks of a nerve enters the epidermis) and ENF end point (termination of the nerve fibres) patterns as realizations of spatial point processes, and develop tools that can be used in the analysis and modelling of ENF patterns. We use spatial summary statistics and shift plots and define a new tool, reactive territory, to study the spatial patterns and to compare the patterns of the two groups. We will also introduce a simple model for these data in order to understand the growth process of the nerve fibres.
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| 5. |
- Andersson, Claes, 1973, et al.
(författare)
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Fidelity and the Speed of the Treadmill: The Combined Impact of Population Size, Transmission Fidelity, and Selection on the Accumulation of Cultural Complexity
- 2016
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Ingår i: American Antiquity. - : Cambridge University Press (CUP). - 0002-7316 .- 2325-5064. ; 81:3, s. 576-590
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Tidskriftsartikel (refereegranskat)abstract
- Human culture signifies the emergence of an entirely new domain of existence: an event in natural history that is paralleled only by the Cambrian Explosion in terms of creativity and scope. The question of how human culture as opposed to its animal counter parts came to become open-endedly creative and cumulative is therefore one of wide and general scientific importance. Several causal factors have been proposed to date to explain this unique quality, including population size, transmission fidelity, pedagogy, and creativity. Inquiries, however, tend to focus exclusively on one factor at a time, leaving us blind to important issues regarding their relative roles and combined action. We here combine two models, one focusing on population size and the other on imitation fidelity, as constraints and enablers of evolutionary cumulativity. We explore how these factors interact to promote and inhibit evolutionary cumulativity and how the synthetic model compares to the original models individually and to empirical and experimental data. We report several findings that do not emerge in the models that we combine individually. For example, group size is found to be important for small but not for larger groups, an observation that moreover substantially improves agreement with data.
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| 6. |
- Andersson, Claes, 1987, et al.
(författare)
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Hierarchical models for epidermal nerve fiber data
- 2018
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Ingår i: Statistics in Medicine. - : Wiley. - 0277-6715 .- 1097-0258. ; 37:3, s. 357-374
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Tidskriftsartikel (refereegranskat)abstract
- While epidermal nerve fiber (ENF) data have been used to study the effects of small fiber neuropathies through the density and the spatial patterns of the ENFs, little research has been focused on the effects on the individual nerve fibers. Studying the individual nerve fibers might give a better understanding of the effects of the neuropathy on the growth process of the individual ENFs. In this study, data from 32 healthy volunteers and 20 diabetic subjects, obtained from suction induced skin blister biopsies, are analyzed by comparing statistics for the nerve fibers as a whole and for the segments that a nerve fiber is composed of. Moreover, it is evaluated whether this type of data can be used to detect diabetic neuropathy, by using hierarchical models to perform unsupervised classification of the subjects. It is found that using the information about the individual nerve fibers in combination with the ENF counts yields a considerable improvement as compared to using the ENF counts only. Copyright © 2017 John Wiley & Sons, Ltd.
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| 7. |
- Andersson, Claes, 1987, et al.
(författare)
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Inference for cluster point processes with over- or under-dispersed cluster sizes
- 2020
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Ingår i: Statistics and Computing. - : Springer Science and Business Media LLC. - 0960-3174 .- 1573-1375. ; 30, s. 1573-1590
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Tidskriftsartikel (refereegranskat)abstract
- Cluster point processes comprise a class of models that have been used for a wide range of applications. While several models have been studied for the probability density function of the offspring displacements and the parent point process, there are few examples of non-Poisson distributed cluster sizes. In this paper, we introduce a generalization of the Thomas process, which allows for the cluster sizes to have a variance that is greater or less than the expected value. We refer to this as the cluster sizes being over- and under-dispersed, respectively. To fit the model, we introduce minimum contrast methods and a Bayesian MCMC algorithm. These are evaluated in a simulation study. It is found that using the Bayesian MCMC method, we are in most cases able to detect over- and under-dispersion in the cluster sizes. We use the MCMC method to fit the model to nerve fiber data, and contrast the results to those of a fitted Thomas process.
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| 8. |
- Andersson, Claes, 1973, et al.
(författare)
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Societal Systems - Complex or worse?
- 2014
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Ingår i: Futures : The journal of policy, planning and futures studies. - : Elsevier BV. - 0016-3287. ; 63, s. 145-157
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Tidskriftsartikel (refereegranskat)abstract
- The basic observation that we explore in this paper is simple but, we argue, rich in consequences: societal systems combine two qualities that are commonly referred to as complexity and complicatedness. We address the problem that societal systems remain recalcitrant despite the development of powerful approaches for dealing with both of these qualities. The root of this problem we identify to be that the combination between complexity and complicatedness is emergent; i.e. fundamentally and irreducibly different from either quality in isolation. This means that neither class of such approaches can be expected to work well on their own. But it also means that the obvious strategy of combining theory for complexity and complicatedness may be much more challenging than envisioned. In short, systems where complexity and complicatedness is mixed ought to be treated as a distinct class of systems. Noting a connection to what has long been called "wicked problems" we hereby outline such a class of systems that we call "wicked systems". We introduce a simple model and heuristic and discuss some implications for theorizing and modeling.
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| 9. |
- Andersson, Claes, 1987
(författare)
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Spatial analysis and modeling of nerve fiber patterns
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Diabetic neuropathy is a condition associated with diabetes affecting the epidermal nerve fibers (ENFs). This thesis presents analysis methods and models for ENF data, with two main puroposes: to find early signs of diabetic neuropathy and to characterize how this condition changes the nerve fiber structure. Early detection is of interest to be able to take measures to slow down the progression of the condition, and a more detailed description of the changes in the nerve fiber structure could improve the understanding of its underlying mechanisms. The ENF samples are mainly analyzed as point patterns, where the points are the locations where nerve fibers enter the epidermis or terminate. The analysis is partly based on existing summary statistics for point patterns, but we also propose a new summary statistic to quantify the proportion of the skin covered by the nerve fibers. Two cluster processes are introduced as models for the patterns consisting only of the locations where the nerve fibers enter the epidermis. For one of the models, a Bayesian hierarchical method for parameter estimation is proposed. A model for the end points is also presented, and non-spatial models for individual nerve fibers, which are used to perform unsupervised classification of the subjects. From the results we find that while all patterns are aggregated, the level of aggregation tends to increase with increased severity of the neuropathy. The results from the modeling indicate that the increased aggregation is caused by a decrease in the number of clusters, while the structure within clusters appears to be similar in all disease groups. The results from the non-spatial analysis indicate that the nerve fibers from healthy subjects tend to extend further than those from subjects with diabetic neuropathy. The use of methods and models developed in this thesis is not limited to ENF data, but can be applied to point pattern data in general. In particular, the models for the base point patterns and the methods for estimating the parameters of these models are contributions to the point process literature.
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| 10. |
- Andersson, Claes, 1987
(författare)
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Statistical methods for early discovery of diabetic neuropathy using epidermal nerve fiber data
- 2016
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The main aim with the work in this thesis is to increase the understanding of the effects diabetic neuropathy has on the epidermal nerve fibers and thereby find methods to detect the disorder at an earlier stage. Epidermal nerve fibers (ENFs) are small sensory nerve fibers in the skin, sensing heat and pain. Earlier diagnosis of the disorder can help to slow down the progression and delay the symptoms. The data used are skin samples from a group of 32 healthy volunteers and 20 diabetic subjects with differently progressed diabetic neuropathy, in which the nerve fibers have been traced using confocal microscopy. One part of the work is based on methods from spatial statistics, considering the points where the nerve fibers enter the epidermis and where they terminate as realizations of point processes. The point patterns obtained from healthy subjects are compared to those of subjects at an early stage of the neuropathy, in terms of spatial summary statistics, including a new tool to quantify the area of the skin covered by a nerve, the \textit{reactive territory}. Significant differences between the groups are found, that has not previously been reported. Moreover, a point process model for the nerve fiber patterns is proposed, to help the understanding of the growth process of the nerve fibers. In the other part of the work, hierarchical models for the nerve fiber segments are proposed, and used to perform unsupervised classification. The results are evaluated in terms of how well the diabetic subjects are separated from the healthy ones. It is found that the results are considerably improved when including the information about the nerve fiber segments, compared to only using the number of nerve fibers.
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| 11. |
- Andersson, Claes, 1973, et al.
(författare)
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Toward a Macroevolutionary Theory of Human Evolution: The Social Protocell
- 2019
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Ingår i: Biological Theory. - : Springer Science and Business Media LLC. - 1555-5550 .- 1555-5542. ; 14, s. 86-102
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Tidskriftsartikel (refereegranskat)abstract
- Despite remarkable empirical and methodological advances, our theoretical understanding of the evolutionary processes that made us human remains fragmented and contentious. Here, we make the radical proposition that the cultural communities within which Homo emerged may be understood as a novel exotic form of organism. The argument begins from a deep congruence between robust features of Pan community life cycles and protocell models of the origins of life. We argue that if a cultural tradition, meeting certain requirements, arises in the context of such a “social protocell,” the outcome will be an evolutionary transition in individuality whereby traditions and hominins coalesce into a macroscopic bio-socio-technical system, with an organismal organization that is culturally inherited through irreversible fission events on the community level. We refer to the resulting hypothetical evolutionary individual as a “sociont.” The social protocell provides a preadapted source of alignment of fitness interests that addresses a number of open questions about the origins of shared adaptive cultural organization, and the derived genetic (and highly unusual) adaptations that support them. Also, social cooperation between hominins is no longer in exclusive focus since cooperation among traditions becomes salient in this model. This provides novel avenues for explanation. We go on to hypothesize that the fate of the hominin in such a setting would be mutualistic coadaptation into a part-whole relation with the sociont, and we propose that the unusual suite of derived features in Homo is consistent with this hypothesis.
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| 12. |
- Andersson, Claes, 1973, et al.
(författare)
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Wickedness and the anatomy of complexity
- 2018
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Ingår i: Futures. - : Elsevier BV. - 0016-3287. ; 95, s. 118-138
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Tidskriftsartikel (refereegranskat)abstract
- Traditional scientific policy approaches and tools are increasingly seen as inadequate, or even counter-productive, for many purposes. In response to these shortcomings, a new wave of approaches has emerged based on the idea that societal systems are irreducibly complex. The new categories that are thereby introduced – like “complex” or “wicked” – suffer, however, by a lack of shared understanding. We here aim to reduce this confusion by developing a meta-ontological map of types of systems that have the potential to “overwhelm us”: characteristic types of problems, attributions of function, manners of design and governance, and generating and maintaining processes and phenomena. This permits us, in a new way, to outline an inner anatomy of the motley collection of system types that we tend to call “complex”. Wicked problems here emerge as the product of an ontologically distinct and describable type of system that blends dynamical and organizational complexity. The framework is intended to provide systematic meta-theoretical support for approaching complexity and wickedness in policy and design. We also points to a potential causal connection between innovation and wickedness as a basis for further theoretical improvement.
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| 13. |
- Ohlsson, Claes, 1965, et al.
(författare)
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Mild stimulatory effect of a probiotic mix on bone mass when treatment is initiated 1.5 weeks after ovariectomy in mice
- 2021
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Ingår i: American Journal of Physiology-Endocrinology and Metabolism. - : American Physiological Society. - 0193-1849 .- 1522-1555. ; 320:3
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Tidskriftsartikel (refereegranskat)abstract
- Studies in humans and rodents show that probiotic bacteria can protect from bone loss caused by sex steroid deficiency. We showed earlier that a mixture of three probiotic bacteria, Lacticaseibacillus paracasei DSM13434, Lactiplantibacillus plantarum DSM 15312, and DSM 15313 (L. mix), protects mice from ovariectomy (ovx)-induced bone loss when treatment was started 2 wk before sham and ovx surgery. In addition, the same probiotic treatment protected against lumbar spine bone loss in early postmenopausal women. In the present study, we wanted to evaluate the therapeutic potential of L. mix by starting treatment 1.5 wk after ovx when most of the rapid bone loss as a result of estrogen deficiency has already occurred. Treatment with L. mix for 5.5 wk increased the trabecular thickness but not the trabecular number in the proximal metaphyseal region of tibia compared with vehicle treatment. Cortical thickness and cortical area of the middiaphyseal part of the tibia were significantly decreased in ovx mice but not in L. mix-treated ovx mice. The bone-protective effects of L. mix in ovx mice were associated with a protection against ovx-induced reduction of the frequency of regulatory T-cells and of the expression of Tgfb in the bone marrow. In conclusion, the probiotic L. mix exerted a mild stimulatory effect on trabecular and cortical bone width when treatment is initiated 1.5 wk after ovariectomy in mice. This effect was associated with effects on bone-protecting regulatory T-cells. The results suggest that L. mix may exert beneficial effects on bone mass when treatment is started after ovariectomy. NEW & NOTEWORTHY The probiotic L. mix exerted a mild stimulatory effect on trabecular and cortical bone width when treatment is initiated 1.5 wk after ovariectomy in mice. This effect was associated with effects on bone-protecting regulatory T-cells. The results suggest that L. mix may exert beneficial effects on bone mass when treatment is started after ovariectomy.
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| 14. |
- Ohlsson, Claes, 1965, et al.
(författare)
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Phosphorylation site S122 in estrogen receptor α has a tissue-dependent role in female mice
- 2020
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Ingår i: FASEB Journal. - 0892-6638 .- 1530-6860. ; 34, s. 15991-16002
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Tidskriftsartikel (refereegranskat)abstract
- Estrogen treatment increases bone mass and reduces fat mass but is associated with adverse effects in postmenopausal women. Knowledge regarding tissue-specific estrogen signaling is important to aid the development of new tissue-specific treatments. We hypothesized that the posttranslational modification phosphorylation in estrogen receptor alpha (ERα) may modulate ERα activity in a tissue-dependent manner. Phosphorylation of site S122 in ERα has been shown in vitro to affect ERα activity, but the tissue-specific role in vivo is unknown. We herein developed and phenotyped a novel mouse model with a point mutation at the phosphorylation site 122 in ERα (S122A). Female S122A mice had increased fat mass and serum insulin levels but unchanged serum sex steroid levels, uterus weight, bone mass, thymus weight, and lymphocyte maturation compared to WT mice. In conclusion, phosphorylation site S122 in ERα has a tissue-dependent role with an impact specifically on fat mass in female mice. This study is the first to demonstrate in vivo that a phosphorylation site in a transactivation domain in a nuclear steroid receptor modulates the receptor activity in a tissue-dependent manner.
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| 15. |
- Selvin, Tove, et al.
(författare)
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Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model
- 2022
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the immunological effects of chemotherapy is of great importance, especially now that we have entered an era where ever-increasing pre-clinical and clinical efforts are put into combining chemotherapy and immunotherapy to combat cancer. Single-cell RNA sequencing (scRNA-seq) has proved to be a powerful technique with a broad range of applications, studies evaluating drug effects in co-cultures of tumor and immune cells are however scarce. We treated a co-culture comprised of human colorectal cancer (CRC) cells and peripheral blood mononuclear cells (PBMCs) with the nucleoside analogue trifluridine (FTD) and used scRNA-seq to analyze posttreatment gene expression profiles in thousands of individual cancer and immune cells concurrently. ScRNA-seq recapitulated major mechanisms of action previously described for FTD and provided new insight into possible treatment-induced effects on T-cell mediated antitumor responses.
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| 16. |
- Törnberg, Petter, 1987, et al.
(författare)
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Modeling the emergence of affective polarization in the social media society
- 2021
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 16:10 October
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Tidskriftsartikel (refereegranskat)abstract
- Rising political polarization in recent decades has hampered and gridlocked policymaking, as well as weakened trust in democratic institutions. These developments have been linked to the idea that new media technology fosters extreme views and political conflict by facilitating self-segregation into “echo chambers” where opinions are isolated and reinforced. This opinion-centered picture has recently been challenged by an emerging political science literature on “affective polarization”, which suggests that current polarization is better understood as driven by partisanship emerging as a strong social identity. Through this lens, politics has become a question of competing social groups rather than differences in policy position. Contrary to the opinion-centered view, this identity-centered perspective has not been subject to dynamical formal modeling, which generally permits hypotheses about micro-level explanations for macro-level phenomena to be systematically tested and explored. We here propose a formal model that links new information technology to affective polarization via social psychological mechanisms of social identity. Our results suggest that new information technology catalyzes affective polarization by lowering search and interaction costs, which shifts the balance between centrifugal and centripetal forces of social identity. We find that the macro-dynamics of social identity is characterized by two stable regimes on the societal level: one fluid regime, in which identities are weak and social connections heterogeneous, and one solid regime in which identities are strong and groups homogeneous. We also find evidence of hysteresis, meaning that a transition into a fragmented state is not readily reversed by again increasing those costs. This suggests that, due to systemic feedback effects, if polarization passes certain tipping points, we may experience run-away political polarization that is highly difficult to reverse.
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