On the performance of four methods for the numerical solution of ecologically realistic size-structured population models

Size-structured population models (SSPMs) are widely used in ecology to account for intraspecific variation in body size. Three characteristic features of size-structured populations are the dependence of life histories on the entire size distribution, intrinsic population renewal through the birth of new individuals, and the potential accumulation of individuals with similar body sizes due to determinate or stunted growth. Because of these three features, numerical methods that work well for structurally similar transport equations may fail for SSPMs and other transport-dominated models with high ecological realism, and thus their computational performance needs to be critically evaluated. Here, we compare the performance of four numerical solution schemes, the fixed-mesh upwind (FMU) method, the moving-mesh upwind (MMU) method, the characteristic method (CM), and the Escalator Boxcar Train (EBT) method, in numerically solving three reference problems that are representative of ecological systems in the animal and plant kingdoms. The MMU method is here applied for the first time to SSPMs, whereas the three other methods have been employed by other authors. Our results show that the EBT method performs best, except for one of the three reference problems, in which size-asymmetric competition affects individual growth rates. For that reference problem, the FMU method performs best, closely followed by the MMU method. Surprisingly, the CM method does not perform well for any of the three reference problems. We conclude that life-history features should be considered when choosing numerical method

Development and psychometric testing of a barriers to HIV testing scale among individuals with HIV infection in Sweden; The Barriers to HIV testing scale-Karolinska version

© 2015 Wiklander et al. Background: Barriers to HIV testing experienced by individuals at risk for HIV can result in treatment delay and further transmission of the disease. Instruments to systematically measure barriers are scarce, but could contribute to improved strategies for HIV testing. Aims of this study were to develop and test a barriers to HIV testing scale in a Swedish context. Methods: An 18-item scale was developed, based on an existing scale with addition of six new items related to fear of the disease or negative consequences of being diagnosed as HIV-infected. Items were phrased as statements about potential barriers with a three-point response format representing not important, somewhat important, and very important. The scale was evaluated regarding missing values, floor and ceiling effects, exploratory factor analysis, and internal consistencies. Results: The questionnaire was completed by 292 adults recently diagnosed with HIV infection, of whom 7 were excluded (≥9 items missing) and 285 were included (≥12 items completed) in the analyses. The participants were 18-70 years old (mean 40.5, SD 11.5), 39 % were females and 77 % born outside Sweden. Routes of transmission were heterosexual transmission 63 %, male to male sex 20 %, intravenous drug use 5 %, blood product/transfusion 2 %, and unknown 9 %. All scale items had <3 % missing values. The data was feasible for factor analysis (KMO = 0.92) and a four-factor solution was chosen, based on level of explained common variance (58.64 %) and interpretability of factor structure. The factors were interpreted as; personal consequences, structural barriers, social and economic security, and confidentiality. Ratings on the minimum level (suggested barrier not important) were common, resulting in substantial floor effects on the scales. The scales were internally consistent (Cronbach's aα 0.78-0.91). Conclusions: This study gives preliminary evidence of the scale being feasible, reliable and valid to identify different types of barriers to HIV testing

Glial nuclear aggregates of superoxide dismutase-1 are regularly present in patients with amyotrophic lateral sclerosis

The most common cause of amyotrophic lateral sclerosis (ALS) is mutations in superoxide dismutase-1 (SOD1). Since there is evidence for the involvement of non-neuronal cells in ALS, we searched for signs of SOD1 abnormalities focusing on glia. Spinal cords from nine ALS patients carrying SOD1 mutations, 51 patients with sporadic or familial ALS who lacked such mutations, and 46 controls were examined by immunohistochemistry. A set of anti-peptide antibodies with specificity for misfolded SOD1 species was used. Misfolded SOD1 in the form of granular aggregates was regularly detected in the nuclei of ventral horn astrocytes, microglia, and oligodendrocytes in ALS patients carrying or lacking SOD1 mutations. There was negligible staining in neurodegenerative and non-neurological controls. Misfolded SOD1 appeared occasionally also in nuclei of motoneurons of ALS patients. The results suggest that misfolded SOD1 present in glial and motoneuron nuclei may generally be involved in ALS pathogenesis

Biodiversity loss through speciation collapse: Mechanisms, warning signals, and possible rescue

Speciation is the process that generates biodiversity, but recent empirical findings show that it can also fail, leading to the collapse of two incipient species into one. Here, we elucidate the mechanisms behind speciation collapse using a stochastic individual-based model with explicit genetics. We investigate the impact of two types of environmental disturbance: deteriorated visual conditions, which reduce foraging ability and impede mate choice, and environmental homogenization, which restructures ecological niches. We find that: (1) Species pairs can collapse into a variety of forms including new species pairs, monomorphic or polymorphic generalists, or single specialists. Notably, polymorphic generalist forms may be a transient stage to a monomorphic population; (2) Environmental restoration enables species pairs to re-emerge from single generalist forms, but not from single specialist forms; (3) Speciation collapse is up to four orders of magnitude faster than speciation, while the re-emergence of species pairs can be as slow as de novo speciation; (4) While speciation collapse can be predicted from either demographic, phenotypic, or genetic signals, observations of phenotypic changes allow the most general and robust warning signal of speciation collapse. We conclude that factors altering ecological niches can reduce biodiversity by reshaping the ecosystem's evolutionary attractors

Branch Thinning and the Large-Scale, Self-Similar Structure of Trees

Branch formation in trees has an inherent tendency toward exponential growth, but exponential growth in the number of branches cannot continue indefinitely. It has been suggested that trees balance this tendency toward expansion by also losing branches grown in previous growth cycles. Here, we present a model for branch formation and branch loss during ontogeny that builds on the phenomenological assumption of a branch carrying capacity. The model allows us to derive approximate analytical expressions for the number of tips on a branch, the distribution of growth modules within a branch, and the rate and size distribution of tree wood litter produced. Although limited availability of data makes empirical corroboration challenging, we show that our model can fit field observations of red maple (Acer rubrum) and note that the age distribution of discarded branches predicted by our model is qualitatively similar to an empirically observed distribution of dead and abscised branches of balsam poplar (Populus balsamifera). By showing how a simple phenomenological assumption—that the number of branches a tree can maintain is limited—leads directly to predictions on branching structure and the rate and size distribution of branch loss, these results potentially enable more explicit modeling of woody tissues in ecosystems worldwide, with implications for the buildup of flammable fuel, nutrient cycling, and understanding of plant growth

libpspm: A feature-rich numerical package for solving physiologically structured population models

For a vast majority of organisms, life-history processes depend on their physiological state, such as body size, as well as on their environment. Size-structured population models, or more generally, physiologically structured population models (PSPMs), have emerged as powerful tools for modelling the population dynamics of organisms, as they account for the dependences of growth, mortality, and fecundity rates on an organism’s physiological state and capture feedbacks between a population’s structure and its environment, including all types of density regulation. However, despite their widespread appeal across biological disciplines, few numerical packages exist for solving PSPMs in an accessible and computationally efficient way. The main reason for this is that PSPMs typically involve solving partial differential equations (PDEs), and no single numerical method works universally best, or even at all, for all PDEs. Here, we present libpspm, a general-purpose numerical library for solving user-defined PSPMs. libpspm provides eight different methods for solving the PDEs underlying PSPMs, including four semi-implicit solvers that can be used for solving stiff problems. Users can choose the desired method without changing the code specifying the PSPM. libpspm allows for predicting the dynamics of multiple physiologically structured or unstructured species, each of which can have its own distinct set of physiological states and demographic functions. By separating model definition from model solution, libpspm can make PSPM-based modelling accessible to non-specialists and thus promote the widespread adoption of PSPMs

Differentiation and displacement: Unpicking the relationship between accounts of illness and social structure

This article seeks to unpack the relationship between social structure and accounts of illness. Taking dentine hypersensitivity as an example, this article explores the perspective that accounts of illness are sense-making processes that draw on a readily available pool of meaning. This pool of meaning is composed of a series of distinctions that make available a range of different lines of communication and action about such conditions. Such lines of communication are condensed and preserved over time and are often formed around a concept and its counter concept. The study of such processes is referred to as semantic analysis and involves drawing on the tools and techniques of conceptual history. This article goes on to explore how the semantics of dentine hypersensitivity developed. It illustrates how processes of social differentiation led to the concept being separated from the more dominant concept of dentine sensitivity and how it was medicalised, scientised and economised. In short, this study seeks to present the story of how society has developed a specific language for communicating about sensitivity and hypersensitivity in teeth. In doing so, it proposes that accounts of dentine hypersensitivity draw on lines of communication that society has preserved over time

Barriers to HIV testing as reported by individuals newly diagnosed with HIV infection in Sweden

Despite the availability of free and anonymous HIV testing almost 60% of Swedish patients are diagnosed late. Identifying predictors of different types of barriers could inform policy makers and health care of interventions to increase testing where needed. This cross-sectional study aimed to describe and analyze barriers to HIV testing as reported by Swedish patients newly diagnosed with HIV infection. N = 285 patients completed the 18-item Barriers to HIV Testing Scale - Karolinska Version. Descriptive analysis and logistic regressions were performed to assess the prevalence of barriers and to identify predictors for the different investigated barriers. Barriers to testing were reported by 60%. Approximately 67% of patients originating from Sweden, 50% from Sub-Saharan Africa and 75% from Eastern European/East Asian countries reported barriers. Patients who were younger and patients who self-initiated HIV testing, had greater odds of reporting a barrier than older individuals and those who were offered a test through screening or by a healthcare professional. To counteract barriers that still exist on an individual level, healthcare-initiated HIV testing could be offered more broadly and information about risks for transmission and effectiveness of HIV treatment still needs to be disseminated among both people born in Sweden and different migrant groups