An agent-based approach to immune modelling

This study focuses on trying to understand why the range of experience with respect to HIV infection is so diverse, especially as regards to the latency period. The challenge is to determine what assumptions can be made about the nature of the experience of antigenic invasion and diversity that can be modelled, tested and argued plausibly. To investigate this, an agent-based approach is used to extract high-level behaviour which cannot be described analytically from the set of interaction rules at the cellular level. A prototype model encompasses local variation in baseline properties contributing to the individual disease experience and is included in a network which mimics the chain of lymphatic nodes. Dealing with massively multi-agent systems requires major computational efforts. However, parallelisation methods are a natural consequence and advantage of the multi-agent approach. These are implemented using the MPI library

Solar Grand Minima and random fluctuations in dynamo parameters

We consider to what extent the long-term dynamics of cyclic solar activity in the form of Grand Minima can be associated with random fluctuations of the parameters governing the solar dynamo. We consider fluctuations of the alpha-coefficient in the conventional Parker migratory dynamo, and also in slightly more sophisticated dynamo models, and demonstrate that they can mimic the gross features of the phenomenon of the occurrence of Grand Minima over a suitable parameter range. The temporal distribution of these Grand Minima appears chaotic, with a more or less exponential waiting time distribution, typical of Poisson processes. In contrast however, the available reconstruction of Grand Minima statistics based on cosmogenic isotope data demonstrates substantial deviations from this exponential law. We were unable to reproduce the non-Poissonic tail of the waiting time distribution either in the framework of a simple alpha-quenched Parker model, or in its straightforward generalization, nor in simple models with feedback on the differential rotation. We suggest that the disagreement may only be apparent and is plausibly related to the limited observational data, and that the observations and results of numerical modeling can be consistent and represent physically similar dynamo regimes.Comment: Solar Physics, in prin

A jump-growth model for predator-prey dynamics: derivation and application to marine ecosystems

This paper investigates the dynamics of biomass in a marine ecosystem. A stochastic process is defined in which organisms undergo jumps in body size as they catch and eat smaller organisms. Using a systematic expansion of the master equation, we derive a deterministic equation for the macroscopic dynamics, which we call the deterministic jump-growth equation, and a linear Fokker-Planck equation for the stochastic fluctuations. The McKendrick--von Foerster equation, used in previous studies, is shown to be a first-order approximation, appropriate in equilibrium systems where predators are much larger than their prey. The model has a power-law steady state consistent with the approximate constancy of mass density in logarithmic intervals of body mass often observed in marine ecosystems. The behaviours of the stochastic process, the deterministic jump-growth equation and the McKendrick--von Foerster equation are compared using numerical methods. The numerical analysis shows two classes of attractors: steady states and travelling waves.Comment: 27 pages, 4 figures. Final version as published. Only minor change

Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content

Article purchased; Published online: 3 August 2017Cassava (Manihot esculenta (L.) Crantz) is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Dry matter content and micronutrient density, particularly of provitamin A, traits that are negatively correlated, are among the primary selection objectives in cassava breeding. This study aimed at identifying genetic markers associated with these traits and uncovering the potential underlying cause of their negative correlation - whether linkage and/or pleiotropy. A genome-wide association mapping using 672 clones genotyped at 72,279 SNP loci was carried out. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness was identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that co-located with the 24.1 Mbp peak for carotenoid content was identified. Haplotypes at these loci explained a large proportion of the phenotypic variability. Evidence of mega-base-scale linkage disequilibrium around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white- and yellow-root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid (phytoene synthase) and starch biosynthesis (UDP-glucose pyrophosphorylase and sucrose synthase) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate on the genetic architecture of carotenoids and dry matter in cassava and provides an opportunity to accelerate genetic improvement of these traits

Relations between lipoprotein(a) concentrations, LPA genetic variants, and the risk of mortality in patients with established coronary heart disease: a molecular and genetic association study

Background: Lipoprotein(a) concentrations in plasma are associated with cardiovascular risk in the general population. Whether lipoprotein(a) concentrations or LPA genetic variants predict long-term mortality in patients with established coronary heart disease remains less clear. Methods: We obtained data from 3313 patients with established coronary heart disease in the Ludwigshafen Risk and Cardiovascular Health (LURIC) study. We tested associations of tertiles of lipoprotein(a) concentration in plasma and two LPA single-nucleotide polymorphisms ([SNPs] rs10455872 and rs3798220) with all-cause mortality and cardiovascular mortality by Cox regression analysis and with severity of disease by generalised linear modelling, with and without adjustment for age, sex, diabetes diagnosis, systolic blood pressure, BMI, smoking status, estimated glomerular filtration rate, LDL-cholesterol concentration, and use of lipid-lowering therapy. Results for plasma lipoprotein(a) concentrations were validated in five independent studies involving 10 195 patients with established coronary heart disease. Results for genetic associations were replicated through large-scale collaborative analysis in the GENIUS-CHD consortium, comprising 106 353 patients with established coronary heart disease and 19 332 deaths in 22 studies or cohorts. Findings: The median follow-up was 9·9 years. Increased severity of coronary heart disease was associated with lipoprotein(a) concentrations in plasma in the highest tertile (adjusted hazard radio [HR] 1·44, 95% CI 1·14–1·83) and the presence of either LPA SNP (1·88, 1·40–2·53). No associations were found in LURIC with all-cause mortality (highest tertile of lipoprotein(a) concentration in plasma 0·95, 0·81–1·11 and either LPA SNP 1·10, 0·92–1·31) or cardiovascular mortality (0·99, 0·81–1·2 and 1·13, 0·90–1·40, respectively) or in the validation studies. Interpretation: In patients with prevalent coronary heart disease, lipoprotein(a) concentrations and genetic variants showed no associations with mortality. We conclude that these variables are not useful risk factors to measure to predict progression to death after coronary heart disease is established. Funding: Seventh Framework Programme for Research and Technical Development (AtheroRemo and RiskyCAD), INTERREG IV Oberrhein Programme, Deutsche Nierenstiftung, Else-Kroener Fresenius Foundation, Deutsche Stiftung für Herzforschung, Deutsche Forschungsgemeinschaft, Saarland University, German Federal Ministry of Education and Research, Willy Robert Pitzer Foundation, and Waldburg-Zeil Clinics Isny

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Open data from the third observing run of LIGO, Virgo, KAGRA, and GEO

The global network of gravitational-wave observatories now includes five detectors, namely LIGO Hanford, LIGO Livingston, Virgo, KAGRA, and GEO 600. These detectors collected data during their third observing run, O3, composed of three phases: O3a starting in 2019 April and lasting six months, O3b starting in 2019 November and lasting five months, and O3GK starting in 2020 April and lasting two weeks. In this paper we describe these data and various other science products that can be freely accessed through the Gravitational Wave Open Science Center at https://gwosc.org. The main data set, consisting of the gravitational-wave strain time series that contains the astrophysical signals, is released together with supporting data useful for their analysis and documentation, tutorials, as well as analysis software packages

Achieving sustainable natural resource management outcomes on the ground: the key elements of stakeholder involvement

Achieving outcomes on the ground is crucial to sustainable natural resource management. Stakeholder involvement is not only a central tenet of sustainable management, it also contributes to outcomes through engendering commitment. This article explores, through three natural resource sectors in Australia, the elements of such involvement contributing to commitment and hence outcomes. The activities of three advisorylconsultative groups from the protected area, agricultural and mining sectors provided the case studies. It is evident from these caseS that perceptions of fairness, identifying a planning process as the 'place to be' and realising mutual benefits were the key elements. Natural reSource managers and opinion leaders can foster these elements by building partnerships, managing impressions and allowing suffiCient time for planning and collaboration

Molecular characterization of the variable domains of an alphaIIbbeta3-specific immunoglobulin M kappa platelet cold agglutinin in a follicular lymphoma patient with treatment refractory autoimmune thrombocytopenia: idiotypic overlap between alphaIIbbeta3 integrin antibodies.

BACKGROUND - Cold hemagglutinins are generally immunoglobulin M (IgM) kappa antibodies reactive at temperatures below 37 degrees C and if of high titer may cause hemolysis. Platelet (PLT) cold agglutinins (CAs) are rare and poorly characterized. A detailed molecular characterization of the variable domains of a pathologic, PLT-reactive, CA is presented. CASE REPORT - A 70-year-old woman was admitted with rectal bleeding accompanied by widespread petechiae, bruising, tongue and buccal mucosa bleeding, and epistaxes and proved refractory to HLA- and HPA-matched PLTs. Detailed investigation showed monoclonal heavy-chain gene rearrangement with an IgM paraprotein of 3.3 g per L and a trace of kappa Bence Jones protein in the urine, compatible with a diagnosis of secretory B-cell non-Hodgkin's lymphoma (B-NHL). PLT antibody (PAIg) investigations revealed a potent IgM kappa PLT CA. Sequencing of the rearranged variable domain genes of the malignant clone together with idiotype-specific antibodies obtained by DNA-based immunization of rabbits and matrix-assisted laser desorption/ionization-time-of-flight analysis of the PAIgM provided a irrefutable link between the thrombocytopenia, the IgM paraprotein, and the PAIgM against alphaIIbbeta3. The thrombocytopenia and bleeding were refractory to standard treatment and PLT transfusion, but treatment with rituximab resulted in a recovery of the PLT count and a complete remission of B-NHL. CONCLUSION - The IgM kappa paraprotein derived from the malignant B-cell clone was a potent and clinically significant CA against alphaIIbbeta3. The testing for PLT CAs in patients with a paraprotein and refractory to matched PLTs may aid the selection of appropriate treatment.</p