Numerical analysis of subcritical Hopf bifurcations in the two-dimensional FitzHugh-Nagumo model.

It had been shown that the transition from a rigidly rotating spiral wave to a meandering spiral wave is via a Hopf bifurcation. Many studies have shown that these bifurcations are supercritical, but, by using simulations in a comoving frame of reference, we present numerical results which show that subcritical bifurcations are also present within FitzHugh-Nagumo. We show that a hysteresis region is present at the boundary of the rigidly rotating spiral waves and the meandering spiral waves for a particular set of parameters, a feature of FitzHugh-Nagumo that has previously not been reported. Furthermore, we present a evidence that this bifurcation is highly sensitive to initial conditions, and it is possible to convert one solution in the hysteresis loop to the other.

Non-random sampling leads to biased estimates of transcriptome association.

Integration of independent data resources across -omics platforms offers transformative opportunity for novel clinical and biological discoveries. However, application of emerging analytic methods in the context of selection bias represents a noteworthy and pervasive challenge. We hypothesize that combining differentially selected samples for integrated transcriptome analysis will lead to bias in the estimated association between predicted expression and the trait. Our results are based on in silico investigations and a case example focused on body mass index across four well-described cohorts apparently derived from markedly different populations. Our findings suggest that integrative analysis can lead to substantial relative bias in the estimate of association between predicted expression and the trait. The average estimate of association ranged from 51.3% less than to 96.7% greater than the true value for the biased sampling scenarios considered, while the average error was - 2.7% for the unbiased scenario. The corresponding 95% confidence interval coverage rate ranged from 46.4% to 69.5% under biased sampling, and was equal to 75% for the unbiased scenario. Inverse probability weighting with observed and estimated weights is applied as one corrective measure and appears to reduce the bias and improve coverage. These results highlight a critical need to address selection bias in integrative analysis and to use caution in interpreting findings in the presence of different sampling mechanisms between groups.

Phenotypic switch to eczema in patients receiving biologics for plaque psoriasis: a systematic review.

The use of biologic therapies for the treatment of chronic plaque psoriasis has been linked to the development of atopic eczema, amongst other cutaneous adverse events. This can cause diagnostic confusion and create difficulty in the management of patients with plaque psoriasis. The main objective of this systematic review was to review all cases of eczema, including atopic eczema, reported in patients treated with biologics for chronic plaque psoriasis. PubMed, Medline and Embase databases were used to identify studies reporting eczema in patients treated with biologic therapy for chronic plaque psoriasis. A total of 92 patients were identified from 24 studies, with patients treated with either: adalimumab; etanercept; infliximab; ixekizumab; secukinumab; or ustekinumab. Factors common to some reported cases include: a prior history of atopy; eosinophilia; raised serum immunoglobulin E. Twenty-three had documented treatment outcomes; 14 had biologic therapy discontinued or switched. Management strategies included topical or oral corticosteroids, and treatment with alternative systemic agents such as ciclosporin or apremilast. This adverse event occurred in 1.0-12.1% of patients within trial data and observational studies. This review demonstrates that there are consistent reports of a switch to an atopic eczema phenotype from psoriasis in patients taking biologics inhibiting tumour necrosis factor alpha and the interleukin (IL)-17/IL-23 axis. The majority stopped the implicated biologic, but conservative management was successful in some cases. Those with an atopic diathesis may be more at risk. Elucidation of mechanisms and risk factors would contribute to optimal therapy selection for individual patients.

Targeted temperature management in patients with intracerebral haemorrhage, subarachnoid haemorrhage, or acute ischaemic stroke: consensus recommendations.

BACKGROUND: A modified Delphi approach was used to identify a consensus on practical recommendations for the use of non-pharmacological targeted temperature management in patients with intracerebral haemorrhage, subarachnoid haemorrhage, or acute ischaemic stroke with non-infectious fever (assumed neurogenic fever). METHODS: Nine experts in the management of neurogenic fever participated in the process, involving the completion of online questionnaires, face-to-face discussions, and summary reviews, to consolidate a consensus on targeted temperature management. RESULTS: The panel's recommendations are based on a balance of existing evidence and practical considerations. With this in mind, they highlight the importance of managing neurogenic fever using a single protocol for targeted temperature management. Targeted temperature management should be initiated if the patient temperature increases above 37.5°C, once an appropriate workup for infection has been undertaken. This helps prevent prophylactic targeted temperature management use and ensures infection is addressed appropriately. When neurogenic fever is detected, targeted temperature management should be initiated rapidly if antipyretic agents fail to control the temperature within 1 h, and should then be maintained for as long as there is potential for secondary brain damage. The recommended target temperature for targeted temperature management is 36.5-37.5°C. The use of advanced targeted temperature management methods that enable continuous, or near continuous, temperature measurement and precise temperature control is recommended. CONCLUSIONS: Given the limited heterogeneous evidence currently available on targeted temperature management use in patients with neurogenic fever and intracerebral haemorrhage, subarachnoid haemorrhage, or acute ischaemic stroke, a Delphi approach was appropriate to gather an expert consensus. To aid in the development of future investigations, the panel provides recommendations for data gathering.

What's new in psoriasis treatment? An analysis of systematic reviews published in 2015.

This review provides a summary of key findings from 27 systematic reviews of 51 articles first published or indexed during 2015, focusing on the treatment of psoriasis and on precision medicine in psoriasis. The evidence supports weight-loss interventions by dieting and exercise for improvement in disease severity in overweight and obese patients with psoriasis. No significant increased risk of serious infections was reported for the biologic therapies adalimumab, etanercept and ustekinumab compared with appropriate comparators. Evidence could not provide reliable estimates of rare adverse events, emphasizing the need for large prospective registries. Polymorphisms in the tumour necrosis factor (TNF)-α gene may confer improved responses to TNF inhibitor (TNFI) therapy, but the studies to date lack power to detect a true association. From the limited available evidence, multidisciplinary management is both more effective and more satisfactory for patients with psoriasis and psoriatic arthritis than conventional consultations. This summary of reviews provides a succinct guide for clinicians and patients wishing to remain up to date with high-quality evidence for the treatment of psoriasis.

HIV-1-negative female sex workers sustain high cervical IFNɛ, low immune activation, and low expression of HIV-1-required host genes.

Sex workers practicing in high HIV endemic areas have been extensively targeted to test anti-HIV prophylactic strategies. We hypothesize that in women with high levels of genital exposure to semen changes in cervico-vaginal mucosal and/or systemic immune activation will contribute to a decreased susceptibility to HIV-1 infection. To address this question, we assessed sexual activity and immune activation status (in peripheral blood), as well as cellular infiltrates and gene expression in ectocervical mucosa biopsies in female sex workers (FSWs; n=50), as compared with control women (CG; n=32). FSWs had low-to-absent HIV-1-specific immune responses with significantly lower CD38 expression on circulating CD4(+) or CD8(+) T-cells (both: P<0.001) together with lower cervical gene expression of genes associated with leukocyte homing and chemotaxis. FSWs also had increased levels of interferon-ɛ (IFNɛ) gene and protein expression in the cervical epithelium together with reduced expression of genes associated with HIV-1 integration and replication. A correlative relationship between semen exposure and elevated type-1 IFN expression in FSWs was also established. Overall, our data suggest that long-term condomless sex work can result in multiple changes within the cervico-vaginal compartment that would contribute to sustaining a lower susceptibility for HIV-1 infection in the absence of HIV-specific responses.

Plasma brain derived neurotrophic factor (BDNF) and response to ketamine in treatment-resistant depression.

Ketamine produces rapid antidepressant effects in treatment-resistant depression (TRD), but the magnitude of response varies considerably between individual patients. Brain-derived neurotrophic factor (BDNF) has been investigated as a biomarker of treatment response in depression and has been implicated in the mechanism of action of ketamine. We evaluated plasma BDNF and associations with symptoms in 22 patients with TRD enrolled in a randomized controlled trial of ketamine compared to an anaesthetic control (midazolam). Ketamine significantly increased plasma BDNF levels in responders compared to non-responders 240 min post-infusion, and Montgomery-Åsberg Depression Rating Scale (MADRS) scores were negatively correlated with BDNF (r=-0.701, p = 0.008). Plasma BDNF levels at 240 min post-infusion were highly negatively associated with MADRS scores at 240 min (r = -0.897, p=.002), 24 h (r = -0.791, p = 0.038), 48 h (r = -0.944, p = 0.001) and 72 h (r = -0.977, p = 0.010). No associations with BDNF were found for patients receiving midazolam. These data support plasma BDNF as a peripheral biomarker relevant to ketamine antidepressant response.

Palmoplantar contractures in childhood: a rare complication of vascular Ehlers-Danlos syndrome.

Although catastrophic vascular complications in vascular Ehlers-Danlos Syndrome (EDS) are well recognized, other complications such as flexion contractures and tendon nodules are rarely reported and poorly characterized. We report a young man with vascular EDS, who developed flexion contractures and tendon nodules, causing considerable disability. Limited management strategies are available for these complications, which have continued to prove a challenge to management.

What's new in psoriasis? An analysis of guidelines and systematic reviews published in 2009-2010.

This review summarizes key clinical findings from 5 guidelines and 21 systematic reviews on psoriasis published or indexed in the period November 2009 to October 2010. The highlights include the British Association of Dermatologists guidelines on the use of biological interventions in psoriasis, and guidelines on the efficacy and use of acitretin. Biological therapies were reviewed for use in specific patient groups (such as those with hepatitis C) and from a health-economics perspective. Another systematic review focused on outcome measures used to assess the severity of psoriasis. Finally, comorbidities including cardiovascular risk were the topic of four systematic reviews.

Computation of the drift velocity of spiral waves using response functions.

Rotating spiral waves are a form of self-organization observed in spatially extended systems of physical, chemical, and biological nature. In the presence of a small perturbation, the spiral wave's center of rotation and fiducial phase may change over time, i.e., the spiral wave drifts. In linear approximation, the velocity of the drift is proportional to the convolution of the perturbation with the spiral's response functions, which are the eigenfunctions of the adjoint linearized operator corresponding to the critical eigenvalues λ=0,±iω . Here, we demonstrate that the response functions give quantitatively accurate prediction of the drift velocities due to a variety of perturbations: a time dependent, periodic perturbation (inducing resonant drift); a rotational symmetry-breaking perturbation (inducing electrophoretic drift); and a translational symmetry-breaking perturbation (inhomogeneity induced drift) including drift due to a gradient, stepwise, and localized inhomogeneity. We predict the drift velocities using the response functions in FitzHugh-Nagumo and Barkley models, and compare them with the velocities obtained in direct numerical simulations. In all cases good quantitative agreement is demonstrated.

Riding a spiral wave: numerical simulation of spiral waves in a comoving frame of reference.

We describe an approach to numerical simulation of spiral waves dynamics of large spatial extent, using small computational grids.

Prediction based classification for longitudinal biomarkers.

Assessment of circulating CD4 count change over time in HIV-infected subjects on antiretroviral therapy (ART) is a central component of disease monitoring. The increasing number of HIV-infected subjects starting therapy and the limited capacity to support CD4 count testing within resource-limited settings have fueled interest in identifying correlates of CD4 count change such as total lymphocyte count, among others. The application of modeling techniques will be essential to this endeavor due to the typically non-linear CD4 trajectory over time and the multiple input variables necessary for capturing CD4 variability. We propose a prediction based classification approach that involves first stage modeling and subsequent classification based on clinically meaningful thresholds. This approach draws on existing analytical methods described in the receiver operating characteristic curve literature while presenting an extension for handling a continuous outcome. Application of this method to an independent test sample results in greater than 98% positive predictive value for CD4 count change. The prediction algorithm is derived based on a cohort of n = 270 HIV-1 infected individuals from the Royal Free Hospital, London who were followed for up to three years from initiation of ART. A test sample comprised of n = 72 individuals from Philadelphia and followed for a similar length of time is used for validation. Results suggest that this approach may be a useful tool for prioritizing limited laboratory resources for CD4 testing after subjects start antiretroviral therapy.

Alternative stable scroll waves and conversion of autowave turbulence.

Rotating spiral and scroll waves (vortices) are investigated in the FitzHugh-Nagumo model of excitable media. The focus is on a parameter region in which there exists bistability between alternative stable vortices with distinct periods. Response functions are used to predict the filament tension of the alternative scrolls and it is shown that the slow-period scroll has negative filament tension, while the filament tension of the fast-period scroll changes sign within a hysteresis loop. The predictions are confirmed by direct simulations. Further investigations show that the slow-period scrolls display features similar to delayed after-depolarization and tend to develop into turbulence similar to ventricular fibrillation (VF). Scrolls with positive filament tension collapse or stabilize, similar to monomorphic ventricular tachycardia (VT). Perturbations, such as boundary interaction or shock stimulus, can convert the vortex with negative filament tension into the vortex with positive filament tension. This may correspond to transition from VF to VT unrelated to pinning.

Estimating and testing haplotype-trait associations in non-diploid populations.

Malaria is an infectious disease that is caused by a group of parasites of the genus Plasmodium. Characterizing the association between polymorphisms in the parasite genome and measured traits in an infected human host may provide insight into disease aetiology and ultimately inform new strategies for improved treatment and prevention. This, however, presents an analytic challenge since individuals are often multiply infected with a variable and unknown number of genetically diverse parasitic strains. In addition, data on the alignment of nucleotides on a single chromosome, which is commonly referred to as haplotypic phase, is not generally observed. An expectation-maximization algorithm for estimating and testing associations between haplotypes and quantitative traits has been described for diploid (human) populations. We extend this method to account for both the uncertainty in haplotypic phase and the variable and unknown number of infections in the malaria setting. Further extensions are described for the human immunodeficiency virus quasi-species setting. A simulation study is presented to characterize performance of the method. Application of this approach to data arising from a cross-sectional study of n=126 multiply infected children in Uganda reveals some interesting associations requiring further investigation.

Computation of the response functions of spiral waves in active media.

Rotating spiral waves are a form of self-organization observed in spatially extended systems of physical, chemical, and biological natures. A small perturbation causes gradual change in spatial location of spiral's rotation center and frequency, i.e., drift. The response functions (RFs) of a spiral wave are the eigenfunctions of the adjoint linearized operator corresponding to the critical eigenvalues lambda=0,+/-iomega. The RFs describe the spiral's sensitivity to small perturbations in the way that a spiral is insensitive to small perturbations where its RFs are close to zero. The velocity of a spiral's drift is proportional to the convolution of RFs with the perturbation. Here we develop a regular and generic method of computing the RFs of stationary rotating spirals in reaction-diffusion equations. We demonstrate the method on the FitzHugh-Nagumo system and also show convergence of the method with respect to the computational parameters, i.e., discretization steps and size of the medium. The obtained RFs are localized at the spiral's core.

Tree-Based Methods for Discovery of Association between Flow Cytometry Data and Clinical Endpoints.

We demonstrate the application and comparative interpretations of three tree-based algorithms for the analysis of data arising from flow cytometry: classification and regression trees (CARTs), random forests (RFs), and logic regression (LR). Specifically, we consider the question of what best predicts CD4 T-cell recovery in HIV-1 infected persons starting antiretroviral therapy with CD4 count between 200 and 350 cell/muL. A comparison to a more standard contingency table analysis is provided. While contingency table analysis and RFs provide information on the importance of each potential predictor variable, CART and LR offer additional insight into the combinations of variables that together are predictive of the outcome. In all cases considered, baseline CD3-DR-CD56+CD16+ emerges as an important predictor variable, while the tree-based approaches identify additional variables as potentially informative. Application of tree-based methods to our data suggests that a combination of baseline immune activation states, with emphasis on CD8 T-cell activation, may be a better predictor than any single T-cell/innate cell subset analyzed. Taken together, we show that tree-based methods can be successfully applied to flow cytometry data to better inform and discover associations that may not emerge in the context of a univariate analysis.

Mixed modeling and multiple imputation for unobservable genotype clusters.

Understanding the genetic contributions to complex diseases will require consideration of interaction across multiple genes and environmental factors. At the same time, capturing information on allelic phase, that is, whether alleles within a gene are in cis (on the same chromosome) or in trans (on different chromosomes), is critical when using haplotypic approaches in disease association studies. This paper proposes a combination of mixed modeling and multiple imputation for assessing high-order genotype-phenotype associations while accounting for the uncertainty in phase inherent in population-based association studies. This method provides a flexible statistical framework for controlling for potential confounders and assessing gene-environment and gene-gene interactions in studies of unrelated individuals where the haplotypic phase is generally unobservable. The proposed method is applied to a cohort of 626 subjects with human immunodeficiency virus (HIV) to assess the potential contribution of four genes, apolipoprotein-C-III, apolipoprotein-E, endothelial lipase and hepatic lipase in predicting lipid abnormalities. A simulation study is also presented to describe the method performance.