A fast MR fingerprinting simulator for direct error estimation and sequence optimization

Magnetic resonance fingerprinting (MRF) is a novel quantitative MR technique that simultaneously provides multiple tissue property maps. When optimizing MRF scans, modeling undersampling errors and field imperfections in cost functions for direct measurement of quantitative errors will make the optimization results more practical and robust. However, optimizing such cost function is computationally expensive and impractical for MRF optimization with tens of thousands of iterations. Here, we introduce a fast MRF simulator to simulate aliased images from actual scan scenarios including undersampling and system imperfections, which substantially reduces computational time and allows for direct error estimation of the quantitative maps and efficient sequence optimization. We evaluate the performance and computational speed of the proposed approach by simulations and in vivo experiments. The simulations from the proposed method closely approximate the signals and MRF maps from in vivo scans, with 158 times shorter processing time than the conventional simulation method using Non-uniform Fourier transform. We also demonstrate the power of applying the fast MRF simulator in MRF sequence optimization. The optimized sequences are validated with in vivo scans to assess the image quality and accuracy. The optimized sequences produce artifact-free T1 and T2 maps in 2D and 3D scans with equivalent mapping accuracy as the human-designed sequence but at shorter scan times. Incorporating the proposed simulator in the MRF optimization framework makes direct estimation of undersampling errors during the optimization process feasible, and provide optimized MRF sequences that are robust against undersampling artifacts and field inhomogeneity.

Automated design of pulse sequences for magnetic resonance fingerprinting using physics-inspired optimization

Magnetic resonance fingerprinting (MRF) is a method to extract quantitative tissue properties such as [Formula: see text] and [Formula: see text] relaxation rates from arbitrary pulse sequences using conventional MRI hardware. MRF pulse sequences have thousands of tunable parameters, which can be chosen to maximize precision and minimize scan time. Here, we perform de novo automated design of MRF pulse sequences by applying physics-inspired optimization heuristics. Our experimental data suggest that systematic errors dominate over random errors in MRF scans under clinically relevant conditions of high undersampling. Thus, in contrast to prior optimization efforts, which focused on statistical error models, we use a cost function based on explicit first-principles simulation of systematic errors arising from Fourier undersampling and phase variation. The resulting pulse sequences display features qualitatively different from previously used MRF pulse sequences and achieve fourfold shorter scan time than prior human-designed sequences of equivalent precision in [Formula: see text] and [Formula: see text] Furthermore, the optimization algorithm has discovered the existence of MRF pulse sequences with intrinsic robustness against shading artifacts due to phase variation.

Effects of setting temperatures in the parallel tempering Monte Carlo algorithm

Parallel tempering Monte Carlo has proven to be an efficient method in optimization and sampling applications. Having an optimized temperature set enhances the efficiency of the algorithm through more-frequent replica visits to the temperature limits. The approaches for finding an optimal temperature set can be divided into two main categories. The methods of the first category distribute the replicas such that the swapping ratio between neighboring replicas is constant and independent of the temperature values. The second-category techniques including the feedback-optimized method, on the other hand, aim for a temperature distribution that has higher density at simulation bottlenecks, resulting in temperature-dependent replica-exchange probabilities. In this paper, we compare the performance of various temperature setting methods on both sparse and fully connected spin-glass problems as well as fully connected Wishart problems that have planted solutions. These include two classes of problems that have either continuous or discontinuous phase transitions in the order parameter. Our results demonstrate that there is no performance advantage for the methods that promote nonuniform swapping probabilities on spin-glass problems where the order parameter has a smooth transition between phases at the critical temperature. However, on Wishart problems that have a first-order phase transition at low temperatures, the feedback-optimized method exhibits a time-to-solution speedup of at least a factor of two over the other approaches.

The potential impact of initiating antiretroviral therapy with integrase inhibitors on HIV transmission risk in British Columbia, Canada

BACKGROUND

Available agents within the integrase strand-transfer inhibitor (INSTI) class have been shown to lead to a faster decay in viral load than other regimens. Therefore, we estimated the potential reduction in HIV transmission risk among antiretroviral-naïve individuals initiating on INSTI-based antiretroviral therapy (ART), focusing on the gay, bisexual and other men who have sex with men (gbMSM) population and various degrees of sexual activity.

METHODS

Using two mathematical models that estimate the HIV transmission risk corresponding to different viral loads, we estimated the average probability of HIV transmission per risky contact for gbMSM during the six months post-ART initiation, stratified by stage of HIV infection, viral load at ART initiation and type of first-line ART (i.e., INSTI or non-INSTI-based ART). This study focused individuals who initiated ART between 2011 and 2016 with at least one year of follow-up in British Columbia, Canada.

FINDINGS

Time to first virologic suppression for INSTI-based regimens was 21.4 days (95% credible interval (CI) 19.9-23.2), compared to 58.6 days (95% CI 54.1-62.2) for non-INSTI regimens. We showed that INSTI-based regimens could reduce the HIV transmission risk by at least 25% among those with viral load ≥ 5 log₁₀ copies/mL at ART initiation.

INTERPRETATION

Initiating ART on INSTI-based regimens has the potential to reduce HIV transmission risk among individuals with high baseline viral load levels, especially among those with high levels of sexual activity.

FUNDING

The British Columbia Ministry of Health, the Canadian Institutes of Health Research, and the Michael Smith Foundation for Health Research.

Two-stage patterning dynamics in conifer cotyledon whorl morphogenesis

Background and Aims

Conifer embryos, unlike those of monocots or dicots, have variable numbers of cotyledons, even within the same species. Cotyledons form in a single whorl on a dome-shaped embryo. The closely spaced cotyledons are not found outside this ring, indicating a radial control on where they can form. Polar transport of the hormone auxin affects outgrowth of distinct cotyledons, but not the radial aspect of the whorl or the within-whorl spacing between cotyledons. A quantitative model of plant growth regulator patterning is needed to understand the dynamics of this complex morphogenetic process.

Methods

A two-stage reaction-diffusion model is developed for the spatial patterning of growth regulators on the embryo surface, with a radial pattern (P1) constraining the shorter-wavelength cotyledon pattern (P2) to a whorl. These patterns drive three-dimensional (3-D) morphogenesis by catalysing local surface growth.

Key Results

Growth driven by P2 generates single whorls across the experimentally observed range of two to 11 cotyledons, as well as the circularly symmetric response to auxin transport interference. These computations are the first corroboration of earlier theoretical proposals for hierarchical control of whorl formation. The model generates the linear relationship between cotyledon number and embryo diameter observed experimentally. This accounts for normal integer cotyledon number selection, as well as the less common cotyledon fusings and splittings observed experimentally. Flattening of the embryo during development may affect the upward outgrowth angle of the cotyledons.

Conclusions

Cotyledon morphogenesis is more complex geometrically in conifers than in angiosperms, involving 2-D patterning which deforms a surface in three dimensions. This work develops a quantitative framework for understanding the growth and patterning dynamics involved in conifer cotyledon development, and applies more generally to the morphogenesis of whorls with many primordia.

Progress towards the United Nations 90-90-90 and 95-95-95 targets: the experience in British Columbia, Canada

Introduction

Antiretroviral therapy (ART) scale‐up is central to the global strategy to control the HIV/AIDS pandemic. To accelerate efforts towards ending the AIDS epidemic, the Joint United Nations Programme on HIV/AIDS released the 90‐90‐90 and 95‐95‐95 targets, which have recently been approved by the United Nations (UN). This study characterizes the province of British Columbia (BC)'s progress towards achieving the UN targets, predicts a trajectory up to 2030 according to each of the individual steps (i.e. %Diagnosed, %On ART and %Virologically Suppressed), and identifies the population sub‐groups at higher risk of not achieving these targets.

Methods

The analyses were based on linked individual‐level datasets of people living with HIV (PLWH) in BC, aged ≥18 months, from 2000 to 2013. Using past trends in HIV prevalence and of each individual UN targets, we forecasted these outcomes until 2030 via generalized additive models. We ran a second set of analyses to assess the associations between individual demographic and behavioural factors and each of the individual steps of the UN targets. Lastly, we performed sensitivity analyses to account for uncertainty associated with prevalence estimates and suppression definitions.

Results

Among the estimated 10666 PLWH in BC in 2013, 82% were diagnosed, 76% of those diagnosed were on ART and 83% of those on ART were virologically suppressed. We identified that females, PLWH aged <30 years and those with unknown risk or who self‐identify as having a history of injection drug use were the population subgroups that experienced the most challenge in engaging on ART and achieving viral suppression. Our model projections suggest that BC will achieve 90%‐91%‐90% and 97%‐99%‐97% by 2020 and 2030 respectively.

Conclusions

As we approach 2020, BC is rapidly moving towards achieving the UN targets. However, region‐specific challenges persist. Identification of remaining regional challenges will be essential to achieving the proposed UN targets and therefore fulfilling the promise to end AIDS as a pandemic by 2030.

Conditions for eradicating hepatitis C in people who inject drugs: A fibrosis aware model of hepatitis C virus transmission

It is estimated that 80% of new hepatitis C virus (HCV) infections occur among people who inject drugs (PWID). Eradicating HCV from this population is key for the complete eradication of the disease, and the advent of simple to use, high efficacy treatments could conceivably make this scenario possible. This paper presents a mathematical model where transmission of HCV is studied in a simulated population of PWID where fibrosis progression is explicitly tracked. The stability thresholds that determine whether HCV will remain endemic or become eradicated were established numerically, and analytically on a reduced version of the model. Conditions on testing and treatment rates for eradication to occur were determined, within the context of the new high efficacy therapies. The results show that HCV eradication in the PWID population of the Vancouver, BC test scenario is achievable, but testing and especially treatment rates will need to increase significantly from current rates. Parameter estimates were drawn from published data.

Are Interferon-Free Direct-Acting Antivirals for the Treatment of HCV Enough to Control the Epidemic among People Who Inject Drugs?

BACKGROUND

Widely access to interferon-free direct-acting antiviral regimens (IFN-free DAA) is poised to dramatically change the impact of the HCV epidemic among people who inject drugs (PWID). We evaluated the long-term effect of increasing HCV testing, treatment and engagement into harm-reduction activities, focused on active PWID, on the HCV epidemic in British Columbia (BC), Canada.

METHODS

We built a compartmental model of HCV disease transmission stratified by disease progression, transmission risk, and fibrosis level. We explored the effect of: (1) Increasing treatment rates from 8 to 20, 40 and 80 per 1000 infected PWID/year; (2) Increasing treatment eligibility based on fibrosis level; (3) Maximizing the effect of testing by performing it immediately upon ending the acute phase; (4) Increasing access to harm-reduction activities to reduce the risk of re-infection; (5) Different HCV antiviral regimens on the Control Reproduction Number Rc. We assessed the impact of these interventions on incidence, prevalence and mortality from 2016 to 2030.

RESULTS

Of all HCV antiviral regimens, only IFN-free DAAs offered a high chance of disease elimination (i.e. Rc < 1), but it would be necessary to substantially increase the current low testing and treatment rates. Assuming a treatment rate of 80 per 1000 infected PWID per year, coupled with a high testing rate, the incidence rate, at the end of 2030, could decrease from 92.9 per 1000 susceptible PWID per year (Status Quo) to 82.8 (by treating only PWID with fibrosis level F2 and higher) or to 65.5 (by treating PWID regardless of fibrosis level). If PWID also had access to increased harm-reduction activities, the incidence rate further decreased to 53.1 per 1000 susceptible PWID per year. We also obtained significant decreases in prevalence and mortality at the end of 2030.

CONCLUSIONS

The combination of increased access to HCV testing, highly efficacious antiviral treatment and harm-reduction programs can substantially decrease the burden of the HCV epidemic among PWID. However, unless we increase the current levels of treatment and testing, the HCV epidemic among PWID in BC, and in other parts of the world with similar epidemiological background, will remain a substantial public health concern for many years.