Parasites on parasites:Coupled fluctuations in stacked contact processes

We present a model for host-parasite dynamics which incorporates both vertical and horizontal transmission as well as spatial structure. Our model consists of stacked contact processes (CP), where the dynamics of the host is a simple CP on a lattice while the dynamics of the parasite is a secondary CP which sits on top of the host-occupied sites. In the simplest case, where infection does not incur any cost, we uncover a novel effect: a non-monotonic dependence of parasite prevalence on host turnover. Inspired by natural examples of hyperparasitism, we extend our model to multiple levels of parasites and identify a transition between the maintenance of a finite and infinite number of levels, which we conjecture is connected to a roughening transition in models of surface growth

Physics of biological evolution

Part I: A remarkable feature of life on Earth is that despite the apparent observed diversity, the underlying chemistry that powers it is highly conserved. From the level of the nucleobases, through the amino acids and proteins they encode, to the metabolic pathways of chemical reactions catalyzed by these proteins, biology often utilizes identical solutions in vastly disparate organisms. This universality is intriguing as it raises the question of whether these recurring features exist because they represent some truly optimal solution to a given problem in biology, or whether they simply exist by chance, having arisen very early in life's history. In this project we consider the universality of metabolism { the set of chemical reactions providing the energy and building blocks for cells to grow and divide. We develop an algorithm to construct the complete network of all possible biochemically feasible compounds and reactions, including many that could have been utilized by life but never were. Using this network we investigate the most highly conserved piece of metabolism in all of biology, the trunk pathway of glycolysis. We design a method which allows a comparison between the large number of alternatives to this pathway and which takes into account both thermodynamic and biophysical constraints, finding evidence that the existing version of this pathway produces optimal metabolic fluxes under physiologically relevant intracellular conditions. We then extend our method to include an evolutionary simulation so as to more fully explore the biochemical space. Part II: Studies of population dynamics have a long history and have been used to understand the properties of complex networks of ecological interactions, extinction events, biological diversity and the transmission of infectious disease. One aspect of these models that is known to be of great importance, but one which nonetheless is often neglected, is spatial structure. Various classes of models have been proposed with each allowing different insights into the role space plays. Here we use a lattice-based approach. Motivated by gene transfer and parasite dynamics, we extend the well-studied contact process of statistical physics to include multiple levels. Doing so generates a simple model which captures in a general way the most important features of such biological systems: spatial structure and the inclusion of both vertical as well as horizontal transmission. We show that spatial structure can produce a qualitatively new effect: a coupling between the dynamics of the infection and of the underlying host population, even when the infection does not affect the fitness of the host. Extending the model to an arbitrary number of levels, we find a transition between regimes where both a finite and infinite number of parasite levels are sustainable, and conjecture that this transition is related to the roughening transition of related surface growth models

Evaluation of Monte Carlo to support commissioning of the treatment planning system of new pencil beam scanning proton therapy facilities

To demonstrate the potential of Monte Carlo (MC) to support the resource-intensive measurements that comprise the commissioning of the treatment planning system (TPS) of new proton therapy facilities.

Approach: Beam models of a pencil beam scanning system (Varian ProBeam) were developed in GATE (v8.2), Eclipse proton convolution superposition algorithm (v16.1, Varian Medical Systems) and RayStation MC (v12.0.100.0, RaySearch Laboratories), using the beam commissioning data. All models were first benchmarked against the same commissioning data and validated on seven spread-out Bragg peak (SOBP) plans. Then, we explored the use of MC to optimise dose calculation parameters, fully explore the performance and limitations of TPS in homogeneous fields and support the development of patient-specific quality assurance (PSQA) processes. We compared the dose calculations of the TPSs against measurements (DDTPSvs.Meas.) or GATE (DDTPSvs.GATE) for an extensive set of plans of varying complexity. This included homogeneous plans with varying field-size, range, width, and range-shifters (RSs) (n=46) and PSQA plans for different anatomical sites (n=11).

Results: The three beam models showed good agreement against the commissioning data, and dose differences of 3.5% and 5% were found for SOBP plans without and with RSs, respectively. DDTPSvs.Meas.and DDTPSvs.GATEwere correlated in most scenarios - for example, in homogeneous fields the Pearson's correlation coefficient was 0.92 and 0.68 for Eclipse and RayStation, respectively. The standard deviation of the differences between GATE and measurements (±0.5% for homogeneous and ±0.8% for PSQA plans) was applied as tolerance when comparing TPSs with GATE. 72% and 60% of the plans were within the GATE predicted dose difference for both TPSs, for homogeneous and PSQA cases, respectively.

Significance: Developing and validating a MC beam model early on into the commissioning of new proton therapy facilities can support the validation of the TPS and facilitate comprehensive investigation of its capabilities and limitations

Radiopaque Nanoparticle and Dipyridamole-loaded Electrospun Polymeric Scaffold as Bioresorbable Drug-Eluting Vascular Graft

https://openworks.mdanderson.org/sumexp22/1080/thumbnail.jp

EVALUATION OF AN END-TO-END RADIOTHERAPY TREATMENT PLANNING PIPELINE FOR PROSTATE CANCER

Radiation treatment planning is a crucial and time-intensive process in radiation therapy. This planning involves carefully designing a treatment regimen tailored to a patient’s specific condition, including the type, location, and size of the tumor with reference to surrounding healthy tissues. For prostate cancer, this tumor may be either local, locally advanced with extracapsular involvement, or extend into the pelvic lymph node chain. Automating essential parts of this process would allow for the rapid development of effective treatment plans and better plan optimization to enhance tumor control for better outcomes. The first objective of this work, to automate the treatment planning process, was the automatic segmentation of critical structures. Delineation of both target and normal tissue structures was necessary to establish the foundation for identifying where radiation must be delivered and what should be spared from excess radiation. Deep learning segmentation models were developed from retrospective CT simulation imaging data and clinical contours to delineate intact, postoperative, and nodal treatment structures for prostate cancer to accomplish this objective. Quality contours were extracted per established contouring guidelines in the literature. Model refinement on a holdout fine-tune dataset was used to verify model contours before quantitative and qualitative evaluation on the holdout test set. Predicted contours resulted in contours comparable in quantitative Dice-Similarity-Coefficient (DSC) and 95% Hausdorff Distance (HD95) to proposed models in literature and clinically usable contours with no more than minor edits upon physician review. The second objective was the automation of Volumetric Modulated Arc Therapy (VMAT) planning for a breadth of prostate treatment scenarios. Development of VMAT plans for intact, postoperative, and nodal involvement treatment cases was necessary for the sequence in daily treatment delivery and the prospective distribution of radiation dose to target and normal tissues. To accomplish this objective, knowledge-based planning models were separately developed to estimate patient-specific DVHs to guide plan optimization for radiation delivery. These two models were then used in this work for end-to-end testing of cases with and without lymph node involvement, including determining if the prostate target is intact or postoperative with or without treatment devices such as hydrogel spacers and rectal balloons. A sequence of iterative optimization runs was created to ensure hotspot reduction and target conformality. The findings demonstrated that plans developed from automatically generated contours were clinically usable with minor edits for intact and postoperative treatments without lymph node involvement. For treatments with lymph node involvement, dose constraints were met for a select set of cases without excessive rectum curvature or excessive bladder descension into the postoperative treatment bed. When comparing auto-segmented to clinical contours, clinical contours experienced similar pass rates as those achieved by auto-segmented contours

Tungsten nanoparticle and polymer blends as novel coating for radiopaque resorbable inferior vena cava filter

https://openworks.mdanderson.org/sumexp22/1148/thumbnail.jp

Energy efficiency and economy-wide rebound effects: a review of the evidence and its implications

The majority of global energy scenarios anticipate a structural break in the relationship between energy consumption and gross domestic product (GDP), with several scenarios projecting absolute decoupling, where energy use falls while GDP continues to grow. However, there are few precedents for absolute decoupling, and current global trends are in the opposite direction. This paper explores one possible explanation for the historical close relationship between energy consumption and GDP, namely that the economy-wide rebound effects from improved energy efficiency are larger than is commonly assumed. We review the evidence on the size of economy-wide rebound effects and explore whether and how such effects are taken into account within the models used to produce global energy scenarios. We find the evidence base to be growing in size and quality, but remarkably diverse in terms of the methodologies employed, assumptions used, and rebound mechanisms included. Despite this diversity, the results are broadly consistent and suggest that economy-wide rebound effects may erode more than half of the expected energy savings from improved energy efficiency. We also find that many of the mechanisms driving rebound effects are overlooked by integrated assessment and global energy models. We therefore conclude that global energy scenarios may underestimate the future rate of growth of global energy demand

Image-Guided Deployment and Monitoring of a Novel Tungsten Nanoparticle-Infused Radiopaque Absorbable Inferior Vena Cava Filter in a Swine Model

PURPOSE: To improve radiopacity of radiolucent absorbable poly-p-dioxanone (PPDO) inferior vena cava filters (IVCFs) and demostrate their effectiveness in clot-trapping ability. MATERIALS AND METHODS: Tungsten nanoparticles (WNPs) were incorporated along with polyhydroxybutyrate (PHB), polycaprolactone (PCL), and polyvinylpyrrolidone (PVP) polymers to increase the surface adsorption of WNPs. The physicochemical and in vitro and in vivo imaging properties of PPDO IVCFs with WNPs with single-polymer PHB (W-P) were compared with those of WNPs with polymer blends consisting of PHB, PCL, and PVP (W-PB). RESULTS: In vitro analyses using PPDO sutures showed enhanced radiopacity with either W-P or W-PB coating, without compromising the inherent physicomechanical properties of the PPDO sutures. W-P- and W-PB-coated IVCFs were deployed successfully into the inferior vena cava of pig models with monitoring by fluoroscopy. At the time of deployment, W-PB-coated IVCFs showed a 2-fold increase in radiopacity compared to W-P-coated IVCFs. Longitudinal monitoring of in vivo IVCFs over a 12-week period showed a drastic decrease in radiopacity at Week 3 for both filters. CONCLUSIONS: The results highlight the utility of nanoparticles (NPs) and polymers for enhancing radiopacity of medical devices. Different methods of incorporating NPs and polymers can still be explored to improve the effectiveness, safety, and quality of absorbable IVCFs

Multiplicity Statistics of Stars in the Sagittarius Dwarf Spheroidal Galaxy: Comparison to the Milky Way

We use time-resolved spectra from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) to examine the distribution of radial velocity (RV) variations in 249 stars identified as members of the Sagittarius (Sgr) dwarf spheroidal (dSph) galaxy by Hayes et al (2020). We select Milky Way (MW) stars that have stellar parameters ($log(g)$, $T_{eff}$, and $[Fe/H]$) similar to those of the Sagittarius members by means of a k-d tree of dimension 3. We find that the shape of the distribution of RV shifts in Sgr dSph stars is similar to that measured in their MW analogs, but the total fraction of RV variable stars in the Sgr dSph is larger by a factor of $\sim 2$. After ruling out other explanations for this difference, we conclude that the fraction of close binaries in the Sgr dSph is intrinsically higher than in the MW. We discuss the implications of this result for the physical processes leading to the formation of close binaries in dwarf spheroidal and spiral galaxies