Stride: a flexible software platform for high-performance ultrasound computed tomography

BACKGROUND AND OBJECTIVE: Advanced ultrasound computed tomography techniques like full-waveform inversion are mathematically complex and orders of magnitude more computationally expensive than conventional ultrasound imaging methods. This computational and algorithmic complexity, and a lack of open-source libraries in this field, represent a barrier preventing the generalised adoption of these techniques, slowing the pace of research, and hindering reproducibility. Consequently, we have developed Stride, an open-source Python library for the solution of large-scale ultrasound tomography problems. METHODS: On one hand, Stride provides high-level interfaces and tools for expressing the types of optimisation problems encountered in medical ultrasound tomography. On the other, these high-level abstractions seamlessly integrate with high-performance wave-equation solvers and with scalable parallelisation routines. The wave-equation solvers are generated automatically using Devito, a domain-specific language, and the parallelisation routines are provided through the custom actor-based library Mosaic. RESULTS: We demonstrate the modelling accuracy achieved by our wave-equation solvers through a comparison (1) with analytical solutions for a homogeneous medium, and (2) with state-of-the-art modelling software applied to a high-contrast, complex skull section. Additionally, we show through a series of examples how Stride can handle realistic numerical and experimental tomographic problems, in 2D and 3D, and how it can scale robustly from a local multi-processing environment to a multi-node high-performance cluster. CONCLUSIONS: Stride enables researchers to rapidly and intuitively develop new imaging algorithms and to explore novel physics without sacrificing performance and scalability. This will lead to faster scientific progress in this field and will significantly ease clinical translation

Sexual Dysfunction and Reproductive Concerns in Young Men Diagnosed With Testicular Cancer: An Observational Study

INTRODUCTION: The survival rates for testicular cancer are excellent; still, there is a lack of knowledge regarding important survivorship issues, such as sexual dysfunction and reproductive concerns. AIM: The aim of this study was to investigate the prevalence and predictors of sexual dysfunction and reproductive concerns and the potential association between these issues in young men ∼2 years after a diagnosis of testicular cancer. METHODS: Data were collected from 111 men (response rate = 50%) diagnosed with testicular cancer at age 16-39. Patients were identified via the Swedish National Quality Registry for Testicular Cancer and approached with a survey, including standardized measures of sexual function, reproductive concerns, body image, and health-related quality of life. The survey was sent to participants approximately 2 years after their cancer diagnosis. Clinical variables were collected from the registry. Predictors were identified by multivariable linear regression analyses. MAIN OUTCOME MEASURES: The main outcomes were sexual function, assessed with the Patient-Reported Outcomes Measurement Information System Sexual Function and Satisfaction measure version 2.0, and reproductive concerns, assessed with the Reproductive Concerns After Cancer scale. RESULTS: Sexual dysfunction was reported by 26% of men, and a high level of reproductive concerns was reported by 28%. Lower satisfaction with sex life was associated with older age (β = -0.41), negative body image (β = -0.42), not having a partner (β = 4.8), and dissatisfaction with sex life before cancer (β = 8.31). Negative body image was associated with reproductive concerns in the dimensions of fertility potential (β = 0.06), partner disclosure (β = 0.08), and child's health (β = 0.07), whereas having had fertility preservation predicted higher levels of concerns with regard to personal health (β = 0.52) and achieving pregnancy (β = 0.53). Clinical variables did not predict either sexual function or reproductive concerns. CLINICAL IMPLICATIONS: Our results show that the majority of young men diagnosed with testicular cancer do not report sexual dysfunction or reproductive concerns 2 years after diagnosis. A sizeable minority, however, does report dysfunction or reproductive concerns, which should be recognized in the follow-up care of this population. STRENGTHS & LIMITATIONS: A strength of the study is the use of high-quality registry data and validated instruments. The lack of Swedish norms for sexual function and reproductive concerns is a possible limitation. CONCLUSION: A subgroup of young men treated for testicular cancer report sexual dysfunction or reproductive concerns approximately 2 years after diagnosis. Factors associated with these issues seem to mainly be psychological, rather than medical, nature. Ljungman L, Eriksson LE, Flynn KE, et al. Sexual Dysfunction and Reproductive Concerns in Young Men Diagnosed With Testicular Cancer: An Observational Study. J Sex Med 2019;16:1049-1059

Decision for reconstructive interventions of the upper limb in individuals with tetraplegia: the effect of treatment characteristics

Objective: To determine the effect of treatment characteristics on the\ud decision for reconstructive interventions for the upper extremities (UE) in\ud subjects with tetraplegia. - \ud Setting: Seven specialized spinal cord injury centres in the Netherlands. - \ud Method: Treatment characteristics for UE reconstructive interventions were\ud determined. Conjoint analysis (CA) was used to determine the contribution\ud and the relative importance of the treatment characteristics on the decision\ud for therapy. Therefore, a number of different treatment scenarios using these\ud characteristics were established. Different pairs of scenarios were presented\ud to subjects who were asked to choose the preferred scenario of each set. - \ud Results: forty nine subjects with tetraplegia with a stable C5, C6 or C7\ud lesion were selected. All treatment characteristics significantly influenced\ud the choice for treatment. Relative importance of treatment characteristics\ud were: intervention type (surgery or surgery with FES implant) 13%, number\ud of operations 15%, in patient rehabilitation period 22%, ambulant\ud rehabilitation period 9%, complication rate 15%, improvement of elbow\ud function 10%, improvement of hand function 15%. In deciding for therapy\ud 40% of the subjects focused on one characteristic. - \ud Conclusion: CA is applicable in Spinal Cord Injury medicine to study the\ud effect of health outcomes and non-health outcomes on the decision for\ud treatment. Non-health outcomes which relate to the intensity of treatment\ud are equally important or even more important than functional outcome in the\ud decision for reconstructive UE surgery in subjects with tetraplegia

The Performance of Private Equity Funds: Does Diversification Matter?

This paper is the first systematic analysis of the impact of diversification on the performance of private equity funds. A unique data set allows the exact evaluation of diversification across the dimensions financing stages, industries, and countries. Very different levels of diversification can be observed across sample funds. While some funds are highly specialized others are highly diversified. The empirical results show that the rate of return of private equity funds declines with diversification across financing stages, but increases with diversification across industries. Accordingly, the fraction of portfolio companies which have a negative return or return nothing at all, increase with diversification across financing stages. Diversification across countries has no systematic effect on the performance of private equity funds

Mitigation of Moral Hazard and Adverse Selection in Venture Capital Financing: The Influence of the Country’s Institutional Setting

A venture capitalist (VC) needs to trade off benefits and costs when attempting to mitigate agency problems in their investor-investee relationship. We argue that signals of ventures complement the VC’s capacity to screen and conduct a due diligence during the pre-investment phase, but its attractiveness may diminish in institutional settings supporting greater transparency. Similarly, whereas a VC may opt for contractual covenants to curb potential opportunism by ventures in the post-investment phase, this may only be effective in settings supportive of shareholder rights enforcement. Using an international sample of VC contracts, our study finds broad support for these conjectures. It delineates theoretical and practical implications for how investors can best deploy their capital in different institutional settings whilst nurturing their relationships with entrepreneurs

Investigation of pathogenic mechanisms in multiple colorectal adenoma patients without germline APC or MYH/MUTYH mutations

Patients with multiple (5–100) colorectal adenomas (MCRAs) often have no germline mutation in known predisposition genes, but probably have a genetic origin. We collected a set of 25 MCRA patients with no detectable germline mutation in APC, MYH/MUTYH or the mismatch repair genes. Extracolonic tumours were absent in these cases. No vertical transmission of the MCRA phenotype was found. Based on the precedent of MYH-associated polyposis (MAP), we searched for a mutational signature in 241 adenomatous polyps from our MCRA cases. Somatic mutation frequencies and spectra at APC, K-ras and BRAF were, however, similar to those in sporadic colorectal adenomas. Our data suggest that the genetic pathway of tumorigenesis in the MCRA patients' tumours is very similar to the classical pathway in sporadic adenomas. In sharp contrast to MAP tumours, we did not find evidence of a specific mutational signature in any individual patient or in the overall set of MCRA cases. These results suggest that hypermutation of APC does not cause our patients' disease and strongly suggests that MAP is not a paradigm for the remaining MCRA patients. Our MCRA patients' colons showed no evidence of microadenomas, unlike in MAP and familial adenomatous polyposis (FAP). However, nuclear β-catenin expression was significantly greater in MCRA patients' tumours than in sporadic adenomas. We suggest that, at least in some cases, the MCRA phenotype results from germline variation that acts subsequent to tumour initiation, perhaps by causing more rapid or more likely progression from microadenoma to macroadenoma

A Method to Study Relaxation of Metastable Phases: Macroscopic Mean-Field Dynamics

We propose two different macroscopic dynamics to describe the decay of metastable phases in many-particle systems with local interactions. These dynamics depend on the macroscopic order parameter $m$ through the restricted free energy $F(m)$ and are designed to give the correct equilibrium distribution for $m$. The connection between macroscopic dynamics and the underlying microscopic dynamic are considered in the context of a projection- operator formalism. Application to the square-lattice nearest-neighbor Ising ferromagnet gives good agreement with droplet theory and Monte Carlo simulations of the underlying microscopic dynamic. This includes quantitative agreement for the exponential dependence of the lifetime on the inverse of the applied field $H$, and the observation of distinct field regions in which the derivative of the lifetime with respect to $1/H$ depends differently on $H$. In addition, at very low temperatures we observe oscillatory behavior of this derivative with respect to $H$, due to the discreteness of the lattice and in agreement with rigorous results. Similarities and differences between this work and earlier works on finite Ising models in the fixed-magnetization ensemble are discussed.Comment: 44 pages RevTeX3, 11 uuencoded Postscript figs. in separate file

Metastable lifetimes in a kinetic Ising model: Dependence on field and system size

The lifetimes of metastable states in kinetic Ising ferromagnets are studied by droplet theory and Monte Carlo simulation, in order to determine their dependences on applied field and system size. For a wide range of fields, the dominant field dependence is universal for local dynamics and has the form of an exponential in the inverse field, modified by universal and nonuniversal power-law prefactors. Quantitative droplet-theory predictions are numerically verified, and small deviations are shown to depend nonuniversally on the details of the dynamics. We identify four distinct field intervals in which the field dependence and statistical properties of the lifetimes are different. The field marking the crossover between the weak-field regime, in which the decay is dominated by a single droplet, and the intermediate-field regime, in which it is dominated by a finite droplet density, vanishes logarithmically with system size. As a consequence the slow decay characteristic of the former regime may be observable in systems that are macroscopic as far as their equilibrium properties are concerned.Comment: 18 pages single spaced. RevTex Version 3. FSU-SCRI-94-1

MYC regulates fatty acid metabolism through a multigenic program in claudin-low triple negative breast cancer

Background: Recent studies have suggested that fatty acid oxidation (FAO) is a key metabolic pathway for the growth of triple negative breast cancers (TNBCs), particularly those that have high expression of MYC. However, the underlying mechanism by which MYC promotes FAO remains poorly understood. Methods: We used a combination of metabolomics, transcriptomics, bioinformatics, and microscopy to elucidate a potential mechanism by which MYC regulates FAO in TNBC. Results: We propose that MYC induces a multigenic program that involves changes in intracellular calcium signalling and fatty acid metabolism. We determined key roles for fatty acid transporters (CD36), lipases (LPL), and kinases (PDGFRB, CAMKK2, and AMPK) that each contribute to promoting FAO in human mammary epithelial cells that express oncogenic levels of MYC. Bioinformatic analysis further showed that this multigenic program is highly expressed and predicts poor survival in the claudin-low molecular subtype of TNBC, but not other subtypes of TNBCs, suggesting that efforts to target FAO in the clinic may best serve claudin-low TNBC patients. Conclusion: We identified critical pieces of the FAO machinery that have the potential to be targeted for improved treatment of patients with TNBC, especially the claudin-low molecular subtype