idmTPreg: Regression Model for Progressive Illness Death Data

The progressive illness-death model is frequently used in medical applications. For example, the model may be used to describe the disease process in cancer studies. We have developed a new R package called idmTPreg to estimate regression coefficients in datasets that can be described by the progressive illness-death model. The motivation for the development of the package is a recent contribution that enables the estimation of possibly time-varying covariate effects on the transition probabilities for a progressive illness-death data. The main feature of the package is that it befits both non-Markov and Markov progressive illness-death data. The package implements the introduced estimators obtained using a direct binomial regression approach. Also, variance estimates and confidence bands are implemented in the package. This article presents guidelines for the use of the package.BERC 2014-2017 SEV-2013-0323 MTM2016-76969-P FP7/2011: Marie Curie Initial Training Network MEDIASRE

Financial toxicity and socioeconomic impact of cancer in Europe

Background: Even with universal health care, patients living with cancer often face substantial treatment-related costs and income loss in Europe. Insights into the socioeconomic impact of cancer within and across countries are needed to create awareness, inform policy, and develop targeted measurement instruments. The SEC study aims to explore the socioeconomic impact and financial toxicity of cancer and identify vulnerable patient groups across Europe. Patients and methods: To investigate experiences of a large number of patients, data were collected in a collaborative effort of hospitals and patient organizations across Europe through convenience sampling. Patients undergoing treatment currently or treated within the past 2 years could participate. A 44-item survey was developed to measure the socioeconomic impact following a cancer diagnosis. The primary outcome was the level of financial toxicity, measured by the Financial Index of Toxicity (FIT) score. To identify vulnerable groups, multiple regression analyses were used to investigate the association between the FIT score, clinical characteristics, and socioeconomic demographics, including cancer type, employment status, and country of residence. Results: A total of 2507 patients across Europe met the inclusion criteria. Fifty-six percent of the patients reported income loss and 86% additional treatment-related expenses. Sixteen percent of patients delayed or avoided medical visits, buying medication, surgery, or other health services. Next to a significant association of the country of residence, our regression models demonstrated that divorced, self-employed patients who were younger (−0.02; P = 0.000) and lower educated (0.75; P = 0.000) with a lower household income (1.21; P = 0.000) and children (0.21; P = 0.000) at the time of diagnosis reported significantly higher FIT scores compared with older patients who were married (−0.56; P = 0.000), retired (−1.55; P = 0.000), or employed (−0.56; P = 0.000). Conclusions: In every European Union country, a substantial number of patients with cancer report serious financial consequences and stress. Further research is critical to inform well-tailored policies and interventions to limit the socioeconomic impact on patients with cancer.</p

An open-source framework for synthetic post-dive Doppler ultrasound audio generation

Doppler ultrasound (DU) measurements are used to detect and evaluate venous gas emboli (VGE) formed after decompression. Automated methodologies for assessing VGE presence using signal processing have been developed on varying real-world datasets of limited size and without ground truth values preventing objective evaluation. We develop and report a method to generate synthetic post-dive data using DU signals collected in both precordium and subclavian vein with varying degrees of bubbling matching field-standard grading metrics. This method is adaptable, modifiable, and reproducible, allowing for researchers to tune the produced dataset for their desired purpose. We provide the baseline Doppler recordings and code required to generate synthetic data for researchers to reproduce our work and improve upon it. We also provide a set of pre-made synthetic post-dive DU data spanning six scenarios representing the Spencer and Kisman-Masurel (KM) grading scales as well as precordial and subclavian DU recordings. By providing a method for synthetic post-dive DU data generation, we aim to improve and accelerate the development of signal processing techniques for VGE analysis in Doppler ultrasound

Taxanes trigger cancer cell killing in vivo by inducing non-canonical T cell cytotoxicity

Although treatment with taxanes does not always lead to clinical benefit, all patients are at risk of their detrimental side effects such as peripheral neuropathy. Understanding the in vivo mode of action of taxanes can help design improved treatment regimens. Here, we demonstrate that in vivo, taxanes directly trigger T cells to selectively kill cancer cells in a non-canonical, T cell receptor-independent manner. Mechanistically, taxanes induce T cells to release cytotoxic extracellular vesicles, which lead to apoptosis specifically in tumor cells while leaving healthy epithelial cells intact. We exploit these findings to develop an effective therapeutic approach, based on transfer of T cells pre-treated with taxanes ex vivo, thereby avoiding toxicity of systemic treatment. Our study reveals a different in vivo mode of action of one of the most commonly used chemotherapies, and opens avenues to harness T cell-dependent anti-tumor effects of taxanes while avoiding systemic toxicity

Taxanes trigger cancer cell killing in vivo by inducing non-canonical T cell cytotoxicity

Although treatment with taxanes does not always lead to clinical benefit, all patients are at risk of their detrimental side effects such as peripheral neuropathy. Understanding the in vivo mode of action of taxanes can help design improved treatment regimens. Here, we demonstrate that in vivo, taxanes directly trigger T cells to selectively kill cancer cells in a non-canonical, T cell receptor-independent manner. Mechanistically, taxanes induce T cells to release cytotoxic extracellular vesicles, which lead to apoptosis specifically in tumor cells while leaving healthy epithelial cells intact. We exploit these findings to develop an effective therapeutic approach, based on transfer of T cells pre-treated with taxanes ex vivo, thereby avoiding toxicity of systemic treatment. Our study reveals a different in vivo mode of action of one of the most commonly used chemotherapies, and opens avenues to harness T cell-dependent anti-tumor effects of taxanes while avoiding systemic toxicity

Oral contraceptive use and ovarian cancer risk for BRCA1/2 mutation carriers: an international cohort study

Background: Ovarian cancer risk in BRCA1 and BRCA2 mutation carriers has been shown to decrease with longer duration of oral contraceptive use. Although the effects of using oral contraceptives in the general population are well established (approximately 50% risk reduction in ovarian cancer), the estimated risk reduction in mutation carriers is much less precise because of potential bias and small sample sizes. In addition, only a few studies on oral contraceptive use have examined the associations of duration of use, time since last use, starting age, and calendar year of start with risk of ovarian cancer. Objective: This study aimed to investigate in more detail the associations of various characteristics of oral contraceptive use and risk of ovarian cancer, to provide healthcare providers and carriers with better risk estimates. Study Design: In this international retrospective study, ovarian cancer risk associations were assessed using oral contraceptives data on 3989 BRCA1 and 2445 BRCA2 mutation carriers. Age-dependent–weighted Cox regression analyses were stratified by study and birth cohort and included breast cancer diagnosis as a covariate. To minimize survival bias, analyses were left truncated at 5 years before baseline questionnaire. Separate analyses were conducted for each aspect of oral contraceptive use and in a multivariate analysis, including all these aspects. In addition, the analysis of duration of oral contraceptive use was stratified by recency of use. Results: Oral contraceptives were less often used by mutation carriers who were diagnosed with ovarian cancer (ever use: 58.6% for BRCA1 and 53.5% BRCA2) than by unaffected carriers (ever use: 88.9% for BRCA1 and 80.7% for BRCA2). The median duration of use was 7 years for both BRCA1 and BRCA2 carriers who developed ovarian cancer and 9 and 8 years for unaffected BRCA1 and BRCA2 carriers with ovarian cancer, respectively. For BRCA1 mutation carriers, univariate analyses have shown that both a longer duration of oral contraceptive use and more recent oral contraceptive use were associated with a reduction in the risk of ovarian cancer. However, in multivariate analyses, including duration of use, age at first use, and time since last use, duration of oral contraceptive use proved to be the prominent protective factor (compared with 10 years [hazard ratio, 0.37; 95% confidence interval, 0.19–0.73]; Ptrend=.008). The inverse association between duration of use and ovarian cancer risk persisted for more than 15 years (duration of ≥10 years; BRCA1 15 years since last use [hazard ratio, 0.56; 95% confidence interval, 0.18–0.59]). Univariate results for BRCA2 mutation carriers were similar but were inconclusive because of limited sample size. Conclusion: For BRCA1 mutation carriers, longer duration of oral contraceptive use is associated with a greater reduction in ovarian cancer risk, and the protection is long term

Barley lesion mimics, supersusceptible or highly resistant to leaf rust and net blotch

Lesion mimic mutants of plants have the feature of spontaneously displaying necrotic spots or bands on their leaves. Lesion mimics have often displayed enhanced resistance to biotrophic pathogens whilst showing increased susceptibility to necrotrophs. This paper identifies three novel, non-allelic mutants of barley (Hordeum vulgare), which spontaneously form necrotic leaf lesions: Necrotic leaf spot 9.3091 (nec9.3091), Mottled leaf 8.1661 (mtt8.1661) and Mottled leaf 9.2721 (mtt9.2721). The Necrotic leaf spot 8.3550 mutant (nec8.3550), formerly known as bst1, was included in the study because it is a lesion mimic mutant belonging to the same original pool. The reactions of the mutants to the biotroph Puccinia hordei and the necrotroph Pyrenophora teres f. sp. teres were investigated. Mutants nec8.3550 and mtt8.1661 were more resistant than the parental Bowman near-isogenic line with the Rph3.c gene (Bowman Rph3.c, NGB 22452) to leaf rust, caused by P.hordei. Mutants nec8.3550, mtt8.1661 and mtt9.2721 were more susceptible than Bowman Rph3.c to net blotch, caused by P.teres f. sp. teres. Autofluorescence was detected in leaf tissues of all mutants. Based on the high expression of the PR1 and Hv-HIR genes, combined with the low susceptibility to P.hordei, nec8.3550 appears to have entered a state of systemic acquired resistance, which is quite distinct from the resistance expressed in mtt8.1661. The latter mutant has low or no expression of PR1 and Hv-HIR genes, yet it is highly resistant to rust. It is also extremely susceptible to net blotch. These mutants can serve as genetic sources of novel disease resistance for barley improvement