Learning why things change: The Difference-Based Causality Learner

In this paper, we present the Difference-Based Causality Learner (DBCL), an algorithm for learning a class of discrete-time dynamic models that represents all causation across time by means of difference equations driving change in a system. We motivate this representation with real-world mechanical systems and prove DBCL's correctness for learning structure from time series data, an endeavour that is complicated by the existence of latent derivatives that have to be detected. We also prove that, under common assumptions for causal discovery, DBCL will identify the presence or absence of feedback loops, making the model more useful for predicting the effects of manipulating variables when the system is in equilibrium. We argue analytically and show empirically the advantages of DBCL over vector autoregression (VAR) and Granger causality models as well as modified forms of Bayesian and constraintbased structure discovery algorithms. Finally, we show that our algorithm can discover causal directions of alpha rhythms in human brains from EEG data

African Land Ecology: Opportunities and Constraints for Agricultural Development

Current agriculture in Sub-Sahara Africa is undeveloped and the Green Revolution has left the continent largely untouched. Poor performance is often related to a number of socio-economic factors. In this paper we argue that there are also some specifities of natural resources, namely local homogeneity and spatial diversity of the pre-dominant Basement Complex soils, that imply that simple fertilizer strategies may not produce the yield increases obtained elsewhere. Keywords: Sub-Sahara Africa, Agro-Ecology, Land use, Land resources, Basement Complex, Green Revolution, Micronutrients, Fertilizer Policy

Building a super-resolution fluorescence cryomicroscope

Correlated super-resolution fluorescence microscopy and cryo-electron microscopy enables imaging with both high labeling specificity and high resolution. Naturally, combining two sophisticated imaging techniques within one workflow also introduces new requirements on hardware, such as the need for a super-resolution fluorescence capable microscope that can be used to image cryogenic samples. In this chapter, we describe the design and use of the “cryoscope”; a microscope designed for single-molecule localization microscopy (SMLM) of cryoEM samples that fits right into established cryoEM workflows. We demonstrate the results that can be achieved with our microscope by imaging fluorescently labeled vimentin, an intermediate filament, within U2OS cells grown on EM grids, and we provide detailed 3d models that encompass the entire design of the microscope

Plant-based dietary patterns and the risk of dementia:a population-based study

Background: Plant-based dietary patterns are increasingly popular in western countries and are supported by many governments and health organisations for their potential beneficial role in the prevention of chronic diseases. Yet, the potential role of plant-based dietary patterns in the development of dementia remains unclear. Objective: To evaluate the association between plant-based dietary patterns and the risk of dementia. Methods: Dietary intake was measured at baseline in 9,543 dementia-free participants (mean age 64 years, birth years 1897–1960, 58% women) of the prospective population-based Rotterdam Study, using food frequency questionnaires. Based on these questionnaires, we calculated an overall plant-based dietary index (PDI), healthy PDI (hPDI) and unhealthy PDI (uPDI), with higher scores reflecting higher consumption of (any, healthy and unhealthy, respectively) plant-based foods and lower consumption of animal-based foods. We analysed the association of the PDIs with incident dementia using Cox proportional hazard models. Results: During a mean follow-up of 14.5 years, 1,472 participants developed dementia. Overall, the PDIs were not associated with the risk of dementia (hazard ratio [95% confidence interval] per 10-point increase: 0.99 [0.91–1.08] for PDI, 0.93 [0.86–1.01] for hPDI, 1.02 [0.94–1.10] for uPDI). However, among men and APOE ε4 carriers, a higher hPDI was linearly associated with a lower risk of dementia (0.86 [0.75–0.99] and 0.83 [0.73–0.95], respectively), while this association was U-shaped among APOE ε4 non-carriers (P value for non-linearity = 0.01). Conclusions:We found no strong evidence for an overall association between plant-based eating and the risk of dementia. Our findings in stratified analyses warranted further investigation.</p

Dairy products and kidney function decline after myocardial infarction:A prospective analysis in the Alpha Omega Cohort

Background &amp; aims: Population-based studies have shown both beneficial and neutral associations between dairy consumption and kidney function outcomes. We investigated the association between dairy products and kidney function decline in drug-treated post-myocardial infarction (MI) patients. Methods: We analysed data of 2169 post–MI patients (aged 60–80 years, 81% male) of the Alpha Omega Cohort. Dietary data were collected at baseline (2002–2006) using a validated 203-item food frequency questionnaire. The 2021 Chronic Kidney Disease Epidemiology (CKD-EPI) equation was used to estimate 40-months change in creatinine-cystatin C based glomerular filtration rate (eGFRcr-cysC, mL/min per 1.73 m2). Beta coefficients and 95% confidence intervals (CIs) for dairy products in relation to annual eGFRcr-cysC change were obtained from multivariable linear regression, adjusted for age, sex, energy intake, and other lifestyle and dietary factors. Results: Baseline energy-adjusted median intakes were 64 g/day for total milk, 20 g/day for hard cheeses, 18 g/day for plain yogurt, and 70 g/day for dairy desserts. Mean ± SD eGFRcr-cysC was 84 ± 20 (13% with CKD), and annual eGFRcr-cysC change was −1.71 ± 3.85. In multivariable models, high vs. low intakes of total milk, cheese, and dairy desserts were not associated with annual eGFRcr-cysC change (βtotal milk: −0.21 [−0.60; 0.19], βcheese: −0.08 [−0.52; 0.36], βdairy desserts: −0.24 [−0.72; 0.24]). High vs. low intake of yogurt was adversely associated with annual eGFRcr-cysC change (βtotal yogurt: −0.50 [−0.91;-0.09]), but subsequent spline analyses showed no clear dose–response association. Conclusions: Intakes of milk, cheese or dairy desserts were not associated with a delayed kidney function decline after MI. The observed adverse association for yogurt should be interpreted with caution. Our findings require confirmation in other cohorts of coronary heart disease patients.</p

Body composition and plasma total-tau, neurofilament light chain, and amyloid-β:A population-based study

A higher body mass at older age has been linked to a lower risk of dementia. This unexpected trend may be explained by age-related lean mass depletion, or methodological issues such as the long preclinical phase of dementia or competing risks. Focusing on preclinical markers of dementia may overcome these issues. Between 2002 and 2005, body composition and plasma total-tau, neurofilament light chain (NfL), amyloid-β40, and amyloid-β42 were measured in 3408 dementia-free participants from the population-based Rotterdam Study. The cross-sectional associations between body composition and plasma markers were determined using linear regression models. Whole body and fat mass, but not lean mass, were positively associated with total-tau, while all these measures were inversely associated with NfL. Apart from an inverse association between lean mass and amyloid-β40, body composition measures were not associated with plasma amyloid-β. Our findings suggest distinct effects of body composition on neurodegeneration.</p

Body composition and plasma total-tau, neurofilament light chain, and amyloid-β:A population-based study

A higher body mass at older age has been linked to a lower risk of dementia. This unexpected trend may be explained by age-related lean mass depletion, or methodological issues such as the long preclinical phase of dementia or competing risks. Focusing on preclinical markers of dementia may overcome these issues. Between 2002 and 2005, body composition and plasma total-tau, neurofilament light chain (NfL), amyloid-β40, and amyloid-β42 were measured in 3408 dementia-free participants from the population-based Rotterdam Study. The cross-sectional associations between body composition and plasma markers were determined using linear regression models. Whole body and fat mass, but not lean mass, were positively associated with total-tau, while all these measures were inversely associated with NfL. Apart from an inverse association between lean mass and amyloid-β40, body composition measures were not associated with plasma amyloid-β. Our findings suggest distinct effects of body composition on neurodegeneration.</p

Associations of dietary patterns with objective and subjective sleep duration and sleep quality in a population-based cohort study

Objective: To examine cross-sectional and longitudinal associations of various types of dietary patterns with self-reported sleep quality and with actigraphy-estimated sleep parameters in the prospective, population-based Rotterdam Study. Methods: For each participant, scores for five different dietary patterns were derived based on food frequency questionnaires; two pre-defined scores developed to estimate adherence to the Dutch dietary guidelines and to the Mediterranean diet; and three data-driven scores indicating a prudent, unhealthy and typical Dutch diet. In 2589 participants (median age 56.9 years; 58 % female), self-rated sleep quality was assessed with the Pittsburgh Sleep Quality Index. In 533 participants, actigraphs were worn for an average of 6.8 days (SD: 0.7) to estimate total sleep time, sleep onset latency, wake after sleep onset, and sleep efficiency. Sleep parameters were measured at baseline and 3–6 years later. Multiple linear regression was used to assess cross-sectional and longitudinal associations. Results: No statistically significant associations between dietary patterns and total sleep time, sleep onset latency, wake after sleep onset, sleep efficiency and subjective sleep quality were observed in cross-sectional or longitudinal analyses. To illustrate, the effect estimate for sleep duration was 2.7 min per night (95 % CI -2.1, 7.5) per 5 point increase in Mediterranean diet score in the cross-sectional analyses. Furthermore, in longitudinal analyses, the effect estimate for sleep duration was −1.0 min per night (95 % CI -5.2, 3.1) per SD increase in the prudent diet. Conclusions: Our results suggest that dietary patterns are not associated with sleep in this population-based cohort study. Trial registration: Netherlands National Trial Register and WHO International Clinical Trials Registry Platform (ICTRP; https://apps.who.int/trialsearch/) shared catalogue number NL6645/NTR6831. Registered November 13th, 2017.</p

Diet quality in relation to kidney function and its potential interaction with genetic risk of kidney disease among Dutch post-myocardial infarction patients

Purpose: We examined the relation between diet quality, its components and kidney function decline in post-myocardial infarction (MI) patients, and we explored differences by genetic risk of chronic kidney disease (CKD). Methods: We analysed 2169 patients from the Alpha Omega Cohort (aged 60–80 years, 81% male). Dietary intake was assessed at baseline (2002–2006) using a validated food-frequency questionnaire and diet quality was defined using the Dutch Healthy Diet Cardiovascular Disease (DHD-CVD) index. We calculated 40-months change in estimated glomerular filtration rate (eGFR, mL/min per 1.73m2). We constructed a weighted genetic risk score (GRS) for CKD using 88 single nucleotide polymorphisms previously linked to CKD. Betas with 95%-confidence intervals (CIs) were obtained using multivariable linear regression models for the association between DHD-CVD index and its components and eGFR change, by GRS. Results: The average DHD-CVD index was 79 (SD 15) points and annual eGFR decline was 1.71 (SD 3.86) mL/min per 1.73 m2. The DHD-CVD index was not associated with annual eGFR change (per 1-SD increment in adherence score: -0.09 [95% CI -0.26,0.08]). Results for adherence to guidelines for red meat showed less annual eGFR decline (per 1-SD: 0.21 [0.04,0.38]), whereas more annual eGFR decline was found for legumes and dairy (per 1-SD: -0.20legumes [-0.37,-0.04] and − 0.18dairy [-0.34,-0.01]). Generally similar results were obtained in strata of GRS. Conclusion: The DHD-CVD index for overall adherence to Dutch dietary guidelines for CVD patients was not associated with kidney function decline after MI, irrespective of genetic CKD risk. The preferred dietary pattern for CKD prevention in CVD patients warrants further research.</p

Associations of dietary patterns with objective and subjective sleep duration and sleep quality in a population-based cohort study

Objective: To examine cross-sectional and longitudinal associations of various types of dietary patterns with self-reported sleep quality and with actigraphy-estimated sleep parameters in the prospective, population-based Rotterdam Study. Methods: For each participant, scores for five different dietary patterns were derived based on food frequency questionnaires; two pre-defined scores developed to estimate adherence to the Dutch dietary guidelines and to the Mediterranean diet; and three data-driven scores indicating a prudent, unhealthy and typical Dutch diet. In 2589 participants (median age 56.9 years; 58 % female), self-rated sleep quality was assessed with the Pittsburgh Sleep Quality Index. In 533 participants, actigraphs were worn for an average of 6.8 days (SD: 0.7) to estimate total sleep time, sleep onset latency, wake after sleep onset, and sleep efficiency. Sleep parameters were measured at baseline and 3–6 years later. Multiple linear regression was used to assess cross-sectional and longitudinal associations. Results: No statistically significant associations between dietary patterns and total sleep time, sleep onset latency, wake after sleep onset, sleep efficiency and subjective sleep quality were observed in cross-sectional or longitudinal analyses. To illustrate, the effect estimate for sleep duration was 2.7 min per night (95 % CI -2.1, 7.5) per 5 point increase in Mediterranean diet score in the cross-sectional analyses. Furthermore, in longitudinal analyses, the effect estimate for sleep duration was −1.0 min per night (95 % CI -5.2, 3.1) per SD increase in the prudent diet. Conclusions: Our results suggest that dietary patterns are not associated with sleep in this population-based cohort study. Trial registration: Netherlands National Trial Register and WHO International Clinical Trials Registry Platform (ICTRP; https://apps.who.int/trialsearch/) shared catalogue number NL6645/NTR6831. Registered November 13th, 2017.</p