Wageningen University & Research

Our research targets the role of forests under the international Paris Climate Agreement, the EU Green Deal and Forest Strategy. In line with the latter objectives, Member States are expected to encourage forest owners to contribute to international climate goals via national strategic plans and new management measures. How forest owners will respond, however, to a range of climate smart forestry (CSF) measures in the near future, is not well known. After postal and email distribution in 2020, 98 Swedish (response rate 21%) and 241 Dutch forest owners (24%) filled out a forest-climate survey. Based upon specific CSF measures, several hypothetical climate-related scenarios were incorporated into the survey. Dutch forest owners are planning to introduce new tree species, more mixed species stands (a gradual shift to broadleaved species) and additional water reservoirs in anticipation of increased drought periods, all part of a hypothetical climate adaptation package for 2030. Swedish forest owners prefer earlier thinning and salvaging activities. Zooming in on Dutch scale differences, small forest owners rely less on current public subsidy packages and show significantly less interest in committing to the adaptation package than large forest owners. In Sweden, preferences for the high forest management intensity scenario is significantly affected by size class: more intensive activities are the least popular with the smallest forest owners. The greatest difference between both countries is the way in which CSF measures should be financially supported. In general, Dutch forest owners would prefer to maintain subsidy schemes but adapt them to new circumstances, while Swedish forest owners benefit from timber and bioenergy markets. At the end there are some suggestions for a monitoring framework for resilient European forests.

Artificial reefs for coral reef restoration are often concrete-based. After concrete is poured, it initially has a high surface pH (approx. 13), which neutralizes within several weeks. During this curing, colonization by marine microalgae is delayed and also macrobenthos such as corals may be impacted. In this study, we evaluated how concrete curing time applied prior to the deployment of artificial reefs affected coral performance. Fragments of five coral species were outplanted onto ordinary Portland concrete discs (n = 10) that had been cured on land. Seven different curing periods were applied, ranging from one day up to four months. The discs with corals were deployed at a Kenyan reef and photographed at the start and end of the experiment. After 1 year, coral cover had increased for four coral species and declined for one, but this was unrelated to concrete curing time. Also, no effect of curing time was seen on the development of other common benthic organisms such as macroalgae or soft corals. We conclude that curing of concrete is unlikely to have any long-term negative impacts on coral performance and therefore, extended curing of artificial reefs prior to coral attachment is unlikely to benefit reef restoration efforts.

Processing large collections of earth observation (EO) time-series, often petabyte-sized, such as NASA’s Landsat and ESA’s Sentinel missions, can be computationally prohibitive and costly. Despite their name, even the Analysis Ready Data (ARD) versions of such collections can rarely be used as direct input for modeling because of cloud presence and/or prohibitive storage size. Existing solutions for readily using these data are not openly available, are poor in performance, or lack flexibility. Addressing this issue, we developed TSIRF (Time-Series Iteration-free Reconstruction Framework), a computational framework that can be used to apply diverse time-series processing tasks, such as temporal aggregation and time-series reconstruction by simply adjusting the convolution kernel. As the first large-scale application, TSIRF was employed to process the entire Global Land Analysis and Discovery (GLAD) ARD Landsat archive, producing a cloud-free bi-monthly aggregated product. This process, covering seven Landsat bands globally from 1997 to 2022, with more than two trillion pixels and for each one a time-series of 156 samples in the aggregated product, required approximately 28 hours of computation using 1248 Intel ® Xeon ® Gold 6248R CPUs. The quality of the result was assessed using a benchmark dataset derived from the aggregated product and comparing different imputation strategies. The resulting reconstructed images can be used as input for machine learning models or to map biophysical indices. To further limit the storage size the produced data was saved as 8-bit Cloud-Optimized GeoTIFFs (COG). With the hosting of about 20 TB per band/index for an entire 30 m resolution bi-monthly historical time-series distributed as open data, the product enables seamless, fast, and affordable access to the Landsat archive for environmental monitoring and analysis applications.

Background Over the course of evolution, insects have seen drastic changes in their mode of development. While insects with derived modes of development have been studied extensively, information on ancestral modes of development is lacking. To address this, we selected a member of one of the earliest lineages of extant flying insects, serving as an outgroup to the modern winged insects, the short germ, non-model mayfly Ephemera vulgata Linnaeus (Insecta: Ephemeroptera, Ephemeridae). We document the embryonic morphology throughout its development and establish a global temporal expression atlas. Results DAPI staining was used to visualise developmental morphology to provide a frame of reference for the sequenced timepoints. A transcriptome was assembled from 3.2 billion Illumina RNAseq reads divided in 12 timepoints with 3 replicates per timepoint consisting of 35,091 putative genes. We identified 6,091 significantly differentially expressed genes (DEGs) and analysed them for broad expression patterns via gene ontology (GO) as well as for specific genes of interest. This revealed a U-shaped relationship between the sum of DEGs and developmental timepoints, over time, with the lowest number of DEGs at 72 hours after egg laying (hAEL). Based on a principal component analysis of sequenced timepoints, overall development could be divided into four stages, with a transcriptional turning point around katatrepsis. Expression patterns of zld and smg showed a persistent negative correlation and revealed the maternal-to-zygotic transition (MZT), occurring 24 hAEL. The onset of development of some major anatomical structures, including the head, body, respiratory system, limb, muscle, and eye, are reported. Finally, we show that the ancestral short germ sequential mode of segmentation translates to a sequential Hox gene activation and find diverging expression patterns for lab and pb. We incorporate these patterns and morphological observations to an overview of the developmental timeline. Conclusions With our comprehensive differential expression study, we demonstrate the versatility of our global temporal expression atlas. It has the capacity to contribute significantly to phylogenetic insights in early-diverging insect developmental biology and can be deployed in both molecular and genomic applications for future research.

Frailty is characterized by loss of physical function and is preferably diagnosed at an early stage (e.g., during pre-frailty). Unfortunately, sensitive tools that can aid early detection are lacking. Blood-based biomarkers, reflecting pathophysiological adaptations before physical symptoms become apparent, could be such tools. We identified candidate biomarkers using a mechanism-based computational approach which integrates a priori defined database-derived clinical biomarkers and skeletal muscle transcriptome data. Identified candidate biomarkers were used as input for a sex-specific correlation analysis, using individual gene expression data from female ( n = 24) and male ( n = 28) older adults (all 75 + years, ranging from fit to pre-frail) and three frailty-related physical parameters. Male and female groups were matched based on age, BMI, and Fried frailty index. The best correlating candidate biomarkers were evaluated, and selected biomarkers were measured in serum. In females, myostatin and galectin-1 and, in males, cathepsin B and thrombospondin-4 serum levels were significantly different between the physically weakest and fittest participants (all p < 0.05). Logistic regression confirmed the added value of these biomarkers in conjunction with age and BMI to predict whether the subjects belonged to the weaker or fittest group (AUC = 0.80 in females and AUC = 0.83 in males). In conclusion, both in silico and in vivo analyses revealed the sex-specificity of candidate biomarkers, and we identified a selection of potential biomarkers which could be used in a biomarker panel for early detection of frailty. Further investigation is needed to confirm these leads for early detection of frailty.

Pathways linking texture and physical properties of bread to eating rate.

Untargeted metabolomics faces researchers with complex processing, analysis, and interpretation tasks. Here, we review computational tools from the perspective of information visualization and underpin its critical role and importance to the field.

In this review essay, I discuss how, in writing this book on how thinking is feeling, Donovan Schaefer is having a passionate love affair with an idea, how he pulls the bow string as far and still not enough to the point of breaking. I have three remarks/points of concern/comments specific to the outline of cogency theory. First, how thinking is feeling? If thinking is feeling is a process, how does it happen? Second, where does reframing science/knowledge as thinking is feeling take us? How can it reframe what we mean by science? And last, who is the thinking-feeling scientist-subject?

Background Anaemia is common in mothers and infants in the first year postpartum, especially in sub-Saharan Africa. We evaluated whether treating anaemia in the second trimester of pregnancy with a single dose of intravenous iron, ferric carboxymaltose, compared with standard-of-care oral iron could alleviate anaemia in postpartum women and their infants. Methods REVAMP (ACTRN12618001268235), an open-label, individually randomised, controlled trial done across nine urban and five rural health centres in Malawi, recruited women if they were in the second trimester of singleton pregnancy, had a capillary haemoglobin concentration of less than 10·0 g/dL, and had a negative malaria rapid diagnostic test. Once enrolled, women were randomly assigned (1:1) to receive intravenous ferric carboxymaltose (20 mg/kg up to 1000 mg) or standard of care (60 mg oral elemental iron twice daily for 90 days); all women received preventive malaria treatment. The primary endpoint of REVAMP was anaemia prevalence at 36 weeks of gestation, with follow-up of mothers and infants until 1 month postpartum. In REVAMP-EXTENDED, women from REVAMP who gave consent, and their infants, were followed up at 3, 6, 9, and 12 months postpartum, and venous blood was collected for haemoglobin, ferritin, and C-reactive protein measurement. Maternal postpartum outcomes comprised prevalence of anaemia (venous haemoglobin concentration <11 g/dL up to and including delivery and <12·0 g/dL postpartum) and haemoglobin concentration, as well as iron status (iron deficiency, defined as serum ferritin <15 μg/L, or <30 μg/L if C-reactive protein >5 mg/L, and iron deficiency anaemia [both iron deficiency and anaemia]). Infant outcomes comprised cord ferritin concentration, and haemoglobin and ferritin concentrations at 1, 3, 6, 9, and 12 months of age. Findings Between Nov 12, 2018, and March 2, 2021, 862 women were randomly assigned in REVAMP, of whom 793 (393 in the ferric carboxymaltose group [376 liveborn infants] and 400 [379 liveborn infants] in the standard-of-care group) provided consent for REVAMP-EXTENDED. At 12 months postpartum, ferritin concentrations were higher (geometric mean ratio 1·47 [95% CI 1·29–1·66], p<0·0001), and prevalence of iron deficiency was lower (prevalence ratio 0·65 [0·48–0·88], p=0·0050), in mothers receiving ferric carboxymaltose than in those receiving standard of care. Anaemia was less common in women who received ferric carboxymaltose than in those who received standard of care at 1 month (prevalence ratio 0·84 [95% CI 0·71–0·98], p=0·027), 3 months (0·75 [0·62–0·91], p=0·0029), and 6 months (0·78 [0·63–0·96], p=0·018) postpartum but not thereafter. There was no evidence of a difference between groups regarding cord ferritin, infant ferritin, or infant haemoglobin concentrations at any timepoint. Benefits on postpartum anaemia were restricted to mothers with baseline iron deficiency. Interpretation Ferric carboxymaltose treatment in the second trimester protected women from postpartum anaemia and iron deficiency but did not affect infant haematological or iron status. Funding Bill & Melinda Gates Foundation. Translation For the Chichewa translation of the abstract see Supplementary Materials section.

Since the early 2010s meat analogues, vegetarian or vegan products that mimic meat as closely as possible, have become an important part of the meat alternative assortment. In this chapter I consider the future of meat analogues. To do so, the timeline of meat analogues and competing alternatives is sketched. I then consider success and potential pitfalls of the meat analogue approach from the point of view of several consumer theories and approaches before arriving at the conclusion that meat analogues successfully address some consumer demands, in particular convenience, and the opportunity to use existing routines, but also hold some latent problems in regard to perceived naturalness and quality. I then outline three scenarios where meat analogues might be superseded, might remain the dominant meat alternative, or be relegated to a more modest role in a larger portfolio of alternatives. Regardless of the future, the role of meat analogues as catalyser for transition towards normalisation of eating meat alternatives cannot be denied.

The random encounter model (REM) estimates animal densities from camera‐trap data by correcting capture rates for a set of biological variables of the animals (average group size, speed and activity level) and characteristics of camera sensors. The REM has been widely used for setups in which cameras are mounted on trees or other structures aimed parallel to the ground. Here, we modify the REM formula to accommodate an alternative field of view acquired with vertically oriented camera traps, a type of deployment used to avoid camera theft and damage. We show how the calculations can be adapted to account for a different detection zone with minor modifications. We find that the effective detection area can be close to a rectangle with dimensions influenced by the properties of the Fresnel lens of the camera's motion sensor, the body mass of different species and the height of the camera. The other REM parameters remain the same. We tested the modified REM (vREM) by applying it to wildlife data collected with vertically oriented camera traps in Bardia National Park, Nepal. We further validated that the effective detection area for the camera model used was best approximated as a rectangle shape using maximum likelihood estimation. Density estimates obtained broadly matched independent density estimates for nine species from the previous studies in Bardia with varying body sizes by four orders of magnitude. We conclude that these modifications allow the REM to be effectively used for mammal density estimation for species with a wide range of body sizes, with vertically oriented camera traps.

Across the lifespan, diet and physical activity profiles substantially influence immunometabolic health. DNA methylation, as a tissue‐specific marker sensitive to behavioral change, may mediate these effects through modulation of transcription factor binding and subsequent gene expression. Despite this, few human studies have profiled DNA methylation and gene expression simultaneously in multiple tissues or examined how molecular levels react and interact in response to lifestyle changes. The Growing Old Together (GOTO) study is a 13‐week lifestyle intervention in older adults, which imparted health benefits to participants. Here, we characterize the DNA methylation response to this intervention at over 750 thousand CpGs in muscle, adipose, and blood. Differentially methylated sites are enriched for active chromatin states, located close to relevant transcription factor binding sites, and associated with changing expression of insulin sensitivity genes and health parameters. In addition, measures of biological age are consistently reduced, with decreases in grimAge associated with observed health improvements. Taken together, our results identify responsive molecular markers and demonstrate their potential to measure progression and finetune treatment of age‐related risks and diseases.

Rewetting peatlands is required to limit carbon dioxide (CO 2 ) emissions, however, raising the groundwater level (GWL) will strongly increase the chance of methane (CH 4 ) emissions which has a higher radiative forcing than CO 2 . Data sets of CH 4 from different rewetting strategies and natural systems are scarce, and quantification and an understanding of the main drivers of CH 4 emissions are needed to make effective peatland rewetting decisions. We present a large data set of CH 4 fluxes (FCH 4 ) measured across 16 sites with eddy covariance on Dutch peatlands. Sites were classified into six land uses, which also determined their vegetation and GWL range. We investigated the principal drivers of emissions and gapfilled the data using machine learning (ML) to derive annual totals. In addition, Shapley values were used to understand the importance of drivers to ML model predictions. The data showed the typical controls of FCH 4 where temperature and the GWL were the dominant factors, however, some relationships were dependent on land use and the vegetation present. There was a clear average increase in FCH 4 with increasing GWLs, with the highest emissions occurring at GWLs near the surface. Soil temperature was the single most important predictor for ML gapfilling but the Shapley values revealed the multi‐driver dependency of FCH 4 . Mean annual FCH 4 totals across all land uses ranged from 90 ± 11 to 632 ± 65 kg CH 4 ha ⁻¹ year ⁻¹ and were on average highest for semi‐natural land uses, followed by paludiculture, lake, wet grassland and pasture with water infiltration system. The mean annual flux was strongly correlated with the mean annual GWL ( R ² = 0.80). The greenhouse gas balance of our sites still needs to be estimated to determine the net climate impact, however, our results indicate that considerable rates of CO 2 uptake and long‐term storage are required to fully offset the emissions of CH 4 from land uses with high GWLs.

In this final Chapter, we synthesise the extensive research conducted throughout the book to address the fundamental question: ‘How can a new conceptualisation of Short Food Supply Chains (SFSCs) in EU regulatory frameworks unlock their full potential to influence and shape the future of sustainable agri-food systems?’. We begin by summarising the main findings of the conceptual and legal analysis, focusing particularly on the role of legal definitions in EU law and their implications for SFSC regulation. We advocate for a flexible approach that strikes a balance between clarity and coherence while allowing for contextual adaptation. Ultimately, we argue that SFSCs can fully realise their potential in shaping sustainable agri-food systems only if a harmonised framework is developed—one that integrates all dimensions of the agri-food system, transcends the traditional separation of the food and agriculture domains in SFSC regulation, and allow for some degree of flexibility.

This Chapter delves into a systematic assessment of the EU food legislation with regard to the concept of Short Food Supply Chain (SFSC). Despite the absence of a specific legal framework for SFSC initiatives within the food domain, various terms in EU food law establish a direct link—a nexus—with the SFSC concept. In this Chapter we identify these nexus terms across key EU food regulations, including the General Food Law Regulation (GFLR), the Food Hygiene Regulation, the Food Information to Consumer Regulation (FICR), the Food Quality Schemes Regulation, and the Organic Regulation. This Chapter examines how each regulation accommodates the unique attributes and needs of small producers within SFSCs. Moving from the question ‘How are SFSCs regulated in the food law domain?’, the analysis reveals a fragmented regulatory landscape characterised by flexibility, exclusion, or derogation from general rules. These exceptions often stem from factors such as the presence of direct producer-consumer interaction, the sale of small quantities of primary products, and the use of traditional local production methods. We conclude by emphasising the critical need for regulatory coherence to support these alternative production and consumption models, particularly in a context where the objective of food law is evolving beyond solely ensuring food safety to also addressing sustainability challenges.

The Farm to Fork (F2F) Strategy, aimed at reshaping EU food systems towards sustainability, represents a new departure point for a change in the food system, aiming to transcend the traditionally sectoral and narrow scope of existing agri-food policies. However, its potential to empower small-scale farmers and foster the development of Short Food Supply Chain (SFSC) initiatives remains questionable. The Chapter examines the F2F Strategy, the legislative initiatives targeting small farmers under its Action Plan, and its interplay with the 2023 Common Agricultural Policy (CAP). The central question guiding our research in this Chapter is: ‘What is the future for SFSC regulation in the current and post-Farm to Fork Strategy Era?’. Our objective is to identify points of convergence and divergence, highlighting the missed opportunities for SFSC operators within the current framework and delineating a possible scenario for the future. In our concluding remarks, we speculate on the post-Farm to Fork Strategy era, proposing the development of a ‘Reconciled F2F Agenda’. This agenda would seek to harmonise the diverse interests of all food system stakeholders and address the needs of small farmers operating at the local level through harmonised and tailored legal actions.

This Chapter scrutinises the impacts of the 2013 and 2023 CAP reforms on the position of small farmers operating at the small scale and local level within the agri-food chain. Traditionally conceptualised as a highly centralised policy, the CAP underwent a significant transformation from the 1990s onwards due to external pressures stemming from economic and environmental concerns, necessitating a reevaluation of its mission. The 2013 CAP aimed to enhance the efficiency and effectiveness of agricultural policy by simplifying administrative procedures while retaining centralised control over the management and oversight of financial support. In contrast, the 2023 reform ushered in a flexible, decentralised, and performance-based policy framework, delegating the responsibility of designing, implementing, and monitoring national agricultural plans to Member States to achieve CAP objectives. Guided by the questions ‘Which regulatory approach concerning the safeguarding and support of small farmers and their small-scale operations was discontinued between the 2013 and 2023 CAP reforms, and why?’, the Chapter delineates the key changes across the two reforms. It evaluates the relevant measures under Pillars I and II of the 2013 CAP and assesses the novelties introduced in the 2023 reform, charting a path forward in the regulation of small farmers and SFSC initiatives in the EU.