Population-aware permutation-based significance thresholds for genome-wide association studies.

Motivation: Permutation-based significance thresholds have been shown to be a robust alternative to classical Bonferroni significance thresholds in genome-wide association studies (GWAS) for skewed phenotype distributions. The recently published method permGWAS introduced a batch-wise approach to efficiently compute permutation-based GWAS. However, running multiple univariate tests in parallel leads to many repetitive computations and increased computational resources.

The Field Automatic Insect Recognition-Device-A Non-Lethal Semi-Automatic Malaise Trap for Insect Biodiversity Monitoring: Proof of Concept.

Field monitoring plays a crucial role in understanding insect dynamics within ecosystems. It facilitates pest distribution assessment, control measure evaluation, and prediction of pest outbreaks. Additionally, it provides important information on bioindicators with which the state of biodiversity and ecological integrity in specific habitats and ecosystems can be accurately assessed.

No Future Growth Enhancement Expected at the Northern Edge for European Beech due to Continued Water Limitation.

With ongoing global warming, increasing water deficits promote physiological stress on forest ecosystems with negative impacts on tree growth, vitality, and survival. How individual tree species will react to increased drought stress is therefore a key research question to address for carbon accounting and the development of climate change mitigation strategies. Recent tree-ring studies have shown that trees at higher latitudes will benefit from warmer temperatures, yet this is likely highly species-dependent and less well-known for more temperate tree species.

Mechanisms determining the multi-diversity of carrion visiting species along a gradient of carrion body mass.

Resource availability and habitat heterogeneity are essential drivers of biodiversity, but their individual roles often remain unclear since both factors are often correlated. Here, we tested the more-individuals hypothesis (MIH) and the habitat-heterogeneity hypothesis (HHH) for bacteria, fungi, dipterans, coleopterans, birds, and mammals on 100 experimentally exposed carcasses ranging by three orders of magnitude in body mass. At the level of each carcass we found marginal or significant support for the MIH for bacteria, fungi, and beetles in spring and significant support for fungi, dipterans, and mammals in summer.

Guiding questions to avoid data leakage in biological machine learning applications.

Machine learning methods for extracting patterns from high-dimensional data are very important in the biological sciences. However, in certain cases, real-world applications cannot confirm the reported prediction performance. One of the main reasons for this is data leakage, which can be seen as the illicit sharing of information between the training data and the test data, resulting in performance estimates that are far better than the performance observed in the intended application scenario.

The benefits of permutation-based genome-wide association studies.

Linear mixed models (LMMs) are a commonly used method for genome-wide association studies (GWAS) that aim to detect associations between genetic markers and phenotypic measurements in a population of individuals while accounting for population structure and cryptic relatedness. In a standard GWAS, hundreds of thousands to millions of statistical tests are performed, requiring control for multiple hypothesis testing. Typically, static corrections that penalize the number of tests performed are used to control for the family-wise error rate, which is the probability of making at least one false positive.

Ways of integrating eating into everyday lives - a qualitative study in Germany.

Background: Food-related behaviour is a very complex topic. A common way to reduce complex issues to their essential content is to create a typology. In Germany, with regard to food-related behaviour, the creation of a typology has often been carried out by commercial research institutes, but also by (international) scientific institutes.

Cover crops support the climate change mitigation potential of agroecosystems.

Cover crops have the potential to mitigate climate change by reducing negative impacts of agriculture on ecosystems. This study is first to quantify the net climate change mitigation impact of cover crops including land-use effects. A systematic literature and data review was conducted to identify major drivers for climate benefits and costs of cover crops in maize (Zea maize L.

Role of CD4 T-cells for regulating splenic myelopoiesis and monocyte differentiation after experimental myocardial infarction.

Myocardial infarction (MI) induces the generation of proinflammatory Ly6C monocytes in the spleen and the recruitment of these cells to the myocardium. CD4 Foxp3 CD25 T-cells (Tregs) promote the healing process after myocardial infarction by engendering a pro-healing differentiation state in myocardial monocyte-derived macrophages. We aimed to study the effects of CD4 T-cells on splenic myelopoiesis and monocyte differentiation.

Comparative phytochemical analysis of cultivated and wild Boiss. & Heldr. subsp. infusions.

The present study focuses on the chemical composition of the infusions of subsp. from cultivated and wild populations using NMR, LC-DAD, LC-HRESIMS, and GC-MS techniques, to reveal possible differences. Mainly carbohydrates, flavonoids, and phenylethanoid glycosides were detected in the H-NMR spectra of both infusions.

Manually annotated and curated Dataset of diverse Weed Species in Maize and Sorghum for Computer Vision.

Sustainable weed management strategies are critical to feeding the world's population while preserving ecosystems and biodiversity. Therefore, site-specific weed control strategies based on automation are needed to reduce the additional time and effort required for weeding. Machine vision-based methods appear to be a promising approach for weed detection, but require high quality data on the species in a specific agricultural area.

Improving Agri-environmental Schemes: Suggestions from Farmers and Nature Managers in a Central European Region.

Agri-environmental schemes (AES) are important policy instruments within the Common Agricultural Policy (CAP) of the European Union for environmental protection. Due to the voluntary nature of AES, their attractiveness to farmers and stakeholders involved in nature management and protection (nature managers) is essential for high participation levels. This study aims to assess farmers' and nature managers' ideas to improve agri-environmental schemes.

Combining machine learning and optimization for the operational patient-bed assignment problem.

Assigning inpatients to hospital beds impacts patient satisfaction and the workload of nurses and doctors. The assignment is subject to unknown inpatient arrivals, in particular for emergency patients. Hospitals, therefore, need to deal with uncertainty on actual bed requirements and potential shortage situations as bed capacities are limited.

Earlier and more uniform spring green-up linked to lower insect richness and biomass in temperate forests.

Urbanization and agricultural intensification are considered the main causes of recent insect decline in temperate Europe, while direct climate warming effects are still ambiguous. Nonetheless, higher temperatures advance spring leaf emergence, which in turn may directly or indirectly affect insects. We therefore investigated how Sentinel-2-derived start of season (SOS) and its spatial variability (SV-SOS) are affected by spring temperature and whether these green-up variables can explain insect biomass and richness across a climate and land-use gradient in southern Germany.

Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats.

Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved.

Usage of Natural Health Products (NHPs) for respiratory diseases: user characteristics and NHP-Consumption behavior during the Covid-19 pandemic in Germany.

Background: Respiratory diseases (RD) can challenge healthcare systems around the globe. Natural health products (NHPs) are popular complementary and alternative medicine options for health issues concerning non-fatal RD. Little is known about the characteristics of the users of RD-NHPs and about their NHP consumption behavior during the Covid-19 pandemic in Germany.

Superior protein thermophilicity prediction with protein language model embeddings.

Protein thermostability is important in many areas of biotechnology, including enzyme engineering and protein-hybrid optoelectronics. Ever-growing protein databases and information on stability at different temperatures allow the training of machine learning models to predict whether proteins are thermophilic. predictions could reduce costs and accelerate the development process by guiding researchers to more promising candidates.

Predicting Gene Regulatory Interactions Using Natural Genetic Variation.

Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype-phenotype map. Although GWAS are usually used to assess simple univariate associations between genetic markers and traits of interest, it is also possible to infer the underlying genetic architecture and to predict gene regulatory interactions. In this chapter, we describe the latest methods and tools to perform GWAS by calculating permutation-based significance thresholds.

Improved weed segmentation in UAV imagery of sorghum fields with a combined deblurring segmentation model.

Background: Efficient and site-specific weed management is a critical step in many agricultural tasks. Image captures from drones and modern machine learning based computer vision methods can be used to assess weed infestation in agricultural fields more efficiently. However, the image quality of the captures can be affected by several factors, including motion blur.

Injurious pecking in organic turkey fattening-effects of husbandry and feeding on injuries and plumage damage of a slow- (Auburn) and a fast-growing (B.U.T.6) genotype.

Injuries and plumage damage (PD) are important indicators of welfare. First priority in turkey fattening is to reduce injurious pecking, which includes aggressive pecking (agonistic behavior) and additionally severe feather pecking (SFP) and cannibalism with their multifactorial reasons. Still, there are few studies available evaluating different genotypes for their welfare status under organic conditions.

Semi-Synthesis of Different Pyranoflavonoid Backbones and the Neurogenic Potential.

Flavonoids and chalcones are known for their manifold biological activities, of which many affect the central nervous system. Pyranochalcones were recently shown to have a great neurogenic potential, which is partly due to a specific structural motif-the pyran ring. Accordingly, we questioned if other flavonoid backbones with a pyran ring as structural moiety would also show neurogenic potential.

easyPheno: An easy-to-use and easy-to-extend Python framework for phenotype prediction using Bayesian optimization.

Summary: Predicting complex traits from genotypic information is a major challenge in various biological domains. With easyPheno, we present a comprehensive Python framework enabling the rigorous training, comparison and analysis of phenotype predictions for a variety of different models, ranging from common genomic selection approaches over classical machine learning and modern deep learning-based techniques. Our framework is easy-to-use, also for non-programming-experts, and includes an automatic hyperparameter search using state-of-the-art Bayesian optimization.

Metabolic Fingerprinting of Different Sideritis Taxa Infusions and Their Neurogenic Activity.

Over the last years, extracts were shown to improve memory. However, their potential to promote the generation of new neurons, starting with the neuronal differentiation of neural stem cells, remains unexplored. Therefore, the present study aimed to evaluate the neurogenic effects of different infusions in neural stem and precursor cells and their impact on cell viability.