Leiden University

Metacontextify: automated environmental annotation of marine metagenomic samples

Abstract Background Environmental metadata is essential for using metagenomic and microbiome data to gain relevant biological insights like relations between the environment and microbial communities, genome content and protein-level adaptations. Unfortunately, obtaining standard...

Uncertainty-Aware Tidal Disruption Event Classification : A Host-Agnostic Probabilistic Random Forest Approach

Abstract The classification of Tidal Disruption Events in large-scale photometric surveys is challenging because deterministic machine learning models produce overconfident misclassifications under varying data quality and low signal-to-noise conditions. Existing lightcurve-based...

Persistent Street Network and Changing Tourism-Related Functional Space: A Case Study of Pingyao, China, 2009–2023

The rise of tourism in historical cities has become a widely observed global phenomenon. As both urban heritage and channels of movement, streets influence the spatial distribution of tourism-related functions. It is important to understand how this influence has evolved over tim...

Childhood facial emotion recognition: Associations with the parental emotional environment and child emotional and behavioral problems

Abstract Impairments in negative facial emotion recognition (FER) are widely reported in children with internalizing and externalizing problems; however, it remains unclear whether these impairments reflect response biases or reduced discrimination accuracy. Children’s emotion so...

Paediatric haematopoietic stem cell transplantation research priorities: Results from an international multi‐stakeholder priority setting partnership

Summary Co‐designed research in paediatric HSCT is limited. We sought to determine research priorities which represent the shared priorities of patients, parents, carers and healthcare professionals (HCP) within Australia, New Zealand, the Netherlands and the United Kingdom. An i...

Steering and Setting Free: Insights From a 20‐Year Retrospective Case Study of a Security and Justice Organization's Digital Transformation

ABSTRACT Advances in digital technologies are expected to fundamentally change how organizations operate and create value. Empirical studies show that public organizations face difficulties organizing and sustaining this digital transformation. To better understand these challeng...

Quantifying pollen and spore morphology using a language model

In a typical systematic paper, specimen morphology is described with natural language, and taxonomic specialists use glossaries of technical terminology to establish and communicate taxon concepts, using morphology to delimit species. Textual descriptions of specimen morphology a...

AdventML: Advanced Enzyme Temperature Prediction with Transformer-Based Embeddings and Resampling Strategies

Abstract Accurate prediction of enzyme optimal catalytic temperature (Topt) is important for enzyme applications, particularly for identifying biocatalysts stable in extreme conditions, but experimental measurement remains costly and time-consuming. Here, we present AdventML, a m...

Spatial variation in liana effects on host‐tree allometry and biomass in an intact tropical forest

Lianas are increasing in abundance across the tropics, yet local spatial variation in their effects on host‐tree allometry and biomass, and the drivers of this variation within forests, remain poorly understood. Using field inventory, drone photogrammetry, and terrestrial laser s...

Electropolymerization Turns an Inactive Molecular Complex into a Water Oxidation Catalyst

Abstract Understanding how structure gives rise to function lies at the heart of catalysis. Yet one of the most fundamental open questions is whether catalytic activity can emerge purely from connectivity, without altering the composition or coordination of the molecular building...

MONKI: a three-dimensional Monte Carlo simulator for transfer of polarised light in planetary atmospheres

Abstract. Spectropolarimetry is a powerful tool for characterising planetary atmospheres and surfaces. For the design and operation of spectro(polari)metric instrumentation, numerically simulated signals of the measured radiation are essential. Here we present MONKI (Monte Carlo...

Redesigned Electricity Institutions with Micro-Nodal Competitive Markets Reduce Electricity Costs Substantially and Induce Dynamic Energy Innovation

The electricity grid is a collective good that tends toward monopoly. It links private electricity generation to private electricity use. Its institutions converged near-globally at the end of the 20th century. Large-scale producers have separated ownership from transmission syst...

Multi-lemma representation of Mandarin noun-noun compounds in speech production: EEG evidence

This study investigated how noun-noun compounds and their syntactic properties are represented in production. Participants’ naming latencies and electrophysiological responses were analysed to investigate the classifier congruency effect in Mandarin Chinese (Wang, M., Chen, Y., &...

Incidence of recurrent major bleeding and its impact on survival in LVAD patients: a multistate analysis

ABSTRACT Introduction Major bleeding frequently complicates the clinical course of left ventricular assist device (LVAD) therapy. However, data on recurrent major bleeding in destination therapy (DT) patients, as well as its impact on survival, is limited. Methods: Single-center...

Beyond the Lockdown: Long-Term Impact of COVID-19 on Registered Domestic Violence in the Netherlands

Domestic violence is a pervasive societal issue impacting millions of people worldwide. While numerous studies have examined the short-term impact of the COVID-19 restrictions on domestic violence, research on its long-term effects remains limited. This study aims to explore the...

Simultaneous PSF Matching via Dual Kernel Optimization

Abstract Standard point spread function (PSF) matching algorithms consider one image as the reference and aim to find a convolution kernel such that, when applied to the reference image, the PSFs of the reference and non-reference images are matched. This method works well if one...

The influence of heteroresistance, growth and antibiotic selection in shaping the invasion dynamics of colistin resistant Pseudomonas aeruginosa

Abstract Heteroresistance, where a small subpopulation of resistant cells coexists within an otherwise susceptible population, plays a critical role in bacterial survival during antibiotic exposure. Yet, its influence on the invasion success of resistant strains remains poorly un...

From silence to sharing: A six-month prospective study on adult disclosure of childhood sexual abuse

Background Disclosure of childhood sexual abuse (CSA) is often assumed to be beneficial. However, prospective research examining outcomes associated with disclosure remains scarce, limiting evidence-based guidance for adults considering disclosure. Objective The primary aim was t...

Plasma metabolomics reveals candidate biomarkers associated with individual treatment response in psoriatic arthritis

Psoriatic arthritis (PsA) is a clinically heterogeneous inflammatory disease for which optimal treatment selection remains unclear. Robust biomarkers that predict treatment response and identify patient-specific factors to inform treatment choice could advance precision medicine...

TLR Signaling Beyond Immunity: Emerging Roles in Cell Migration, Metabolism, Development, and Host–Microbiome Crosstalk

Recent findings support a broader view of TLR signaling as an integrative signaling hub that links immunity with cell migration, metabolism, development, and host–microbiome crosstalk. In cell migration, TLRs exert context-dependent effects through chemokine receptor regulation,...