bluuebunny/crossref_metadata_2025_split huggingface dataset:
WormTracer: A precise method for worm posture analysis using temporal continuity
Authors: Kuze Koyo , Tazawa Ukyo T. , Suwazono Karin , Toyoshima Yu , Iino Yuichi 
Published: December 2023

AbstractThis study introduces WormTracer, a novel algorithm designed to accurately quantify temporal evolution of worm postures. Unlike conventional methods that analyze individual images separately, WormTracer estimates worm centerlines within a sequence of images concurrently. This process enables the resolution of complex postures that are difficult to assess when treated as isolated images. The centerlines obtained through WormTracer exhibit higher accuracy compared to those acquired using conventional methods. By applying principal component analysis to the centerlines obtained by WormTracer, we successfully generated new eigenworms, a basic set of postures, that enables a more precise representation of worm postures than existing eigenworms.Author summaryC. elegansis a valuable model organism for comprehensive understanding of genes, neurons and behavior. Quantification of behavior is essential for clarifying these relationships, and posture information plays a crucial role in the analyses. However, accurately quantifying the posture ofC. elegansfrom video images of worms is challenging, and while various methods have been developed to date, they have their own limitations.In this study, we developed an analytical tool called WormTracer, which can obtain worm centerlines more accurately than conventional methods, even when worms assume complex postures. Using this tool, we successfully obtained new eigenworms, basis postures of a worm, that can more accurately reproduce various postures than conventional eigenworms. WormTracer and the new eigenworms will be valuable assets for future quantitative studies on worm locomotion and sensorimotor behaviors.
Evolution of apoptotic signalling pathways within lophotrochozoans
Authors: Horkan Helen R , Popgeorgiev Nikolay , Vervoort Michel , Gazave Eve , Krasovec Gabriel 
Published: December 2023

AbstractApoptosis is the main form of regulated cell death in metazoans. Apoptotic pathways are well characterised in nematode, fly and mammals, leading to a vision of the conservation of apoptotic pathways in metazoans. However, we recently showed that intrinsic apoptosis is in fact divergent among metazoans. In addition, extrinsic apoptosis is poorly studied in non-mammalian animals, making its evolution unclear. Consequently, our understanding of apoptotic signalling pathways evolution is a black-box which must be illuminated by extending research to new biological systems. Lophotrochozoans are a major clade of metazoans which, despite their considerable biological diversity and key phylogenetic position as sister group of ecdysozoans (i.e.fly, nematode), are poorly explored, especially regarding apoptosis mechanisms. Traditionally each apoptotic signalling pathway was considered to rely on a specific initiator Caspase, associated with an activator. To shed light on apoptosis evolution in animals, we explored the evolutionary history of initiator Caspases, Caspase activators and the BCL-2 family (which control mitochondrial apoptotic pathway) in lophotrochozoans using phylogenetic analysis and protein interaction predictions. We discovered a diversification of initiator Caspases in molluscs, annelids and brachiopods, and the loss of key extrinsic apoptosis components in platyhelminths, along with the emergence of a clade specific Caspase with an ankyrin pro-domain. Taken together, our data show a specific history of apoptotic actors’ evolution in lophotrochozoans, further demonstrating the appearance of distinct apoptotic signalling pathways during metazoan evolution.Significance statementApoptosis, a form of programmed cell death, has been long studied in model organisms such as fly, mouse, and in humans. The restricted focus on these models has led to an overall view that the evolution of genes involved in apoptosis is highly conserved across all animals. The advent of next generation sequencing has led to a boom in the omics data available across the tree of life. Thanks to this, we explored the evolution of key genes involved in apoptosis in the clade Lophotrochozoa (i.e.molluscs, annelids, flatworms, brachiopods), one of the three large clades that make up bilaterian animals. We found a complex evolutionary history of apoptosis genes, with multiple losses, gains, divergences and redundancies, highlighting the value of exploring gene evolution and apoptotic mechanisms in Lophotrochozoans.
Sampling the Zebrafish gut Microbiota – A Genome Resolved Metagenomic Approach
Authors: Thormar Eiríkur Andri , Hansen Søren Blikdal , Jørgensen Louise von Gersdorff , Limborg Morten T. 
Published: December 2023

ABSTRACTThe zebrafish is a promising model organism in the field of functional microbiota research. However, studies on the functional landscape of the zebrafish gut microbiota through shotgun based metagenomics are scarce. Thus, there is a lack of consensus regarding an appropriate sampling method that accurately represents the zebrafish gut microbiota. To address this, we sought to systematically test and evaluate four different methods of sampling the zebrafish gut microbiota: collection of feces from the tank, the whole gut, intestinal content and the application of ventral pressure to facilitate extrusion of gut material. In addition, we included water samples as an environmental control to address the potential influence of the environmental microbiota on the data interpretation. To compare these sampling methods in a context of microbiota-based studies we employed a combination of genome resolved metagenomics and 16S metabarcoding techniques. We observed differences among sample types on all levels including sampling, bioinformatic processing, metagenome co-assemblies, generation of metagenome-assembled genomes (MAGs), functional potential, MAG coverage and micro-diversity. Furthermore, our comparison to the environmental control demonstrated the potential impact of the environmental contamination on data interpretation. The findings emphasise the importance of considering the choice of sampling method. While all sample types tested are informative about the zebrafish gut microbiota, the optimal sample type depends on the specific objectives of the study.
Interspecific relationships in a suboptimal habitat, an unexpected ally for the survival of the threatened Tenerife speckled lizard (Gallotia intermedia)
Authors: Albaladejo-Robles Gonzalo , Escánez Alejandro , Perera-Castro Alicia V. 
Published: December 2023

AbstractAnthropogenic-driven environmental changes are pushing species to the limits of their habitats. More often species are restricted to relic or suboptimal habitats that present the minimum requirements to sustain species populations. In this scenario of accelerated environmental change and biodiversity loss, is fundamental to understand why species can survive in such suboptimal conditions. We conduct an isotopic trophic analysis along with a behavioural experiment to show how novel ecological interactions allow an endangered species to maintain stable populations in suboptimal habitats. We show how the Tenerife speckled lizard (Gallotia intermedia), a critically endangered endemic reptile from Tenerife Island (Canary Islands), can maintain stable populations in relic habitats thanks to its interactions with the yellow-legged gull (Larus michahellis) colony. A stable isotope analysis revealed thatG. intermediarelies on marine subsidies for its diet and that the foraging area of this reptile is likely to be restricted to the limits ofL. michahellisbreeding colony. Furthermore, an antipredator behaviour analysis showed thatL. michahellisdisplayed a strong anti-predator or mobbing response against cats, one of the main threats forG. intermedia, thus potentially providing some protection to the reptiles inhabiting the seabird colony. Our results show how unusual and poorly studied biotic interactions can provide valuable resources and conditions for the conservation of a critically endangered species inhabiting a suboptimal or relict habitat.
High resolution optical spectroscopy for the evaluation of cannabidiol efficiency as a radiation therapy support of peripheral nervous system tumors
Authors: Chrabąszcz Karolina , Pogoda Katarzyna , Cieżak Klaudia , Panek Agnieszka , Kwiatek Wojciech M. 
Published: December 2023

AbstractAn increasing number of scientific papers discuss the promising therapeutic potential of cannabidiol (CBD) not only for the treatment of cancer, but also for asthma and neurodegenerative disorders. This happens mainly due to its proven anticancer, anti-inflammatory, and antioxidant properties. In the field of cancer research, the use of CBD has already been investigated on malignant tumors of the central nervous system, like gliomas. So far, CBD has not yet been explored in the therapy of peripheral nervous system (PNS) tumors. Peripheral nerves reside outside the central nervous system, therefore peripheral nerve tumors can occur anywhere in the body. When the tumor develops within large blood vessels, spinal nerves or involves more than one peripheral nerve, radiotherapy is recommended. Due to high doses of ionizing radiation, complications such as dizziness, damage to adjacent nerves, or malignancy of the lesion may occur. Therefore, it is important to develop a treatment scheme that efficiently reduces tumor volume while maintaining the normal functions of the surrounding cells and decrease the side effects. Herein, we proposed to combine hyperspectral imaging using Raman and FTIR spectroscopy and AFM-IR technique as a novel approach to monitor the therapeutic efficacy of CBD. Performed studies reviled the dual effect of CBD, that protects normal cells from ionizing radiation and increases its toxicity in cancer cells.
Predicting Anorexia Nervosa and Autistic Characteristics in Individuals with Anorexia Nervosa from Resting State Cyclic Connectivity
Authors: Halls Daniel , Leppanen Jenni , Williams Steve , Tchanturia Kate 
Published: December 2023

AbstractBackgroundResting state functional Magnetic Resonance Imaging (rsfMRI) differences have been reported in individuals with anorexia nervosa (AN). However, methodological issues limit inferences, the dynamic cyclic nature of the resting state signal has not been explored, neither has the association with known elevated autistic characteristics.Methods92 participants, 65 Individuals with AN and 27 controls underwent rsfMRI. Cyclic analysis was conducted to obtain pairwise relationships between regions. Classification of group and regression to predict autistic characteristics within the AN group was conducted, with model weights being explored to ascertain the most predictive pairwise relationships.ResultsPairwise relationships in the temporal, dorsal and ventral attention networks were most predictive of group. The anterior intraparietal sulcus, salience, dorsal attention, auditory dorsal posterior cingulate cortex, and ventral attention networks were most predictive of autistic characteristics.DiscussionSeveral distinct pairwise relationships predicting group and autistic characteristics were found, however, the global disruption of the temporal ordering of the cyclic wave, and variation in temporal ordering across resting state scan are also a neurophenotype in individuals with AN and the relationship to autistic characteristics. Characteristics associated with AN and autism are also predicted by distinct neural regions.
Modeling Sex Differences in the Effects of Diuretics in Renal Epithelial Transport during Angiotensin II-induced Hypertension
Authors: Zheng Kaixin , Layton Anita T. 
Published: December 2023

AbstractChronic angiotensin II (AngII) infusion is an experimental model that induces hypertension in rodents. The natriuresis, diuresis, and blood pressure responses differ between males and females, perhaps unexpectedly, given the rodent kidney, which plays a key role in blood pressure regulation, exhibit marked sex differences. Those sex differences include morphology, hemodynamics, and, under healthy (undrugged) conditions, solute and electrolyte transporter abundance. Notably, compared to the male rat nephron, the female rat nephron exhibits lower Na+/H+exchanger 3 (NHE3) activity along the proximal tubule, but higher Na+transporter activities along the distal segments. AngII infusion-induced hypertension induces a pressure natriuretic response that reduces NHE3 activity and shifts Na+transport capacity downstream, to different extents in the two sexes. The goals of this study are (i) to understand how the sexually dimorphic responses differentially impact segmental electrolyte transport following a 14- day AngII infusion, and (ii) to identify and explain any sex differences in the effects of loop diuretics, thiazide diuretics, and K+-sparing diuretics. To achieve those goals, we developed sex-specific computational models of renal epithelial transport of electrolytes and water. Model simulations suggest that the NHE3 downregulation in the proximal tubule is a major contributor to natriuresis and diuresis in hypertension, with a stronger effect in males. Due to the downstream shift of Na+transport load in hypertension, all three diuretic classes are predicted to induce stronger natriuretic and diuretic effects under hypertension compared to normotension, especially in females.New and NoteworthySex differences in the prevalence of hypertension are found in humans and animal models. The kidney, which plays an important role in blood pressure regulation, exhibits sex differences in morphology, hemodynamics, and membrane transporter distributions. This computational modeling study provides insights into how the sexually dimorphic responses to a 14-day angiotensin II infusion differentially impact segmental electrolyte transport. Simulations results also explain sex differences in the effects of loop diuretics, thiazide diuretics, and K+-sparing diuretics.
Fatty Acid Metabolism and The Oxidative Stress Response Support Bacterial Predation
Authors: Jain Rikesh , Le Nguyen-Hung , Bertaux Lionel , Baudry Jean , Bibette Jérôme , Denis Yann , Habermann Bianca H. , Mignot Tâm 
Published: December 2023

AbstractDespite growing awareness of their importance in soil ecology, the genetic and physiological traits of bacterial predators are still relatively poorly understood. In the course of aMyxococcus xanthuspredator evolution experiment, we discovered a class of genotypes leading to enhanced predation against diverse species. RNA-seq analysis demonstrated that this phenotype is linked to the constitutive activation of a predation-specific program. Functional analysis of the mutations accumulated across the evolutionary time in a two- component system and Acyl-CoA-manipulating enzymes revealed the critical roles of fatty acid metabolism and antioxidant gene induction. The former likely adapts the predator to metabolites derived from the prey while the latter protects predatory cells from reactive oxygen species (ROS) generated by prey cells under stress and released upon lysis during predation. These findings reveal interesting parallels between bacterial predator-prey dynamics and pathogen-host cell interactions.Significance StatementThis study illuminates the largely unexplored genetic and metabolic strategies used by bacterial predators in soil ecosystems. Through experimental evolution inMyxococcus xanthus, we discovered that more efficient predators accumulate mutations that activate a genetic program for predation. This program simultaneously triggers a metabolic shift favoring fatty acid degradation for energy production and upregulates antioxidant gene expression, enhancing protection against reactive oxygen species generated during prey cell lysis. This adaptive mechanism proves advantageous across a wide range of prey species, suggesting that metabolic adaptation plays a crucial role in the evolutionary trajectory of bacterial predators within their natural ecological niche.
Restoring Protein Glycosylation with GlycoShape
Authors: Ives Callum M , Singh Ojas , D’Andrea Silvia , Fogarty Carl A , Harbison Aoife M , Satheesan Akash , Tropea Beatrice , Fadda Elisa 
Published: December 2023

AbstractDuring the past few years, we have been witnessing a revolution in structural biology. Leveraging on technological and computational advances, scientists can now resolve biomolecular structures at the atomistic level of detail by cryogenic electron microscopy (cryo-EM) and predict 3D structures from sequence alone by machine learning (ML). One technique often supports the other to provide the view of atoms in molecules required to capture the function of molecular machines. An example of the extraordinary impact of these advances on scientific discovery and on public health is given by how structural information supported the rapid development of COVID-19 vaccines based on the SARS-CoV-2 spike (S) glycoprotein. Yet, none of these new technologies can capture the details of the dense coat of glycans covering S, which is responsible for its natural, biologically active structure and function and ultimately for viral evasion. Indeed, glycosylation, the most abundant post-translational modification of proteins, is largely invisible through experimental structural biology and in turn it cannot be reproduced by ML, because of the lack of data to learn from. Molecular simulations through high-performance computing (HPC) can fill this crucial information gap, yet the computational resources, the users’ skills and the long timescales involved limit applications of molecular modelling to single study cases. To broaden access to structural information on glycans, here we introduce GlycoShape (https://glycoshape.org) an open access (OA) glycan structure database and toolbox designed to restore glycoproteins to their native functional form by supplementing the structural information available on proteins in public repositories, such as the RCSB PDB (www.rcsb.org) and AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/), with the missing glycans derived from over 1 ms of cumulative sampling from molecular dynamics (MD) simulations. The GlycoShape Glycan Database (GDB) currently counts over 435 unique glycans principally covering the human glycome and with additional structures, fragments, and epitopes from other eukaryotic and prokaryotic organisms. The GDB feeds into Re-Glyco, a bespoke algorithm in GlycoShape designed to rapidly restore the natural glycosylation to protein 3D structures and to predictN-glycosylation occupancy, where unknown. Ultimately, integration of GlycoShape with other OA protein structure databases can provide a step-change in scientific discovery, from the structural and functional characterization of the active form of biomolecules, all the way down to pharmacological applications and drug discovery.
Polymorphism-aware models in RevBayes: Species trees, disentangling Balancing Selection and CG-biased gene conversion
Authors: Braichenko Svitlana , Borges Rui , Kosiol Carolin 
Published: December 2023

AbstractThe role of balancing selection is a long-standing evolutionary puzzle. Balancing selection is a crucial evolutionary process that maintains genetic variation (polymorphism) over extended periods of time; however, detecting it poses a significant challenge. Building upon the polymorphismaware phylogenetic models (PoMos) framework rooted in the Moran model, we introduce Po-MoBalance model. This novel approach is designed to disentangle the interplay of mutation, genetic drift, directional selection (GC-biased gene conversion), along with the previously unexplored balancing selection pressures on ultra-long timescales comparable with species divergence times by analysing multi-individual genomic and phylogenetic divergence data. Implemented in the open-source RevBayes Bayesian framework, PoMoBalance offers a versatile tool for inferring phylogenetic trees as well as quantifying various selective pressures. The novel aspect of our approach in studying balancing selection lies in PoMos’ ability to account for ancestral polymorphisms and incorporate parameters that measure frequency-dependent selection, allowing us to determine the strength of the effect and exact frequencies under selection. We implemented validation tests and assessed the model on the data simulated with SLiM and a custom Moran model simulator. Real sequence analysis ofDrosophilapopulations reveals insights into the evolutionary dynamics of regions subject to frequency-dependent balancing selection, particularly in the context of sex-limited colour dimorphism inDrosophila erecta.
Evaluation of phenotypic and genotypic methods for the identification and characterisation of bacterial isolates recovered from catheter-associated urinary tract infections
Authors: Varney Adam M. , Mannix-Fisher Eden , Thomas Jonathan C. , McLean Samantha 
Published: December 2023

AbstractPurposeUrinary tract infections are the most common type of hospital-acquired infection, up to 80% of which are associated with catheterisation. The present study evaluates phenotypic and genomic characterisation of a panel of catheter associated urinary tract infection isolates from a UK hospital.MethodsStrains were identified and characterised utilising a range of phenotypic and genomic techniques to understand where methodologies agree. The effect of medium composition on growth and biofilm formation phenotype was also determined to evidence the importance of assay design in characterisation of bacterial isolates.ResultsNo consensus was observed for any of the CAUTI isolates across five identification methods, including biochemical testing, MALDI and sequencing technologies. Comparison of EUCAST antimicrobial susceptibility testing and genotypic data for antibiotic resistance showed high concordance where strains were phenotypically resistant to multiple antibiotic classes, however discordance increased for strains that were phenotypically sensitive to range of antibiotics. Phenotypic analysis of bacterial pathogens often relies on the use of rich laboratory media; however, we observed significant differences in growth rate and biofilm formation within a range of media, with a trend towards comparatively low planktonic growth and significant biofilm biomass formation in artificial urine.ConclusionThis study emphasises potential pitfalls of relying on a single method of species identification, with only whole genome sequencing providing accurate identification of isolates to species level. Furthermore, it highlights the continuing importance of utilising phenotypic methods to understand antibiotic resistance within clinical settings and of utilising clinically relevant conditions for pathogen characterisation.
Modulating social learning-induced evaluation updating during human sleep
Authors: Chen Danni , Xia Tao , Yao Ziqing , Zhang Lingqi , Hu Xiaoqing 
Published: December 2023

AbstractPeople often change their evaluations upon learning about their peers’ evaluations, i.e., social learning. Given sleep’s vital role in consolidating daytime experiences, sleep may facilitate social learning and thereby further changing people’s evaluations. Combining a social learning task and the sleep-based targeted memory reactivation technique, we asked whether social learning-induced evaluation changes can be modulated during sleep. After participants indicated their initial evaluation for snacks, they learned about their peers’ evaluation while hearing the snacks’ spoken names. During the post-learning non-rapid-eye-movement sleep, we re-played half of the snack names (i.e., cued snack) to reactivate the associated peers’ evaluations. Upon waking up, we found that the social learning-induced evaluation changes further enlarged for both cued and uncued snacks. Examining sleep electroencephalogram (EEG) activity revealed that cue-elicited delta-theta EEG power and the overnight N2 sleep spindle density predicted post-sleep evaluation changes for cued but not for uncued snacks. Our findings suggested that sleep-mediated memory reactivation processes could strengthen social learning-induced evaluation changes.