bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjusted vascular contractility relies on integrity of progranulin pathway: Insights into mitochondrial function
Authors: Singh Shubhnita , Bruder-Nascimento Ariane , Costa Rafael M. , Alves Juliano V. , Bharathi Sivakama , Goetzman Eric S. , Bruder-Nascimento Thiago 
Published: November 2023

AbstractObjectiveCardiovascular disease (CVD) is a global health crisis and a leading cause of mortality. The intricate interplay between vascular contractility and mitochondrial function is central to CVD pathogenesis. The progranulin gene (GRN) encodes glycoprotein progranulin (PGRN), a ubiquitous molecule with known anti-inflammatory property. However, the role of PGRN in CVD remains enigmatic. In this study, we sought to dissect the significance of PGRN in the regulation vascular contractility and investigate the interface between PGRN and mitochondrial quality.MethodOur investigation utilized aortae from male and female C57BL6/J wild-type (PGRN+/+) and B6(Cg)-Grntm1.1Aidi/J (PGRN−/−) mice, encompassing wire myograph assays to assess vascular contractility and primary aortic vascular smooth muscle cells (VSMCs) for mechanistic insights.ResultsOur results showed suppression of contractile activity in PGRN-/- VSMCs and aorta, followed by reduced α-smooth muscle actin expression. Mechanistically, PGRN deficiency impaired mitochondrial oxygen consumption rate (OCR), complex I activity, mitochondrial turnover, and mitochondrial redox signaling, while restoration of PGRN levels in aortae from PGRN-/- mice via lentivirus delivery ameliorated contractility and boosted OCR. In addition, VSMC overexpressing PGRN displayed higher mitochondrial respiration and complex I activity accompanied by cellular hypercontractility. Furthermore, increased PGRN triggered lysosome biogenesis by regulating transcription factor EB and accelerated mitophagy flux in VSMC, while treatment with spermidine, an autophagy inducer, improved mitochondrial phenotype and enhanced vascular contractility. Finally, angiotensin II failed to induce vascular contractility in PGRN-/- suggesting a key role of PGRN to maintain the vascular tone.ConclusionOur findings suggest that PGRN preserves the vascular contractility via regulating mitophagy flux, mitochondrial complex I activity, and redox signaling. Therefore, loss of PGRN function appears as a pivotal risk factor in CVD development.
Pushing the boundaries of MEG based on optically pumped magnetometers towards early human life
Authors: Corvilain Pierre , Wens Vincent , Bourguignon Mathieu , Capparini Chiara , Fourdin Lauréline , Ferez Maxime , Feys Odile , De Tiège Xavier , Bertels Julie 
Published: November 2023

AbstractCharacterizing the early development of the human brain is critical from both fundamental and clinical perspectives. However, existing neuroimaging techniques are either not well suited to infants or have limited spatial or temporal resolution. The advent of optically pumped magnetometers (OPMs) has revolutionized magnetoencephalography (MEG) by enabling wearable and thus more naturalistic recordings while maintaining excellent sensitivity and spatiotemporal resolution. Nevertheless, its adaptation to studying neural activity in infancy poses several challenges. In this work, we present an original close-to-scalp OPM-MEG setup that successfully recorded brain responses to sounds in newborns. We exposed one-month-old infants to continuous streams of tones and observed significant evoked responses, which peaked ∼250 ms poststimulus at bilateral auditory cortices. When tones were presented at a steady fixed pace with an oddball tone every fourth tone, significant neural responses were found both at the frequency of the standard tones (3 Hz) and of the oddball tones (0.75 Hz). The latter reflects the ability of the newborn brain to detect auditory change and synchronize to regular auditory patterns. Additional analyses support the added value of triaxial OPMs to increase the number of channels on small heads. Finally, OPM-MEG responses were validated with those obtained from the same participants using an adult-sized cryogenic MEG. This study demonstrates the applicability of OPM-MEG to study early postnatal periods; a crucial step towards future OPM investigations of typical and pathological early brain development.
Leaderless consensus decision-making determines cooperative transport direction in weaver ants
Authors: Carlesso Daniele , Stewardson Madelyne , Garnier Simon , Feinerman Ofer , Reid Chris R. 
Published: November 2023

AbstractAnimal groups need to achieve and maintain consensus to minimise conflict among individuals and prevent group fragmentation. An excellent example of a consensus challenge is cooperative transport, where multiple individuals cooperate to move a large item together. This behavior, regularly displayed by ants and humans only, requires individuals to agree on which direction to move in. Unlike humans, ants cannot use verbal communication but most likely rely on private information and/or mechanical forces sensed through the carried item to coordinate their behaviour. Here we investigated how groups of weaver ants achieve consensus during cooperative transport using a tethered-object protocol, where ants had to transport a prey item that was tethered in place with a thin string. This protocol allows the decoupling of the movement of informed ants from that of uninformed individuals. We showed that weaver ants pool together the opinions of all group members to increase their navigational accuracy. We confirmed this result using a symmetry-breaking task, in which we challenged ants with navigating an open-ended corridor. Weaver ants are the first reported ant species to use a ‘wisdom of the crowd’ strategy for cooperative transport, demonstrating that consensus mechanisms may differ according to the ecology of each species.
Soil health increases primary productivity across Europe
Authors: Romero Ferran , Labouyrie Maëva , Orgiazzi Alberto , Ballabio Cristiano , Panagos Panos , Jones Arwyn , Tedersoo Leho , Bahram Mohammad , Guerra Carlos A. , Eisenhauer Nico , Tao Dongxue , Delgado-Baquerizo Manuel , García-Palacios Pablo , van der Heijden Marcel G.A. 
Published: November 2023

AbstractA healthy soil is at the core of sustainable management and policy, but its importance for plant productivity across environmental gradients and land-use types remains poorly understood. To address this gap, we conducted a pan-European field study including 588 sites from 27 countries to investigate the link between soil health and primary productivity across three major land-use types: woodlands, grasslands, and croplands. We found that mean soil health (a composite index based on soil properties, biodiversity, and plant disease control) in woodlands was 31.4% higher than in grasslands, and 76.1% higher than in croplands. Soil health was positively linked to cropland and grassland productivity at the continental scale. Woodland productivity was best explained by climate. Among microbial diversity indicators, we observed a positive association between the richness of Acidobacteria, Firmicutes, and Proteobacteria and primary productivity. Among microbial functional groups, we found that nitrogen-fixing bacteria and mycorrhizal fungi positively related to primary productivity in croplands and grasslands, while plant pathogens showed a negative relationship. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types.
Brain Injury Knowledge Ontology (BIKO) for traumatic brain injury: Formalizing concepts and methods used in translational traumatic brain injury research
Authors: Surles-Zeigler Monique C. , Sincomb Troy , Dixon C Edward , Imam Fahim , Gillespie Tom , Grethe Jeffrey S. , Ferguson Adam R. , Martone Maryann E. 
Published: November 2023

AbstractTraumatic brain injury (TBI) is an insult to the brain resulting from an external force and is a significant cause of morbidity and mortality in the United States. No effective clinical therapeutics currently exist for this injury. Although several therapies and procedures have been deemed successful for TBI treatment in preclinical research studies, they have yet to be translated into human patients. These discouraging results have left many scientists questioning the role of animal models in drug discovery for TBI.One major hurdle in translating the knowledge obtained in the laboratory to the clinic is the methodological variance across these studies. This variance can hinder the ability to draw conclusions from conflicting studies and aggregate data across various research studies, which ultimately impedes the ability to aggregate data across these studies. Therefore, addressing this variance is crucial for bridging the gap between the laboratory and the clinic. The increasing volume of papers and associated data being published every day makes this hurdle even more difficult to overcome. The initial steps to address these knowledge gaps are identifying these studies and creating a shared knowledge framework for mapping their terminology. We are developing the Brain Injury Knowledge Ontology (BIKO) to create a standardized model to describe methods and outcome measures used within preclinical and clinical TBI therapy studies to facilitate comparison across studies and models. The first version of BIKO focuses on modeling the major preclinical TBI models, e.g., Controlled Cortical Impact Model, Fluid Percussion Model, and Weight-Drop Model), major neurological injuries related to these models and their relationship to clinical pathophysiology. We show how BIKO provides a machine-readable way to represent the methodologies used in TBI therapeutic studies to compare models across clinically relevant features.
The laminar pattern of proprioceptive activation in human primary motor cortex
Authors: Knudsen Lasse , Guo Fanhua , Huang Jiepin , Blicher Jakob U. , Lund Torben E. , Zhou Yan , Zhang Peng , Yang Yan 
Published: November 2023

AbstractThe primary motor cortex (M1) has traditionally been viewed as a motor output generator. However, its vital role in proprioceptive somatosensation is increasingly being recognized. Yet, our understanding of proprioceptive somatosensation in M1 at the laminar scale is limited, largely due to methodological challenges. Empirical findings in primates and rodents suggest a pronounced role of superficial cortical layers, but the involvement of deep layers has yet to be examined in humans. Submillimeter resolution fMRI has emerged in recent years, paving the way for the study of layer-dependent activity in humans (laminar fMRI). In the present study, laminar fMRI was employed to investigate the laminar pattern of proprioceptive somatosensation on M1 deep layer activation using passive finger movements as proprioceptive stimulation. Significant M1 deep layer activation was observed in response to proprioceptive stimulation across 10 healthy subjects using vascular space occupancy (VASO) at 7T. For further validation, two additional subjects were scanned using a balanced steady-state free precession (bSSFP) sequence with ultrahigh (0.3 mm) in-plane resolution, yielding converging results. These results were interpreted in the light of previous laminar fMRI studies and the active inference account of motor control. We suggest that a considerable proportion of M1 deep layer activation is due to proprioceptive influence and that deep layers of M1 constitute a key component in proprioceptive circuits.
GRable version 1.0: A software tool for site-specific glycoform analysis with improved MS1-based glycopeptide detection with parallel clustering and confidence evaluation with MS2 information
Authors: Nagai-Okatani Chiaki , Tominaga Daisuke , Tomioka Azusa , Sakaue Hiroaki , Goda Norio , Ko Shigeru , Kuno Atsushi , Kaji Hiroyuki 
Published: November 2023

ABSTRACTHigh-throughput intact glycopeptide analysis is crucial for elucidating the physiological and pathological status of the glycans attached to each glycoprotein. Mass spectrometry-based glycoproteomic methods are challenging because of the diversity and heterogeneity of glycan structures. Therefore, we have developed an MS1-based site-specific glycoform analysis method named “Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile (Glyco-RIDGE)” for a more comprehensive analysis. This method detects glycopeptide signals as a cluster based on the mass and chromatographic properties of glycopeptides and then searches for each combination of core peptides and glycan compositions by matching their mass and retention time differences. Here we developed a novel browser-based software named GRable for semi-automated Glyco-RIDGE analysis with significant improvements in glycopeptide detection algorithms, including “parallel clustering.” This unique function improved the comprehensiveness of glycopeptide detection and allowed the analysis to focus on specific glycan structures, such as pauci-mannose. The other notable improvement is evaluating the “confidence level” of the GRable results, especially using MS2 information. This function facilitated reduced misassignment of the core peptide and glycan composition and improved the interpretation of the results. Additional improved points are: “correction function” for accurate monoisotopic peak picking; one-to-one correspondence of clusters and core peptides even for multiply sialylated glycopeptides; and “inter-cluster analysis” function for understanding the reason for detected but unmatched clusters. The significance of these improvements was demonstrated using purified and crude glycoprotein samples, showing that GRable allowed site-specific glycoform analysis of intact sialylated glycoproteins on a large scale and in depth. Therefore, this software will help to analyze the status and changes in glycans to obtain biological and clinical insights into protein glycosylation by complementing the comprehensiveness of MS2-based glycoproteomics. GRable can run freely online using a web browser via the GlyCosmos Portal (https://glycosmos.org/grable).Graphical Abstract
Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer
Authors: Raynal Flavien , Sengupta Kaustav , Plewczynski Dariusz , Aliaga Benoît , Pancaldi Vera 
Published: November 2023

AbstractCancer cells are highly plastic, allowing them to adapt to changing conditions. Genes related to basic cellular processes evolved in ancient species, while more specialized genes appeared later with multicellularity (metazoan genes) or even after mammals evolved. Transcriptomic analyses have shown that ancient genes are up-regulated in cancer, while metazoan-origin genes are inactivated. Despite the importance of these observations, the underlying mechanisms remain unexplored. Here, we study local and global epigenomic mechanisms that may regulate genes from specific evolutionary periods. Using evolutionary gene age data, we characterize the epigenomic landscape, gene expression regulation, and chromatin organization in three cell types: human embryonic stem cells, normal B-cells, and primary cells from Chronic Lymphocytic Leukemia, a B-cell malignancy. We identify topological changes in chromatin organization during differentiation observing patterns in Polycomb repression and RNA Polymerase II pausing, which are reversed during oncogenesis. Beyond the non-random organization of genes and chromatin features in the 3D epigenome, we suggest that these patterns lead to preferential interactions among ancient, intermediate, and recent genes, mediated by RNA Polymerase II, Polycomb, and the lamina, respectively.Our findings shed light on gene regulation according to evolutionary age and suggest this organization changes across differentiation and oncogenesis.
Molecular epidemiology of Cercospora leaf spot on resistant and susceptible sugar beet hybrids
Authors: Chen Chen , Keunecke Harald , Neu Enzo , Kopisch-Obuch Friedrich J. , McDonald Bruce A. , Stapley Jessica 
Published: November 2023

AbstractCercospora leaf spot (CLS), caused byCercospora beticola, is a major foliar disease impacting sugar beet production worldwide. The development of new resistant sugar beet hybrids is a powerful tool to better manage the disease, but it is unclear how these hybrids affect CLS epidemiology. We used a molecular epidemiology approach to study natural epidemics of CLS affecting two susceptible and two resistant sugar beet hybrids at two field sites.Infected plants were geotagged on a weekly basis. Isolations ofC. beticolawere made from infected leaves and genotyped using six simple sequence repeat loci to identify clones. We determined that CLS epidemics had a later onset in plots planted to resistant hybrids, but once the pathogen established an infection, there was little difference between resistant and susceptible hybrids in the probability of localized spread and dispersal. We found that different clones often infected the same leaf and that clusters of infected plants were often colonized by a mixture of clones. There was little overall difference in genetic diversity between resistant and susceptible hybrids, however genotypic evenness differed at one site. In this site we found one genotype restricted to the resistant cultivars at a high frequency. At the end of the epidemic infections were not randomly distributed across the fields and we found that a single clone could spread over a distance of 100 m during a growing season.
A dipteran parasite regulates 20E synthesis and antibacterial activity of the host for development through inducing host nitric oxide production
Authors: Dai Minli , Jiang Zhe , Li Fanchi , Wei Jing , Li Bing 
Published: November 2023

AbstractParasites primarily rely on the host to survive, and have evolved diverse survival strategies. In the present study, we report a specific survival strategy of a dipteran parasiteExorista sorbillans(Diptera: Tachinidae), which is a potential biological control agent for agricultural pests and a pest in sericulture. We found that the expression levels of host nitric oxide synthase (NOS) and nitric oxide (NO) production were increased afterE. sorbillansinfection. Reducing NOS expression and NO production with a NOS inhibitor (L-NAME) in infected hosts significantly impeded the growth ofE. sorbillanslarvae. Moreover, the 20-hydroxyecdysone (20E) biosynthesis of infected hosts was elevated with increasing NO production, and inhibiting NOS expression also lowered 20E biosynthesis. More importantly, induced NO synthesis was required to eliminate intracellular bacterial pathogens that presumably competed for shared host resources. Inhibiting NOS expression down-regulated the transcription of antimicrobial peptide genes and increased the number of bacteria in infected hosts. Collectively, this study revealed a new perspective on the role of NO in host-parasite interactions and a novel mechanism for parasite regulation of host to support its development.Author summaryParasites are ubiquitous on earth and diverse, and have evolved various strategies to match their own specific requirements for survival within the host. In this study, we found thatExorista sorbillans, an endoparasite of many agricultural pests and the main insect pest in sericulture, used a novel strategy to manipulate its host NO synthesis for survival within its hostBombyx mori. Specifically, NOS expression and the production of NO in the host were up-regulated byE. sorbillansinfection, which benefited larvalE. sorbillansdevelopment. Meanwhile, increased NO production in host activated 20E synthesis of parasitized hosts and triggered the expression of AMPs against the invasion of pathogenic bacteria to avoid nutritional competence in the host. Our study provides innovative insights into the mechanisms by which a parasite manipulates host NO production for development and may help to expand our knowledge of other parasitic systems.
Terrestrial land cover shapes fish diversity in major subtropical rivers
Authors: Zhang Heng , Blackman Rosetta C. , Furrer Reinhard , Osathanunkul Maslin , Brantschen Jeanine , Di Muri Cristina , Harper Lynsey R. , Hänfling Bernd , Niklaus Pascal A. , Pellissier Loïc , Schaepman Michael E. , Zong Shuo , Altermatt Florian 
Published: November 2023

AbstractFreshwater biodiversity is critically affected by human modifications of terrestrial land use and land cover (LULC)1,2. Yet, knowledge of the spatial extent and magnitude of LULC-aquatic biodiversity linkages is still surprisingly limited, impeding the implementation of optimal management strategies3. Here, we compiled fish diversity data across a 160,000-km2subtropical river catchment in Thailand characterized by exceptional biodiversity4yet intense anthropogenic alterations5, and attributed fish species richness and community composition to contemporary terrestrial LULC across the catchment. We estimated a spatial range of LULC effects extending up to about 20 km upstream from sampling sites, and explained nearly 60 % of the variance in the observed species richness, associated with major LULC categories including croplands, forest, and urban areas. We find that integrating both spatial range and magnitudes of LULC effects is needed to accurately predict fish species richness. Further, projected LULC changes showcase future gains and losses of fish species richness across the river network and offer a scalable basis for riverine biodiversity conservation and land management, allowing for potential mitigation of biodiversity loss in highly diverse yet data-deficient tropical to sub-tropical riverine habitats.
A single changing hypernetwork to represent (social-)ecological dynamics
Authors: Gaucherel C. , Cosme M. , Noûs C. , Pommereau F. 
Published: November 2023

AbstractTo understand and manage (social-)ecological systems, we need an intuitive and rigorous way to represent them. Recent ecological studies propose to represent interaction networks into modular graphs, multiplexes and higher-order interactions. Along these lines, we argue here that non-dyadic (non-pairwise) interactions are common in ecology and environmental sciences, necessitating fresh concepts and tools for handling them. In addition, such interaction networks often change sharply, due to appearing and disappearing species and components. We illustrate in a simple example that any ecosystem can be represented by a single hypergraph, here called the ecosystem hypernetwork. Moreover, we highlight that any ecosystem hypernetwork exhibits a changing topology summarizing its long term dynamics (e.g., species extinction/invasion, pollutant or human arrival/migration). Qualitative and discrete-event models developed in computer science appear suitable for modeling hypergraph (topological) dynamics. Hypernetworks thus also provide a conceptual foundation for theoretical as well as more applied studies in ecology (at large), as they form the qualitative backbone of ever-changing ecosystems.