bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal and spatial variability in availability bias has consequences for marine bird abundance estimates during the non-breeding season
Authors: Dunn Ruth E , Duckworth James , O’Brien Susan , Furness Robert W , Buckingham Lila , Daunt Francis , Bogdanova Maria , Green Jonathan A. 
Published: March 2024

AbstractTo effectively monitor how marine ecosystems are being reshaped by anthropogenic pressures, we require understanding of species abundances and distributions. Due to their socio-economic and ecological value, predatory species are often at the forefront of survey efforts. However, survey data are only valuable if they can reliably be converted into estimates of underlying distributions.We consider at-sea surveys of marine predators that often inform ecological impact assessments of offshore windfarms. These surveys are subject to a form of detection bias called ‘availability bias’ whereby individuals which are submerged below the surface are consequently ‘unavailable’ for detection. Although correction factors are commonly used in these surveys, they are currently based on limited data that may not be species-, time-, or area-specific. Here, we use time-depth-recorder data to investigate variation in marine bird availability bias.We found that the proportion of diving marine birds submerged below the sea surface during daylight hours, and therefore unavailable to be counted during surveys, varied by species, month, and area. For three of our focal species wintering around northwest Europe (Atlantic puffin, common guillemot, razorbill) our results were different to comparable values previously used to correct for the availability bias, whereas no correction factors are regularly used for the fourth species (red-throated diver). We now present availability bias correction factors that are species- and month-specific to the areas the study populations use during their non-breeding seasons: the North Sea, the north and west coasts of the UK, the Baltic Sea, and Icelandic coastal waters.Synthesis and applications:Variation in the proportion of daylight hours that marine birds spent submerged lead to differences in availability bias correction factors, thereby impacting estimations of their abundances. We encourage use of correction factors that use data from the species, marine area, and month during which surveys are conducted to provide more accurate abundance estimates. Using more relevant correction factors will result in increasingly accurate abundance and distribution estimates of diving marine birds, with relevance for a range of applications including planning for offshore windfarm developments, the designation and monitoring of protected areas, and understanding environmental change.
Comparative Evaluation of Bioinformatic Pipelines for Full-Length Viral Genome Assembly
Authors: Zsichla Levente , Zeeb Marius , Fazekas Dávid , Áy Éva , Müller Dalma , Metzner Karin J. , Kouyos Roger , Müller Viktor 
Published: March 2024

AbstractThe increasingly widespread application of next-generation sequencing (NGS) in clinical diagnostics and epidemiological research has generated a demand for robust, fast, automated, and user-friendly bioinformatic workflows. To guide the choice of tools for the assembly of full-length viral genomes from NGS datasets, we assessed the performance and applicability of four widely adopted bioinformatic pipelines (shiver - for which we created a user-friendly Dockerized version, referred to as dshiver; SmaltAlign, viral-ngs, and V-pipe) using both simulated datasets and real-world HIV-1 paired-end short- read sequences and default settings.All four pipelines produced high-quality consensus genome assemblies and minority variant calls when the reference sequence used for assembly had high similarity to the analyzed sample. However, while shiver and SmaltAlign showed robust performance also with more divergent samples (non-matching subtypes), viral-ngs and V-Pipe proved to be sensitive to genetic distance from the reference sequence. With empirical datasets, SmaltAlign and viral-ngs exhibited substantially shorter runtime compared to V-Pipe and shiver. In terms of applicability, V-Pipe provides the broadest functionalities; SmaltAlign and dshiver combine user-friendliness with robustness; while the use of viral-ngs requires a less computational resources compared to other tools.To conclude, all four pipelines can perform well in terms of quality metrics; however, the reference sequence needs to be adjusted to closely match the sample data for viral-ngs and V-Pipe. Differences in user-friendliness and runtime may guide the choice of the pipeline in a particular setting. The new Dockerized version of shiver offers ease of use in addition to the accuracy and robustness of the original pipeline.
Spatial integration of sensory input and motor output inPseudomonas aeruginosachemotaxis through colocalized distribution
Authors: Wu Zhengyu , Tian Maojin , Fu Sanyuan , Chen Min , Zhang Rongjing , Yuan Junhua 
Published: March 2024

AbstractThe opportunistic pathogenPseudomonas aeruginosaserves as a model organism for studying multiple signal transduction pathways. The chemoreceptor cluster, a core component of the chemotaxis pathway, is assembled from hundreds of proteins. The unipolar distribution of receptor clusters has long been recognized, yet the precise mechanism governing their assembly remains elusive. Here, we directly observed the relative positions of the flagellar motor and chemoreceptor cluster using flagellar filament labeling and gene editing techniques. Surprisingly, we found that both are located at the same cell pole, with the distribution pattern controlled by the polar anchor protein FlhF. Additionally, the efficient assembly of the chemoreceptor cluster is partially dependent on the integrity of the motor structure. Furthermore, we discovered that overexpression of the chemotaxis regulatory protein CheY leads to high intracellular levels of the second messenger c-di-GMP, triggering cell aggregation. Therefore, the colocalization of the chemoreceptor cluster and flagellum inP. aeruginosaserves to avoid cross-pathway signaling interference, enabling cells to conduct various physiological activities in an orderly manner.
Engineered Migrasomes: A Robust, Thermally Stable Vaccination Platform
Authors: Wang Dongju , Wang Haifang , Wan Wei , Zhu Zihui , Sho Takami , Zheng Yi , Zhang Xing , Dou Longyu , Ding Qiang , Yu Li , Liu Zhihua 
Published: March 2024

AbstractThe burgeoning abilities of pathogens and tumor cells to evade immune responses underscore the urgent need for innovative vaccination platforms based on a variety of biological mechanisms. The current logistical challenges associated with cold-chain (i.e. low-temperature) transportation particularly impacts access to vaccines in the global south. We recently discovered organelles called migrasomes, and herein we investigate the potential of migrasomes as an alternative vaccination platform. Their inherent stability and their enrichment with immune-modulating molecules make migrasomes promising candidates, but their low yield presents a hurdle. We address this problem through our engineered migrasome-like vesicles (eMigrasomes), which emulate the biophysical attributes of natural migrasomes with substantially improved yield. We show that eMigrasomes loaded with a model antigen elicit potent antibody responses and maintain stability at room temperature. We demonstrate that eMigrasomes bearing the SARS-CoV-2 Spike protein induce robust humoral protection against the virus. Our study demonstrates the potential of eMigrasome-based vaccines as a unique, robust, and accessible alternative to traditional methods.
Convergent evolution during host range expansion and virulence increase in aSalmonellabacteriophage
Authors: Maurin Amandine , Vasse Marie , Breyton Cécile , Zarate-Chaves Carlos , Bouzidi Sarah , Hayer Juliette , Dainat Jacques , Mesleard-Roux Margaux , Weill François-Xavier , Bravo Ignacio G. , Feugier Alexandre , Froissart Rémy 
Published: March 2024

AbstractViral host range expansion is predicted to evolve at the cost of reduced mean fitness. We investigated the adaptive walks of a virulent phage (Tequintavirus) in a spatially variable environment composed of four susceptible bacterial isolates and four resistant ones (Salmonella entericaserotype Tennessee, sequence types ST5018 and ST319 respectively). Starting from a single ancestral phage, we evolved multiple independent populations through serial passages on non-coevolving bacteria, following the Appelmans protocol. The phage populations evolved an expanded host range and increased virulence. Whole-genome sequencing revealed recurrent parallel mutations across populations (i.e. convergent evolution), particularly in genes encoding exo- and endo-nucleases, dUTPase, and caudal proteins. Notably, two parallel mutations in the gene coding for theLong Tail Fibrebecame fixed early in the evolutionary trajectories. Reverse-genetics experiments introducing these mutations into the ancestral genome expanded the host range but yielded only marginal increases in virulence, highlighting the effect of compensatory mutations.Abstract FigureHighlightsA phage (Tequintavirus) was evolved on susceptible and resistantSalmonella entericastrainsExperimentally evolved phage populations displayed expanded host range and increased virulenceConvergent evolution revealed adaptive mutations modifying receptor recognition in caudal proteinsReverse-genetic showed implication of two Long Tail Fibre mutations in host range expansionIn BriefGeneralism is traditionally predicted to evolve at the cost of lower mean fitness. Contrary to this textbook view, we demonstrate that generalist phages with expanded host range and increased virulence can readily evolvein vitroand be purposely optimized for phage therapy applications.
Two-photon excitation two-dimensional fluorescence spectroscopy (2PE-2DFS) of the fluorescent nucleobase 6-MI
Authors: Albrecht Claire S. , Scatena Lawrence F. , von Hippel Peter H. , Marcus Andrew H. 
Published: March 2024

ABSTRACTBase stacking is fundamentally important to the stability of double-stranded DNA. However, few experiments can directly probe the local conformations and conformational fluctuations of the DNA bases. Here we report a new spectroscopic approach to study the local conformations of DNA bases using the UV-absorbing fluorescent guanine analogue, 6-methyl isoxanthopterin (6-MI), which can be used as a site-specific probe to label DNA. In these experiments, we apply a two-photon excitation (2PE) approach to two-dimensional fluorescence spectroscopy (2DFS), which is a fluorescence-detected nonlinear Fourier transform spectroscopy. In 2DFS, a repeating sequence of four collinear laser pulses (with center wavelength ∼ 675 nm and relative phases swept at radio frequencies) is used to excite the lowest energy electronic-vibrational (vibronic) transitions of 6-MI (with center wavelength ∼ 340 nm). The ensuing low flux fluorescence is phase-synchronously detected at the level of individual photons and as a function of inter-pulse delay. The 2PE transition pathways that give rise to electronically excited state populations include optical coherences between electronic ground and excited states and non-resonant (one-photon-excited) virtual states. Our results indicate that 2PE-2DFS experiments can provide information about the electronic-vibrational spectrum of the 6-MI monomer, in addition to the conformation-dependent exciton coupling between adjacent 6-MI monomers within a (6-MI)2dimer. In principle, this approach can be used to determine the local base-stacking conformations of (6-MI)2dimer-substituted DNA constructs.
Infiltrative classical monocyte-derived andSPP1lipid-associated macrophages mediate inflammation and fibrosis in ANCA-associated glomerulonephritis
Authors: Vegting Yosta , Jongejan Aldo , Neele Annette E , Claessen Nike , Sela Gal , Prange Koen H M , Kers Jesper , Roelofs Joris J T H , van der Heijden Joost W , de Boer Onno J , Remmerswaal Ester B M , Vogt Liffert , Bemelman Frederike J , de Winther Menno P J , Moerland Perry D , Hilhorst Marc L 
Published: March 2024

AbstractBackgroundKidney macrophage infiltration is a histological hallmark of vasculitic lesions and is strongly linked to disease activity in anti-neutrophil cytoplasmic antibodies (ANCA)-associated glomerulonephritis (AGN). The precise mechanisms by which kidney macrophages influence local inflammation and long-term damage remain largely unknown.MethodsHere, we investigate kidney macrophage diversity using single-cell transcriptome analysis of 25,485 freshly retrieved unfrozen, high-quality kidney CD45+immune cells from five AGN patients, a lupus nephritis and nephrectomy control. Detailed subclustering of myeloid cells was performed to identify disease-specific macrophage subtypes. Next, transcriptome differences between macrophage subsets and disease serotypes were assessed. Findings were validated by immunostainings of an extended cohort of kidney biopsies and flow cytometric analysis of peripheral blood monocytes.ResultsFour main macrophage subsets were identified, including a classical monocyte-derived macrophage (MDM) subset expressing a chemotactic (CXCL2, CXCL3, CXCL8,CCL3) and pro-inflammatory (IL1β, TNF) set of markers and a osteopontin/SPP1+lipid-associated macrophage (SPP1LAMs) subtype exhibiting distinctive upregulation of fibrotic genesets. AGN samples revealed a markedly increased proportion of CD163+macrophages, predominantly composed of classical MDMs, accompanied by resident-likeC1Qmacrophages, andSPP1LAMs. An analogous trend was observed in the expansion of peripheral blood classical monocytes during active disease. The proteinase 3 (PR3)-AGN subtype exhibited heightened classical MDM infiltration and markers of acute inflammation, while interferon signaling and markers of chronicity were reduced compared to myeloperoxidase (MPO)-AGN.ConclusionsOur findings highlight the expression of inflammatory and fibrotic genes by kidney macrophage subsets in AGN. Classical monocyte dysregulation might contribute to inflammation in the pathogenesis of AGN. Targeting these specific monocyte/macrophage subsets may potentially control the inflammatory cascade and attenuate resulting fibrosis in AGN and kidney disease in general.Key points- Classical monocyte-derived macrophages are predominant in ANCA-associated glomerulonephritis and exhibit chemotactic and pro-inflammatory markers- Osteopontin/SPP1+lipid-associated macrophages (SPP1LAMs) show distinctive upregulation of fibrotic genesets- Understanding of the macrophage immune response supports exploration of macrophage-directed therapies for the treatment of autoimmune kidney diseases
Genetic signatures in the highly virulent subtype B HIV-1 conferring immune escape to V1/V2 and V3 broadly neutralizing antibodies
Authors: Marichannegowda Manukumar , Heredia Alonso , Wang Yin , Song Hongshuo 
Published: March 2024

AbstractHIV-1 is considered to become less susceptible to existing neutralizing antibodies over time. Our study on the virulent B (VB) HIV-1 identified genetic signatures responsible for immune escape from broadly neutralizing antibodies (bNAbs) targeting V1/V2 and V3 glycan epitopes. We found that the absence of N295 and N332 glycans in the high mannose patch, which are crucial for neutralization by V3 glycan bNAbs and are typically conserved in subtype B HIV-1, is a notable feature in more than half of the VB variants. Neutralization assays confirmed that the loss of these two glycans in VB HIV-1 leads to escape from V3 glycan bNAbs. Additionally, all VB variants we investigated have an insertion in V2, contributing to immune escape from V1/V2 bNAbs PG9 and PG16. These findings suggest potential co-evolution of HIV-1 virulence and antigenicity, underscoring the need to monitor both the pathogenicity and neutralization susceptibility of newly emerged HIV-1 strains.
The chromokinesin Kid (KIF22) forms a homodimer, moves processively along microtubules and transports double-strand DNA
Authors: Niwa Shinsuke , Furusaki Natsuki , Kita Tomoki , Suzuki Yuki , Chiba Kyoko 
Published: March 2024

AbstractDuring prometaphase in mitosis, chromosomes are pushed toward the spindle equator. The chromokinesin Kid, also known as KIF22, moves chromosomes along spindle microtubules during prometaphase. Kid has long been considered as a monomeric and non-processive motor, different from typical kinesins. In this study, we demonstrate that the full-length Kid forms a homodimer and moves processively along microtubules. A conserved coiled-coil domain within the stalk region of Kid is not only capable of homodimer formation, but is also required for the processivity of Kid. Furthermore, the neck linker and coiled-coil domains of Kid could add processive activity to the motor domain of KIF1A, suggesting that Kid contains a functional neck linker and dimerization capability, a prerequisite for the processivity of kinesin motor domains. The full-length Kid, containing a helix-hairpin-helix domain, can transport double-strand DNA along microtubules in vitro. These findings collectively suggest the reclassification of Kid as a processive motor that transports DNA along microtubules.
Searching thePinus taedafoliar mycobiome for emerging pathogens among brown spot needle blight and needlecast outbreaks in the Southeast United States
Authors: Meinecke Colton D. , Niyas Afaq M.M. , McCarty Elizabeth , Quesada Tania , Smith Jason A. , Villari Caterina 
Published: March 2024

AbstractNeedle pathogens cause the discoloration, death, or premature abscission of conifer foliage, which reduce growth and vigor, and repeated defoliation may eventually result in tree mortality. Since 2016, forest managers in the southeast United States have reported an increasing scale, frequency, and severity of needle disease outbreaks on the region’s principal timber species, loblolly pine (Pinus taedaL.). These recent outbreaks are raising concern throughout the region, as needle diseases are not traditionally considered a threat toP. taeda.Lecanosticta acicola(Thum.) Syd., the native causal agent of brown-spot needle blight, has been recovered from some outbreaks, however, the full array of fungi associated with symptoms has not been explored. In this research,P. taedafoliage was collected from affected stands throughout the region and analyzed to identify fungi associated with needle disease symptoms. We employed both targeted molecular diagnostics, to confirm the presence or absence ofL. acicola, and DNA metabarcoding, to characterize the foliar mycobiome and screen for other potential pathogens.Lecanosticta acicolawas detected among symptomatic needles from multiple states, particularly in western portions of theP. taedarange but rarely from stands in eastern states. Fungal ITS1 metabarcoding revealed multiple pathogens in symptomatic needles and identified associations between known pathogens fungi and differing symptoms. Additionally, the fungal community composition of needles varied with patterns of symptom presentation. This study is the first regionwide assessment of fungi associated with recent large-scale needle disease outbreaks onP. taedaand identifies multiple pathogens that warrant study in greater detail.
San Min and its Spencerian origin
Authors: Liang Bin , Moltow David , Richey Stephanie 
Published: March 2024

PurposeThe aim of this article is two-fold. First, it offers a unique account of San Min, the prototype of the current Chinese educational principle proposed by Yan Fu (1854–1921) that aimed at improving people’s physical, intellectual and moral capacities. This system of educational thinking has received only marginal attention in Anglophone research literature. Second, given the influence of Yan Fu’s interpretation and promulgation of Herbert Spencer’s educational philosophy during that period, it investigates the extent to which San Min is derived from Spencer’s educational thought (the “Spencerian Triad”). This article focusses on how Yan Fu adapted the ideas of San Min from Spencer’s account.Design/methodology/approachThis article considers Yan Fu’s principle of San Min in relation to Spencer’s educational triad through a close reading and comparison of key primary texts (including Yan Fu’s original writing). It explores the similarities and differences between each account of education’s goals and its proposed means of attainment.FindingsYan Fu’s principle of San Min is shown to have been adapted from the Spencerian Triad. However, using the theory of Social Organism, Yan Fu re-interpreted Spencer’s individual liberty as liberty for the nation. While Spencer’s goal was to empower individuals, Yan Fu aimed to serve collective independence, wealth and power.Originality/valueThis article addresses oversights concerning San Min’s Western origins in the Spencerian Triad and its influence on Chinese education under Yan Fu’s sway. It is significant because San Min is still at the core of the current Chinese educational policy.
Optimal integration decision of industrial internet platform for third-party components in two-sided networks
Authors: Feng Nan , Zhang Lei , Liu Xin , Xie Jing 
Published: March 2024

PurposeWith the development of digitalization and interconnection, there is a growing need for enterprise customers to ensure the compatibility of the third-party components they are using in the manufacturing process, thus raising the integration requirements for the Industrial Internet platform and its third-party developers. Therefore, our study investigates the optimal integration decision of the Industrial Internet platform while considering its access price, the integration cost, and the net utility derived by enterprise customers from the third-party components.Design/methodology/approachWe model a two-sided Industrial Internet platform that connects customers on the demand side to the developers on the supply side. We then explore the integration decision of the Industrial Internet platform and its important factors by solving the optimal profit function.FindingsFirst, despite the high integration cost of third-party developers, the platform still chooses to integrate when enterprise customers derive high utility from the third-party components. Second, due to the compatibility effect, charging the enterprise customers a higher price may reduce the platform profits when these customers derive low utility from the third-party components. Third, the platform profits will increase along with the integration cost of third-party developers when it is low in the case where enterprise customers derive low utility from third-party components.Originality/valueOur findings offer insightful takeaways for the Industrial Internet platform when making integration decisions.