bluuebunny/crossref_metadata_2025_split huggingface dataset:
Humoral and cellular response induced by a second booster of an inactivated SARS-CoV-2 vaccine in adults
Authors: Melo-González Felipe , Méndez Constanza , Peñaloza Hernán F , Schultz Bárbara M , Piña-Iturbe Alejandro , Ríos Mariana , Moreno-Tapia Daniela , Pereira-Sánchez Patricia , Leighton Diane , Orellana Claudia , Covarrubias Consuelo , Gálvez Nicolás MS , Soto Jorge A , Duarte Luisa F , Rivera-Pérez Daniela , Vázquez Yaneisi , Cabrera Alex , Bustos Sergio , Iturriaga Carolina , Urzua Marcela , Navarrete María S , Rojas Álvaro , Fasce Rodrigo , Fernández Jorge , Mora Judith , Ramírez Eugenio , Gaete-Argel Aracelly , Acevedo Mónica , Valiente-Echeverría Fernando , Soto-Rifo Ricardo , Weiskopf Daniela , Grifoni Alba , Sette Alessandro , Zeng Gang , Meng Weining ,   CoronaVac03CL Study Group, González-Aramundiz José V , González Pablo A , Abarca Katia , Bueno Susan M , Kalergis Alexis M 
Published: August 2022

SummaryThe SARS-CoV-2 Omicron variant has challenged the control of the COVID-19 pandemic even in highly vaccinated countries. While a second booster of mRNA vaccines improved the immunity against SARS-CoV-2, the humoral and cellular responses induced by a second booster of an inactivated SARS-CoV-2 vaccine have not been studied. In the context of a phase 3 clinical study, we report that a second booster of CoronaVac® increased the neutralizing response against the ancestral virus yet showed poor neutralization against the Omicron variant. Additionally, isolated PBMCs displayed equivalent activation of specific CD4+ T cells and IFN-γ production when stimulated with a mega-pool of peptides derived from the spike protein of the ancestral virus or the Omicron variant. In conclusion, a second booster dose of CoronaVac® does not improve the neutralizing response against the Omicron variant compared with the first booster dose, yet it helps maintaining a robust spike-specific CD4+ T cell response.
Macrolinguistic function in temporal lobe epilepsy: a reinterpretation of circumstantiality
Authors: D’Aprano Fiore , Malpas Charles B. , Roberts Stefanie E. , Saling Michael M. 
Published: August 2022

AbstractIndividuals with temporal lobe epilepsy (TLE) often have an impairment of conversational language manifesting as verbosity and attributable to disruption of cognitive-linguistic networks. The micro- and macrolinguistic underpinnings of this disturbance, and the role of epilepsy and cognitive variables, are yet to be explored. We examined the elicited language output of 16 individuals with TLE and 14 healthy controls under separate monologic discourse tasks: a structured and constrained context, elicited by description of the ‘Cookie Theft’ picture, and an unstructured, unconstrained context, elicited by description of a ‘Typical Day’. We hypothesised that language output in the unstructured context would be characterised by verbosity to a greater extent than language elicited in a structured context. Following transcription and coding, detailed multi-level discourse analysis suggested that a constrained context gives rise to microlinguistic disturbances in individuals with TLE, reducing fluency, with more pauses and fillers. Under an unconstrained context, as anticipated, classical aspects of verbosity emerge in those with TLE, manifesting as longer speaking time, a longer duration of pauses, and a higher proportion of repetitive or redundant statements. Macrolinguistic elements such as coherence and informativeness are widely impacted, particularly disturbing language formulation. Correlations suggest that microlinguistic disturbances are closely linked with the immediate impact of seizures on cognitive-linguistic function, while macrolinguistic disturbances are more broadly impacted by disorder severity and word retrieval deficits. These findings suggest that different psycholinguistic impairments emerge as a function of differing linguistic challenges imposed by constrained and unconstrained conversational contexts. We conclude that these patterns reflect a dynamic linguistic system taking shape under specific contextual conditions.HighlightsA multi-centre multi-level discourse analysis was carried out to examine language in temporal lobe epilepsy (TLE).Distinct linguistic impairments reflect task demands which differentially affect micro- and macrolinguistic features.In constrained conditions, individuals with TLE exhibit microlinguistic disturbances mainly affecting their fluency and output clarity.In unconstrained conditions, they are verbose and have disturbed coherence where they produce more content that is repetitive or redundant.
Allometric equation for the commonest palm in the Central Congo Peatlands,Raphia laurentiiDe Wild
Authors: Bocko Yannick Enock , Loubota Panzou Grace Jopaul , Dargie Greta Christina , Wenina Mampouya Yeto Emmanuel , Mbemba Mackline , Joël Loumeto Jean , Lewis Simon L. 
Published: August 2022

AbstractThe world’s largest tropical peatland lies in the central Congo Basin.Raphia laurentiiDe Wild. is a palm which forms dominant to mono-dominant stands across ca. 45 % of the peatland area. However, a lack of allometric equation for this canopy-forming trunkless palm with fronds up to 20 m long, means that this it is currently excluded from aboveground biomass (AGB) estimates for these peatland ecosystems. Here we develop an allometric equation forR. laurentii, by destructively sampling 90R. laurentiistipes (across six mean petiole diameter size classes of: 2-4 cm, 4-5 cm, 5-6 cm, 6-7 cm, >8 cm) in a peat swamp forest, in the Likouala Department, Republic of the Congo. Prior to destructive sampling, the five parameters were measured for each stipe: diameter at stem base, mean diameter of the palm fronds, total diameter of the palm fronds (TDpf), total height and number of palm fronds. After destructive sampling and before weighing each individual was separated into the stem and the following palm frond categories: sheath, petiole, rachis and leaflets. We fitted a linear model relatingAGBto each independent predictor variable separately to assess the best variable, finding that palm fronds represented at least 77 % of the totalAGBin each diameter classes. We found thatTDpfwas the best single predictor variable forR. laurentii AGB. We provide a series of equations, based on samplingR. laurentiiwith fronds ≥2 cm diameter or ≥5 cm diameters. The best allometric equation was:AGB=Exp(−2.691 + 1.425 × ln (TDpf) + 0.695 ×ln(H) + 0.395 × ln (WD).. A monodominant 1 ha plot near the harvesting site had a palm AGB of 60.8 Mg ha-1, similar to theAGBof the trees in the same plot, at 86.2 Mg ha-1. Accounting for theAGBof palms is important, and can now be estimated using the allometric equations developed here.
Long-term temporal stability of peripheral blood DNA methylation alterations in patients with inflammatory bowel disease
Authors: Joustra Vincent , Li Yim Andrew Y.F. , Hageman Ishtu , Levin Evgeni , Adams Alex , Satsangi Jack , de Jonge Wouter J. , Henneman Peter , D’Haens Geert 
Published: August 2022

AbstractIntroductionThere is great current interest in the potential application of DNA methylation alterations in peripheral blood leukocytes (PBL) as biomarkers of susceptibility, progression and treatment response in inflammatory bowel disease (IBD). However, the intra-individual stability of PBL methylation in IBD has not been characterised. Here, we studied the long-term stability of all probes located on the Illumina HumanMethylation EPIC BeadChip array.MethodsWe followed a cohort of 46 adult IBD patients (36 Crohn’s disease (CD), 10 ulcerative colitis (UC), median age 44 (IQR: 27-56), 50% female) that received standard care without any intervention at the Amsterdam UMC. Paired PBL samples were collected at two time points with a median 7 (range: 2-9) years in between. Differential methylation and intra-class correlation (ICC) analyses were used to identify time-associated differences and temporally stable CpGs, respectively.ResultsAround 60% of all EPIC array loci presented poor intra-individual stability (ICC <0.50); 78.114 (≈9%) showed good (ICC 0.75 – 0.89); and 41.274 (≈5%) excellent (ICC ≥0.90) stability. Focusing on previously identified consistently differentially methylated positions indicated that 22 CD-, 11 UC-, and 24 IBD-associated loci demonstrated high stability (ICC ≥0.75) over time; of these, we observed a marked stability of CpG loci associated to the HLA genes.ConclusionOur data provide insight into the long-term stability of the PBL DNA methylome within an IBD context, facilitating the selection of biologically relevant and robust IBD-associated epigenetic biomarkers with increased potential for independent validation. These data also have potential implications in understanding disease pathogenesis.
Epigenetic variations are accompanying landmarks of freshwater adaptation in threespine sticklebacks
Authors: Golden Artemiy , Starshin Alexey , Mazur Alexandr , Mugue Nikolai , Kaplun Daria , Artemov Artem , Khrameeva Ekaterina , Prokhortchouk Egor 
Published: August 2022

ABSTRACTFor evolutionary biology, the phenotypic consequences of epigenetic variations and their potential contribution to adaptation and diversification are pressing issues. Marine and freshwater sticklebacks represent an ideal model for studying both genetic and epigenetic components of phenotypic plasticity that allow fish to inhabit water with different salinity. Here, we applied single-cell genomics (scRNA-seq and scATAC-seq) and whole-genome bisulfite sequencing to characterize intercellular variability in transcription, the abundance of open chromatin regions, and CpG methylation level in gills of marine and freshwater stickleback morphs. We found little difference in overall transcriptional variance between the morphs but observed significant changes in chromatin openness variance. In addition, genomic divergence islands (DIs) coincided with regions of increased methylation entropy in freshwater fish. Moreover, analysis of transcription factor binding sites within DIs revealed that СTCF motifs around marker SNPs were significantly enriched within the region. Altogether, our data show that increased epigenetic variance accompanies the adaptation of marine sticklebacks to freshwater.
VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
Authors: Rangel-Pineros Guillermo , Almeida Alexandre , Beracochea Martin , Sakharova Ekaterina , Marz Manja , Muñoz Alejandro Reyes , Hölzer Martin , Finn Robert D. 
Published: August 2022

AbstractThe study of viral communities has revealed the enormous diversity and impact these biological entities have on a range of different ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterization of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterization of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities and a large metagenomics study. The results showed that VIRify was able to identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an accuracy of at least 95.5%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them.
Age-associated reduction of nuclear shape dynamics in excitatory neurons of the visual cortex
Authors: Frey Tanita , Murakami Tomonari , Maki Koichiro , Kawaue Takumi , Sugai Ayaka , Nakazawa Naotaka , Adachi Taiji , Kengaku Mineko , Ohki Kenichi , Gotoh Yukiko , Kishi Yusuke 
Published: August 2022

AbstractNeurons decline in their functionality over time, and age-related neuronal alterations are associated with phenotypes of neurodegenerative diseases. In non-neural tissues, an infolded nuclear shape has been proposed as a hallmark of aged cells and neurons with infolded nuclei have also been reported to be associated with neuronal activity. Here, we perform time-lapse imaging in the visual cortex ofNex-Cre;SUN1-GFPmice. Nuclear infolding was observed within 15 minutes of stimulation in young nuclei, while the aged nuclei were already infolded pre-stimulation and showed reduced dynamics of the morphology. In young nuclei, the depletion of the stimuli restored the nucleus to a spherical shape and reduced the dynamic behavior, suggesting that nuclear infolding is a reversible process. We also found the aged nucleus to be stiffer than the young one, further relating to the age-associated loss of nuclear shape dynamics. We reveal temporal changes in the nuclear shape upon external stimulation and observe that these morphological dynamics decrease with age.
Growth hormone remodels the 3D-structure of the mitochondria of inflammatory macrophages and promotes metabolic reprogramming
Authors: Palacios Blanca Soler , Villares Ricardo , Lucas Pilar , Miguel-Rodríguez-Frade José , Cayuela Ana , Piccirillo Jonathan G , Lombardía Manuel , Gestoso David Delgado , Risco Cristina , Corrales Fernando , Sorzano Carlos Oscar S. , Martínez Nuria , Conesa José Javier , Iborra Francisco J. , Mellado Mario 
Published: August 2022

AbstractMacrophages are a heterogeneous population of innate immune cells that support tissue homeostasis through their involvement in tissue development and repair, and pathogen defense. Emerging data reveal that metabolism may control macrophage polarization and function and, conversely, phenotypic polarization may drive metabolic reprogramming. Here, using biochemical analysis, correlative cryogenic fluorescence microscopy and cryo-focused ion-beam scanning electron microscopy, we demonstrate that growth hormone (GH) functions as a metabolic modulator to reprogram inflammatory GM-CSF-primed monocyte-derived macrophages (GM-MØ). We found that exogenous treatment of GM-MØ with recombinant human GH suppressed glycolysis, lactate production and non-mitochondrial respiration, and enhanced mitochondrial oxidative phosphorylation. Likewise, GH treatment augmented mitochondrial volume and altered mitochondrial dynamics, including the remodeling of the inner membrane to increase the density of cristae. Our data demonstrate that GH likely serves a modulatory role in the metabolism of inflammatory macrophages and suggest that metabolic reprogramming of macrophages should be considered a new target to intervene in multiple inflammatory diseases.
No evidence for cognitive impairment in an experimental rat model of knee osteoarthritis and associated chronic pain
Authors: Gonçalves Sara , Hathway Gareth J. , Woodhams Stephen G. , Chapman Victoria , Bast Tobias 
Published: August 2022

ABSTRACTAlthough chronic pain states have been associated with impaired cognitive functions, including memory and cognitive flexibility, the cognitive effects of osteoarthritis (OA) pain remain to be clarified. The aim of this study was to measure cognitive function in the mono-iodoacetate (MIA) rat model of chronic OA-like knee pain.We used young adult male Lister hooded rats, which are well suited for cognitive testing. Rats received either a unilateral knee injection of MIA (3mg/50µL) or saline as control. Joint pain at rest was assessed for up to 12 weeks using weight-bearing asymmetry, and referred pain at a distal site using determination of hindpaw withdrawal thresholds (PWT). The watermaze delayed-matching-to-place (DMP) test of rapid place learning, novel object recognition (NOR) memory assay and an operant response-shift and -reversal task were used to measure memory and behavioural flexibility. Open field locomotor activity, startle response, and prepulse inhibition (PPI) were also measured for comparison.MIA-injected rats showed markedly reduced weight-bearing on the injured limb, as well as pronounced cartilage damage and synovitis, but interestingly no changes in PWT. Rearing was reduced, but otherwise locomotor activity was normal and no changes in startle and PPI were detected. MIA-injected rats had intact watermaze DMP performance, suggesting no substantial change in hippocampal function, and there were no changes in NOR memory or performance on the operant task of behavioural flexibility. Our finding that OA-like pain does not alter hippocampal function, unlike other chronic pain conditions, is consistent with human neuroimaging findings.
Bayesian inference reveals a complex evolutionary history of belemnites
Authors: Stevens Kevin , Pohle Alexander , Hoffmann René , Immenhauser Adrian 
Published: August 2022

ABSTRACTBelemnites are an extinct group of Mesozoic coleoid cephalopods, common in Jurassic and Cretaceous marine sedimentary rocks. Despite their significance, their total group phylogeny has rarely been considered in recent decades. In contrast, most researchers restricted the assignment of families to one of the two usually recognized subgroups, the Belemnitina and the Belemnopseina. As for many fossil cephalopods, researchers have been reluctant to employ modern phylogenetic methods to illuminate belemnites’ evolutionary history.To overcome the “dead end” of belemnite systematics, we performed the first tip-dated Bayesian analysis of belemnite phylogeny. In our analysis, the Aulacoceratida are found as the monophyletic sister group to belemnites. The Sinobelemnitidae are resolved as paraphyletic and fall outside the Belemnitina and Belemnopseina, which make up the remaining belemnites. Belemnitina is restricted to Jurassic species with generally no or apical furrows. Holcobelidae are the earliest branching Belemnopseina. Cylindroteuthidssensu lato(including Oxyteuthidae) are nested within Belemnopseina, contrary to the common hypothesis placing them within the Belemnitina. Duvaliidae and Dicoelitidae are recovered as members of the Belemnopseina, but their precise relationship has to be evaluated based on more taxa and additional characters. We introduce the well-supported unranked clade Pseudoalveolata, which includes Dimitobelidae, Belemnitellidae, and members of the paraphyletic “Belemnopseidae”.The phylogeny presented here, based on reproducible and quantitative methods, contrasts with the usually applied authoritative “stratophenetic” approach to belemnite systematics, based on the overemphasis of single characters. This result is considered the basis for future studies on belemnite phylogeny, allowing for a rigorous testing of evolutionary hypotheses.PLAIN LANGUAGE SUMMARYBelemnites were common extinct cephalopods that were closely related to today’s squid and cuttlefish. The most common fossil remains of belemnites are bullet-shaped calcitic “cones” (rostrum) that cover their internal shells. Belemnites’ evolutionary history is not well known. Our study revealed an evolutionary tree of belemnites based on the statistical analysis of morphological features of the rostrum and calibrated to the known geological ages of the studied belemnite species. This approach was for the first time applied to belemnites and changed several aspects that were believed about their evolution.
Immunohistochemical diagnosis of Trypanosoma vivax in experimentally infected sheep tissues
Authors: do Nascimento Luiz Flávio Nepomuceno , de Cristo Thierry Grima , Franco Cintia , Salbego Fabiano Zanini , Tamanho Renato Batista , Casagrande Renata Assis , Bittar Joely Ferreira Figueiredo , Miletti Luiz Claudio 
Published: August 2022

ABSTRACTTrypanosoma vivax is one of the main species responsible for animal African trypanosomiasis in West Africa and has a marked economic impact on livestock in Sub-Saharan Africa and South America endemic countries. In this work, T. vivax was demonstrated by immunohistochemical technique in formalin-fixed paraffin-embedded in tissues of experimentally infected sheep using polyclonal antibodies produced against formalin-fixed trypomastigotes. T. vivax was observed within multiple small and medium-size vessels from multiple organs, including the liver and kidneys. The immunostaining was evidenced in an intense cherry red. This is the first immunohistochemical experiment that shows T. vivax in fixed tissues.
Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA cluster biogenesis in mosquitoes
Authors: Qu Jieqiong , Betting Valerie , van Iterson Ruben , Kwaschik Florence M. , van Rij Ronald P. 
Published: August 2022

SummaryThe piRNA pathway in mosquitoes differs substantially from other model organisms, with an expanded PIWI gene family and functions in antiviral defense. Here, we defined core piRNA clusters as small RNA source loci that showed ubiquitous expression in both somatic and germline tissues. These core piRNA clusters were enriched for non-retroviral endogenous viral elements (nrEVEs) in antisense orientation and depended on key biogenesis factors, Nxf1, Veneno, Tejas, Yb, and Shutdown. Combined transcriptome and chromatin state analyses identified transcriptional readthrough as a conserved mechanism for piRNA cluster biogenesis in Aedes aegypti, Aedes albopictus, Culex quinquefasciatus, and Anopheles gambiae. Comparative analyses between two Aedes mosquitoes suggested that piRNA clusters function as traps for nrEVEs, allowing adaptation to environmental challenges such as virus infection. Our systematic transcriptome and chromatin state analyses lay the foundation for studies of gene regulation, genome evolution and piRNA functions in these important vector species.Graphical abstractHighlightsCore piRNA clusters showed ubiquitous expression in both somatic and germline tissues in four vector mosquitoes.Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA biogenesis.Biogenesis of cluster-derived piRNAs depends on key factors, Nxf1, Veneno, Tejas, Yb, and Shutdown.piRNA clusters function as traps for viral elements downstream of conserved set of genes in Aedes mosquitoes