bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early impact of the COVID-19 pandemic and social distancing measures on routine childhood vaccinations in England, January to April 2020
Authors: McDonald Helen I , Tessier Elise , White Joanne M , Woodruff Matthew , Knowles Charlotte , Bates Chris , Parry John , Walker Jemma L , Scott J. Anthony , Smeeth Liam , Yarwood Joanne , Ramsay Mary , Edelstein Michael 
Published: May 2020

AbstractElectronic health records were used to assess the early impact of COVID-19 on routine childhood vaccination in England to 26 April 2020.MMR vaccination counts fell from February 2020, and in the three weeks after introduction of social distancing measures were 19.8% lower (95% CI −20.7 to −18.9%) than the same period in 2019, before improving in mid-April. A gradual decline in hexavalent vaccination counts throughout 2020 was not accentuated on introduction of social distancing.
The rise of the three-spined stickleback – eco-evolutionary consequences of a mesopredator release
Authors: Eriksson Britas Klemens , Yanos Casey , Bourlat Sarah , Donadi Serena , Fontaine Michael C. , Hansen Joakim P. , Jakubavičiūtė Eglė , Kiragosyan Karine , Maan Martine E. , Merilä Juha , Austin Åsa N. , Olsson Jens , Reiss Katrin , Sundblad Göran , Bergström Ulf , Eklöf Johan S. 
Published: May 2020

AbstractDeclines of large predatory fish due to overexploitation are restructuring food webs across the globe. It is now becoming evident that restoring these altered food webs requires addressing not only ecological processes, but evolutionary ones as well, because human-induced rapid evolution may in turn affect ecological dynamics. In the central Baltic Sea, abundances of the mesopredatory fish, the three-spined stickleback (Gasterosteus aculeatus), have increased dramatically during the past decades. Time-series data covering 22 years show that this increase coincides with a decline in the number of juvenile perch (Perca fluviatilis), the most abundant predator of stickleback along the coast. We studied the interaction between evolutionary and ecological effects of this mesopredator take-over, by surveying the armour plate morphology of stickleback and the structure of the associated food web. First, we investigated the distribution of different stickleback phenotypes depending on predator abundances and benthic production; and described the stomach content of the stickleback phenotypes using metabarcoding. Second, we explored differences in the relation between different trophic levels and benthic production, between bays where the relative abundance of fish was dominated by stickleback or not; and compared this to previous cage-experiments to support causality of detected correlations. We found two distinct lateral armour plate phenotypes of stickleback, incompletely and completely plated. The proportion of incompletely plated individuals increased with increasing benthic production and decreasing abundances of adult perch. Stomach content analyses showed that the completely plated individuals had a stronger preference for invertebrate herbivores (amphipods) than the incompletely plated ones. In addition, predator dominance interacted with ecosystem production to determine food web structure and the propagation of a trophic cascade: with increasing production, biomass accumulated on the first (macroalgae) and third (stickleback) trophic levels in stickleback-dominated bays, but on the second trophic level (invertebrate herbivores) in perch-dominated bays. Since armour plates are defence structures favoured by natural selection in the presence of fish predators, the phenotype distribution suggest that a novel low-predation regime favours sticklebacks with less armour. Our results indicate that an interaction between evolutionary and ecological effects of the stickleback take-over has the potential to affect food web dynamics.
Redox state changes of mitochondrial cytochromes in brain and breast cancers by Raman spectroscopy and imaging
Authors: Abramczyk Halina , Surmacki Jakub Maciej , Brozek-Pluska Beata 
Published: May 2020

AbstractThis paper presents a non-invasive approach to study redox status of cytochromesin vitrohuman brain cells of normal astrocytes (NHA), astrocytoma (CRL-1718), glioblastoma (U87- MG) and medulloblastoma (Daoy), and human breast cells of normal cells (MCF10A), slightly malignant cells (MCF7) and highly aggressive cells (MDA-MB-231), in vivo animal models, andex vivobrain and breast tissues surgically resected human specimens by means of Raman microspectroscopy at 355 nm, 532 nm, 785 nm and endospectroscopic Raman probe at 785 nm. Here we show that the amount of reduced cytochrome becomes abnormally high in human brain tumors and breast cancers. In contrast, the amount of reduced cytochrome c is lower in cancer cells when compared to the normal one atin vitroconditions when the effect of microenvironment is eliminated. Mitochondrial dysfunction and alterations in the chemical composition of the nucleus, mitochondria, lipid droplets, cytoplasm in single cells have been detected by Raman imaging. Incubationin vitrowith retinoic acid increases the amount of reduced cytochrome c.
Memory consolidation and improvement by synaptic tagging and capture in recurrent neural networks
Authors: Luboeinski Jannik , Tetzlaff Christian 
Published: May 2020

AbstractThe synaptic-tagging-and-capture (STC) hypothesis formulates that at each synapse the concurrence of a tag with protein synthesis yields the maintenance of changes induced by synaptic plasticity. This hypothesis provides a biological principle underlying the synaptic consolidation of memories that is not verified for recurrent neural circuits. We developed a theoretical model integrating the mechanisms underlying the STC hypothesis with calcium-based synaptic plasticity in a recurrent spiking neural network. In the model, calcium-based synaptic plasticity yields the formation of strongly interconnected cell assemblies encoding memories, followed by consolidation through the STC mechanisms. Furthermore, we find that the STC mechanisms have an up to now undiscovered effect on memories – with the passage of time they modify the storage of memories, such that after several hours memory recall is significantly improved. This kind of memory enhancement can provide a new principle for storing information in biological and artificial neural circuits.
An evolutionarily conserved metallophosphodiesterase is a determinant of lifespan inDrosophila
Authors: Gupta Kriti , Janardan Vishnu , Banerjee Sanghita , Chakrabarti Sveta , Srinivas Swarna , Mahishi Deepthi , Raghu Padinjat , Visweswariah Sandhya S. 
Published: May 2020

AbstractEvolutionarily conserved genes usually have a critical role to play during organismal aging and longevity. Here, we show that a previously uncharacterized Class III metallophosphoesterase inDrosophila, an ortholog of the MPPED1 and MPPED2 proteins in mammals, is necessary for optimal lifespan. dMPPED is the product of the geneCG16717and hydrolyzed a variety of phosphodiester substrates in a metal-dependent manner.dMPPEDwas expressed widely during development and in the adult fly. Deletion of the gene in flies dramatically reduced lifespan, without affecting development or fecundity. Longevity was restored on ubiquitous expression of the protein, and neuronal expression of both wild type and the catalytically inactive form of dMPPED was also able to restore normal lifespan. Overexpression of the protein, both ubiquitously and neuronally in wild type flies extended lifespan by ~ 20%. RNA-seq analysis ofdMPPEDKOflies revealed mis-regulation of innate immune pathways, a number of transcription factors and genes earlier reported to affect aging and lifespan. Importantly, neuronal expression of mammalian MPPED2 was able to rescue lifespan indMPPEDKOflies, but not extend lifespan in wild type flies. This reports the first description of the biological role of an evolutionarily conserved metallophosphoesterase that may serve as a scaffolding protein in diverse signaling pathways to modulate longevity in the fly.
Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data
Authors: Tanevski Jovan , Flores Ricardo Omar Ramirez , Gabor Attila , Schapiro Denis , Saez-Rodriguez Julio 
Published: May 2020

AbstractThe advancement of technologies to measure highly multiplexed spatial data requires the development of scalable methods that can leverage the spatial information. We present MISTy, a flexible, scalable and explainable machine learning framework for extracting interactions from any spatial omics data. MISTy builds multiple views focusing on different spatial or functional contexts to dissect different effects, such as those from direct neighbours versus those from distant cells. MISTy can be applied to different spatially resolved omics data with dozens to thousands of markers, without the need to perform cell-type annotation. We evaluate the performance of MISTy on anin silicodataset and demonstrate its applicability on three breast cancer datasets, two measured by imaging mass cytometry and one by Visium spatial transcriptomics. We show how we can estimate interactions coming from different spatial contexts that we can relate to tumor progression and clinical features. Our analysis also reveals that the estimated interactions in triple negative breast cancer are associated with clinical outcomes which could improve patient stratification. Finally, we demonstrate the flexibility of MISTy to integrate different kinds of views by modeling activities of pathways estimated from gene expression in a spatial context to analyse intercellular signaling.
Electrophysiological and behavioral indices of cognitive conflict processing across adolescence
Authors: Overbye Knut , Walhovd Kristine B. , Fjell Anders M. , Tamnes Christian K. , Huster Rene J. 
Published: May 2020

ABSTRACTCognitive control enables goal-oriented adaptation to a fast-changing environment and has a slow developmental trajectory that spans into young adulthood. The specifics of this development are still poorly understood, as are the neurodevelopmental mechanisms that drive it. In a cross-sectional sample of participants 8-19 years old (n = 108), we used blind source separation of EEG data recorded in a Flanker task to derive electrophysiological measures of attention and the processing of cognitive conflict, including a frontal negative component corresponding to the N2 and a parietal positive component corresponding to the P3. Additionally, we examined multiple behavioral measures of interference control derived from the Flanker, Stroop, and Anti-saccade tasks. We found a positive association between age and the amplitude of the parietal positive component, while there was no relationship between age and the amplitude of the frontal negative component. A stronger frontal negative amplitude was, however, age-independently related to better performance on both Stroop and Anti-saccade measures of interference control. Finally, we examined post-conflict behavioral adjustment on the Flanker task. A Gratton effect was found with slower reaction times on current congruent and better accuracy on current incongruent trials when preceded by incongruent as opposed to congruent trials. The Gratton effect on accuracy was positively associated with age. Together, the findings suggest a multifaceted developmental pattern in neurocognitive mechanisms for conflict processing across adolescence, with a more protracted development of the parietal positive compared to the frontal negative component.
SARS-CoV-2 Spike Glycoprotein and ACE2 interaction reveals modulation of viral entry in wild and domestic animals
Authors: Praharaj Manas Ranjan , Garg Priyanka , Kesarwani Veerbhan , Topno Neelam A , Khan Raja Ishaq Nabi , Sharma Shailesh , Panigrahi Manjit , Mishra B P , Mishra Bina , Sai kumar G , Gandham Ravi Kumar , Singh Raj Kumar , Majumdar Subeer , Mohapatra Trilochan 
Published: May 2020

AbstractBackgroundSARS-CoV-2 is a viral pathogen causing life-threatening disease in human. Interaction between spike protein of SARS-CoV-2 and ACE2 receptor on the cells is a potential factor in the infectivity of a host. The interaction of SARS-CoV-2 spike receptor-binding domain with its receptor - ACE2, in different hosts was evaluated to understand and predict viral entry. The protein and nucleotide sequences of ACE2 were initially compared across different species to identify key differences among them. The ACE2 receptor of various species was homology modeled (6LZG, 6M0J, and 6VW1 as a reference), and its binding ability to the spike ACE2 binding domain of SARS-CoV-2 was assessed. Initially, the spike binding parameters of ACE2 of known infected and uninfected species were compared with each Order (of animals) as a group. Finally, a logistic regression model vis-a-vis the spike binding parameters of ACE2 (considering data against 6LZG and 6M0J) was constructed to predict the probability of viral entry in different hosts.ResultsPhylogeny and alignment comparison did not lead to any meaningful conclusion on viral entry in different hosts. Out of several spike binding parameters of ACE2, a significant difference between the known infected and uninfected species was observed for six parameters. However, these parameters did not specifically categorize the Orders (of animals) into infected or uninfected. The logistic regression model constructed revealed that in the mammalian class, most of the species of Carnivores, Artiodactyls, Perissodactyls, Pholidota, and Primates had high probability of viral entry. However, among the primates, African Elephant had low probability of viral entry. Among rodents, hamsters were highly probable for viral entry with rats and mice having a medium to low probability. Rabbits have a high probability of viral entry. In Birds, ducks have a very low probability, while chickens seemed to have medium probability and turkey showed the highest probability of viral entry.ConclusionsMost of the species considered in this study showed high probability of viral entry. This study would prompt us to closely follow certain species of animals for determining pathogenic insult by SARS-CoV-2 and for determining their ability to act as a carrier and/or disseminator.
Comment on ‘Initiation of chromosome replication controls both division and replication cycles inE. colithrough a double-adder mechanism’
Authors: Le Treut Guillaume , Si Fangwei , Li Dongyang , Jun Suckjoon 
Published: May 2020

AbstractWitzet al. recently performed single-cell mother machine experiments to track growth and the replication cycle inE. coli. They analyzed the correlation structure of selected parameters using both their data and published data, and concluded thatE. colicell-size control is implemented at replication initiation, which challenged the newly emerged division-centric mechanism of cell-size control in bacteria. We repeated Witz et al.’s analysis, and performed additional experiments and analytical calculations. These results explain Witz et al.’s observation and in fact support the division-centric model.
The enemy of my enemy is my friend: Nematode infection of pollinating and non-pollinating fig wasps has net benefits for the fig-fig wasp pollination mutualism
Authors: Van Goor Justin , Piatscheck Finn , Houston Derek D. , Nason John D. 
Published: May 2020

AbstractMutualistic associations between species pairs are ubiquitous in nature but are also components of broader organismal community networks. These community-level associations have shaped the evolution of individual mutualisms through interspecific interactions ranging from secondarily mutualistic to intensely antagonistic. Our understanding of this complex context remains limited because identifying species interacting with focal mutualists and assessing their associated fitness benefits and costs is difficult, especially over space and through time. Here, we focus on a community comprised of a fig and fig wasp mutualist, eight non-pollinating fig wasp (NPFW) commensals/antagonists, and a nematode previously believed to be associated only with the pollinator wasp mutualist. Through repeated sampling and field experiments, we identified that all NPFWs are targets for infection by this nematode. Further, this infection can impact NPFWs more severely than either mutualistic partner, suggesting a novel role of density-dependent facultative mutualism between fig and wasp mutualists and the nematode.
Pulmonary infection interrupts acute cutaneous wound healing through disruption of chemokine signals
Authors: Crane Meredith J. , Xu Yun , Monaghan Sean F. , Hall Benjamin M. , Albina Jorge E. , Henry William L. , Tran Holly L. , Chhabria Karisma R. P. , Jordon Alexander R. D. , Carlsen Lindsey , Jamieson Amanda M. 
Published: May 2020

SummaryStudies of the immune response typically focus on single-insult systems, with little known about how multi-insult encounters are managed. Pneumonia in patients recovering from surgery is a clinical situation that exemplifies the need for the patient to mount two distinct immune responses. Examining this, we have determined that poor wound healing is an unreported complication of pneumonia in laparotomy patients. Using mouse models, we found that lung infection suppressed the trafficking of innate leukocytes to wounded skin, while pulmonary resistance to the bacterial infection was maintained. The dual insults caused distinct systemic and local changes to the inflammatory response, the most striking being a rapid and sustained decrease in chemokine levels at the wound site of mice with pneumonia. Remarkably, replenishing wound chemokine levels completely rescued the wound-healing rate in mice with a pulmonary infection. These findings have broad implications for understanding the mechanisms guiding the innate immune system to prioritize inflammatory sites.One Sentence SummaryChemokine-mediated signaling drives the prioritization of innate immune responses to bacterial pulmonary infection over cutaneous wound healing.HighlightsHuman laparotomy patients with pneumonia have an increased rate of incision dehiscence, and this observation can be recapitulated in mouse models of bacterial lung infections and skin wounds.Lung infection causes rapid and sustained suppression of skin wound chemokine and inflammatory cytokine production as well as leukocyte recruitment.Unique systemic shifts in the immune compartment occur with two inflammatory insults, including the cytokine/chemokine signature and the mobilization, recruitment, and phenotype of innate leukocytes.Restoration of chemokine signaling in the wounds of mice that have a lung infection results in increased neutrophil trafficking to the wound site and rescues the rate of healing.Graphical Abstract
Genome-wide mapping of histone modifications in two species ofLeptosphaeria maculansshowing contrasting genomic organization and host specialization
Authors: Soyer J.L. , Clairet C. , Gay E.J. , Lapalu N. , Rouxel T. , Stukenbrock E.H. , Fudal I. 
Published: May 2020

AbstractIn plant-associated fungi, the role of the epigenome is increasingly recognized as an important regulator of genome structure and of the expression of genes involved in interaction(s) with the host plant. Two closely-related phytopathogenic species,Leptosphaeria maculans‘brassicae’ (Lmb) andL. maculans‘lepidii’ (Lml) exhibit a large conservation of genome synteny but contrasting genome structure. Lmb has undergone massive invasion of its genome by transposable elements amounting to one third of its genome and clustered in large TE-rich regions on chromosomal arms, while Lml genome has only a small amount of repeats (3% of the genome). Previous studies showed that the TE-rich regions of Lmb harbour a few species-specific effector genes, expressed during plant infection. The distinct genome structures shown by Lmb and Lml thus provides an excellent model for comparing the organization of pathogenicity/effector genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation during axenic culture, targeting either histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyse the influence of chromatin organisation on gene expression. In both species, we found that facultative heterochromatin landscapes associated with H3K27me3-domains are enriched with genes lacking functional annotation, including numerous candidate effector and species-specific genes. Notably, orthologous genes located in H3K27me3-domains in both species are enriched with genes encoding putative proteinaceous and metabolic effectors. These genes are mostly silenced in axenic growth conditions and are likely to be involved in interaction with the host. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3-domains associated with TE-rich regions that contain numerous species-specific effector-encoding genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection, and the selective advantage to the fungus to host effector genes in H3K9me3- or H3K27me3-domains.
Design issues and solutions for stop-signal data from the Adolescent Brain Cognitive Development [ABCD] study
Authors: Bissett Patrick G. , Hagen McKenzie P. , Jones Henry M. , Poldrack Russell A. 
Published: May 2020

AbstractThe Adolescent Brain Cognitive Development (ABCD) study is an unprecedented longitudinal neuroimaging sample that tracks the brain development of over 10,000 9-10 year olds through adolescence. At the core of this study are the three tasks that are completed repeatedly within the MRI scanner, one of which is the stop-signal task. In analyzing the available stopping experimental code and data, we identified a set of design issues that we believe significantly compromise its value. These issues include but are not limited to: variable stimulus durations that violate basic assumptions of dominant stopping models, trials in which stimuli are incorrectly not presented, and faulty stop-signal delays. We present eight issues, show their effect on the existing ABCD data, suggest prospective solutions including task changes for future data collection and preliminary computational models, and suggest retrospective solutions for data users who wish to make the most of the existing data.