bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward a synthesis of phytoplankton community composition methods for global-scale application
Authors: Kramer Sasha J. , Bolaños Luis M. , Catlett Dylan , Chase Alison P. , Behrenfeld Michael J. , Boss Emmanuel S. , Crockford E. Taylor , Giovannoni Stephen J. , Graff Jason R. , Haëntjens Nils , Karp-Boss Lee , Peacock Emily E. , Roesler Collin S. , Sosik Heidi M. , Siegel David A. 
Published: September 2023

AbstractThe composition of the marine phytoplankton community has been shown to impact many biogeochemical processes and marine ecosystem services. A variety of methods exist to characterize phytoplankton community composition (PCC), with varying degrees of taxonomic resolution. Accordingly, the resulting PCC determinations are dependent on the method used. Here, we use surface ocean samples collected in the North Atlantic and North Pacific Oceans to compare high performance liquid chromatography (HPLC) pigment-based PCC to four other methods: quantitative cell imaging, flow cytometry, and 16S and 18S rRNA amplicon sequencing. These methods allow characterization of both prokaryotic and eukaryotic PCC across a wide range of size classes. PCC estimates of many taxa resolved at the class level (e.g., diatoms) show strong positive correlations across methods, while other groups (e.g., dinoflagellates) are not well captured by one or more methods. Since variations in phytoplankton pigment concentrations are related to changes in optical properties, this combined dataset expands the potential scope of ocean color remote sensing by associating PCC at the genus- and species-level with group- or class-level PCC from pigments. Quantifying the strengths and limitations of pigment-based PCC methods compared to PCC assessments from amplicon sequencing, imaging, and cytometry methods is the first step toward the robust validation of remote sensing approaches to quantify PCC from space.
WITHDRAWN: How antimicrobial heteroresistance promotes bacterial adaptation to antimicrobial therapy – or not
Authors: Liao Junqi , Nyhoegen Christin , Uecker Hildegard , Schulenburg Hinrich 
Published: September 2023

Withdrawal StatementThe authors have withdrawn their manuscript owing to inconsistencies of results during a re-assessment of the experimental work, which now question main conclusions drawn and which require additional experiments. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author
Sound elicits stereotyped facial movements that provide a sensitive index of hearing abilities
Authors: Clayton Kameron K. , Stecyk Kamryn S. , Guo Anna A. , Chambers Anna R. , Chen Ke , Hancock Kenneth E. , Polley Daniel B. 
Published: September 2023

SUMMARYSound elicits rapid movements of muscles in the face, ears, and eyes that protect the body from injury and trigger brain-wide internal state changes. Here, we performed quantitative facial videography from mice resting atop a piezoelectric force plate and observed that broadband sounds elicit rapid, small, and highly stereotyped movements of a facial region near the vibrissae array. Facial motion energy (FME) analysis revealed sensitivity to far lower sound levels than the acoustic startle reflex and greater reliability across trials and mice than sound-evoked pupil dilations or movement of other facial and body regions. FME tracked the low-frequency envelope of sounds and could even decode speech phonemes in varying levels of background noise with high accuracy. FME growth slopes were disproportionately steep in mice with autism risk gene mutations and noise-induced sensorineural hearing loss, providing an objective behavioral measure of sensory hyper-responsivity. Increased FME after noise-induced cochlear injury was closely associated with the emergence of excess gain in later waves of the auditory brainstem response, suggesting a midbrain contribution. Deep layer auditory cortex units were entrained to spontaneous facial movements but optogenetic suppression of cortical activity facilitated – not suppressed – sound-evoked FME, suggesting the auditory cortex is a modulator rather than a mediator of sound-evoked facial movements. These findings highlight a simple involuntary behavior that is more sensitive and integrative than other auditory reflex pathways and captures higher-order changes in sound processing from mice with inherited and acquired hearing disorders.
Phase separation of S-RNase promotes self-incompatibility inPetunia hybrida
Authors: Tian Huayang , Zhang Hongkui , Huang Huaqiu , Zhang Yu’e , Xue Yongbiao 
Published: September 2023

SummarySelf-incompatibility (SI) is an intraspecific reproductive barrier widely present in angiosperms. The SI system with the broadest occurrence in angiosperms is based on anS-RNaselinked to a cluster of multipleS-locus F-box(SLF) genes found in the Solanaceae, Plantaginaceae, Rosaceae, and Rutaceae. Recent studies reveal that non-self S-RNase is degraded by the SCFSLF-mediated ubiquitin-proteasome system in a collaborative manner inPetunia, but how self-RNase functions largely remains mysterious. Here, we show that S-RNases form S-RNase condensates (SRCs) in the self-pollen tube cytoplasm through phase separation and their disruption breaks SI in self-incompatiblePetunia hybrida.We further find that the pistil SI factors of a small asparagine-rich protein HT-B and thioredoxin h (Trxh) together with a reduced state of the pollen tube all promote the expansion of SRCs, which then sequester several actin binding proteins, including the actin polymerization factor PhABRACL, whose actin polymerization activity is reduced by S-RNase in vitro. Meanwhile, we find that S-RNase variants lacking condensation ability fail to recruit PhABRACL and are unable to induce actin foci formation required for the pollen tube growth inhibition. Taken together, our results demonstrate that phase separation of S- RNase promotes SI response inP. hybrida, revealing a new mode of S-RNase action.
Disease trajectories in hospitalized COVID-19 patients are predicted by clinical and peripheral blood signatures representing distinct lung pathologies
Authors: Da Silva Filho João , Herder Vanessa , Gibbins Matthew P. , dos Reis Monique Freire , Melo Gisely Cardoso , Haley Michael J. , Judice Carla Cristina , Val Fernando Fonseca Almeida , Borba Mayla , Tavella Tatyana Almeida , de Sousa Sampaio Vanderson , Attipa Charalampos , McMonagle Fiona , de Lacerda Marcus Vinicius Guimaraes , Costa Fabio Trindade Maranhão , Couper Kevin N. , Monteiro Wuelton Marcelo , de Lima Ferreira Luiz Carlos , Moxon Christopher Alan , Palmarini Massimo , Marti Matthias 
Published: September 2023

SummaryLinking clinical biomarkers and lung pathology still is necessary to understand COVID-19 pathogenesis and the basis of progression to lethal outcomes. Resolving these knowledge gaps enables optimal treatment approaches of severe COVID-19. We present an integrated analysis of longitudinal clinical parameters, blood biomarkers and lung pathology in COVID-19 patients from the Brazilian Amazon. We identified core signatures differentiating severe recovered patients and fatal cases with distinct disease trajectories. Progression to early death was characterized by rapid and intense endothelial and myeloid activation, presence of thrombi, mostly driven by SARS-CoV-2+macrophages. Progression to late death was associated with systemic cytotoxicity, interferon and Th17 signatures and fibrosis, apoptosis, and abundant SARS-CoV-2+epithelial cells in the lung. Progression to recovery was associated with pro-lymphogenic and Th2-mediated responses. Integration of ante-mortem clinical and blood biomarkers with post-mortem lung-specific signatures defined predictors of disease progression, identifying potential targets for more precise and effective treatments.
How immunity shapes the long-term dynamics of seasonal influenza
Authors: Eales Oliver , Shearer Freya , McCaw James 
Published: September 2023

AbstractSince its emergence in 1968, influenza A H3N2 has caused yearly epidemics in temperate regions. While infection confers immunity against antigenically similar strains, new antigenically distinct strains that evade existing immunity regularly emerge (‘antigenic drift’). Immunity at the individual level is complex, depending on an individual’s lifetime infection history. An individual’s first infection with influenza typically elicits the greatest response with subsequent infections eliciting progressively reduced responses (‘antigenic seniority’). The combined effect of individual-level immune responses and antigenic drift on the epidemiological dynamics of influenza are not well understood. Here we develop an integrated modelling framework of influenza transmission, immunity, and antigenic drift to show how individual-level exposure, and the build-up of population level immunity, shape the long-term epidemiological dynamics of H3N2. Including antigenic seniority in the model, we observe that following an initial decline after the pandemic year, the average annual attack rate increases over the next 80 years, before reaching an equilibrium, with greater increases in older age-groups. Our analyses suggest that the average attack rate of H3N2 is still in a growth phase. Further increases, particularly in the elderly, may be expected in coming decades, driving an increase in healthcare demand due to H3N2 infections.We anticipate our findings and methodological developments will be applicable to other antigenically variable pathogens. This includes the recent pandemic pathogens influenza A H1N1pdm09, circulating since 2009, and SARS-CoV-2, circulating since 2019. Our findings highlight that following the short-term reduction in attack rates after a pandemic, if there is any degree of antigenic seniority then a resurgence in attack rates should be expected over the longer-term. Designing and implementing studies to assess the dynamics of immunity for H1N1pdm09, SARS-CoV-2, and other antigenically variable pathogens may help anticipate any long-term rises in infection and health burden.
UK and US risk factors for hearing loss in neonatal intensive care unit infants
Authors: Thornton Sally K , Hoare Derek J , Yates Alice M , Willis Karen R , Scutt Polly , Kitterick Padraig T , Dixit Abhijit , Jayasinghe Dulip S 
Published: September 2023

AbstractImportanceEarly detection and intervention of hearing loss may mitigate negative effects on children’s development. Children who were admitted to the neonatal intensive care unit (NICU) as babies are particularly susceptible to hearing loss and risk factors are vital for surveillance.Design, Setting and ParticipantsThis single-centre retrospective cohort study included data from 142 inborn infants who had been admitted to the NICU in a tertiary regional referral centre. Data were recorded for 71 infants with confirmed permanent congenital hearing loss hearing loss. To determine impact of NICU admission independently of prematurity babies were individually matched with 71 inborn infants on gestational age, birthweight, and sex.Main Outcomes and MeasuresNeonatal indicators were recorded for all children with permanent congenital hearing loss. Presence of UK and US risk factors for hearing loss were collected on the neonatal population with hearing loss and for the matched controls.ResultsA fifth (21%) of babies with hearing loss had one or more UK risk factors whereas most (86%) had at least one US risk factor. False positives would be evident if US factors were used whereas the matched controls had no UK risk factors. Ten babies who at birth had no UK or US risk factors did not have any significant neonatal indicators identified in their records, one was ventilated for one day and two had a genetic anomaly.Conclusions and RelevanceCurrent risk factors for hearing loss we identified for follow-up in this high-risk group are highly specific for congenital hearing loss. UK risk factors were highly specific for hearing loss but not sensitive and conversely, US risk factors are sensitive but not specific so false positives would be recorded. A national study of neonatal indicators could provide the utility to test which combinations of risk factors provide high sensitivity without losing specificity.Key pointsCurrent risk factors listed in UK guidance were highly specific for congenital hearing loss but not sensitive meaning cases would be missed. US risk factors were more sensitive for hearing loss but not very specific indicating false positives would be made in this population.Neonates with hearing loss who wouldnothave been identified solely according to US or UK risk factors were born close to term and had few neonatal indicators identified.
Inhibition of Replication Origins and ATR Synergistically Activates the Innate Immune System in Cancer Cells
Authors: Doberstein Kai , Panther Johannes , Berlit Sebastian , Tuschy Benjamin , Sütterlin Marc , Marmé Frederik 
Published: September 2023

AbstractSufficient numbers of activated replication origins are essential for successful DNA replication. While normal cells load replication origins in abundance to the genome, cancer cells often load fewer origins of replication due to genomic alterations such asCCNE1amplifications.Here we exploit this feature to sensitize cancer cells to ATR inhibition.We show by using siRNA and small molecules that the inhibition of origin activation as well as the reduction of replication origins itself sensitizes ovarian cancer cell lines against ATR inhibition by inducing genomic instability. We further show that in ovarian cancer cells this combinatorial approach leads to an increased genomic instability which manifests in an increase of micronuclei that consequently activate the innate immune system through the cGAS-STING pathway. Notably, no activation of the innate immune system was observed in immortalized fallopian tube cells. However, overexpression of Cyclin E1 in this model leads to a marked increase in genomic instability and innate immune activation.Here we provide preclinical evidence to increase the therapeutic efficacy of ATR inhibitors. Additionally, this approach could help to activate innate immunity and increase T-cell immune infiltration in tumors, providing a rationale for a combination with immune checkpoint inhibitors.
“Surviving and Thriving”: Evidence for Cortical GABA Stabilization in Cognitively-Intact Oldest-Old Adults
Authors: Britton MK , Jensen G , Edden RA , Puts NA , Nolin SA , Merritt SS , Rezaei RF , Forbes M , Johnson KJ , Bharadwaj PK , Franchetti MK , Raichlen DA , Jessup CJ , Hishaw GA , Van Etten EJ , Gudmundson AT , Murali-Manohar S , Cowart H , Trouard TP , Geldmacher DS , Wadley VG , Alperin N , Levin BE , Rundek T , Visscher KM , Woods AJ , Alexander GE , Cohen RA , Porges EC 
Published: September 2023

AbstractCortical GABA levels are reduced in older age; age-related differences in GABA may be associated with age-related cognitive change. The nature of age-related GABA differences in the highest-functioning stratum of the oldest-old (85+) population is not yet known. We extend our previously-reported Individual Participant Data Meta-Analysis of GABA levels (Porges et al., 2021) across the lifespan with four novel datasets sampling the cognitively-intact oldest-old. The slope of age-related GABA differences in cognitively-intact oldest-old adults flattens after roughly age 80. We interpret these findings as an effect of survivorship: inclusion in the study required intact cognition, and too great a reduction of GABA levels may not be compatible with neurophysiological function needed for intact cognition. This work contributes to a growing body of evidence suggesting that successful cognitive aging may require intact GABAergic function, as well as further characterizing successful aging amongst oldest-old adults.
How do life history traits influence the environment’s effect on population synchrony? Insights from European birds and insects
Authors: Martin Ellen C. , Hansen Brage Bremset , Lee Aline Magdalena , Herfindal Ivar 
Published: September 2023

AbstractPopulations closer together in space are more likely to experience shared environmental fluctuations. This correlation in experienced environmental conditions is the main driver of spatial population synchrony, defined as the tendency for geographically separate populations of the same species to exhibit parallel fluctuations in abundance over time. Moran’s theorem states that spatially distinct populations are expected to show the same synchrony in their population dynamics as the synchrony in their environment. However, this is rarely the case in the wild, and the population synchrony of different species inhabiting the same area is rarely similar. These species-specific differences in how the environment synchronizes populations can be due to life history traits that make some species more susceptible to environmental stochasticity, such as reduced mobility or faster pace of life. In this study, we compiled long-term annual abundance datasets on European birds and insects (Lepidopterasp. andBombussp.) to identify how environmental synchrony (i.e., positively spatially correlated fluctuations in the environment, also called the Moran effect) affects species population synchrony. As expected, the environment synchronized populations of both birds and insects. Populations experiencing correlated fluctuations in precipitation or temperature had higher synchrony in annual population growth rates. Birds were more strongly synchronized by temperature, while precipitation was a stronger driver of synchrony in insects. In birds, species with short generation times had a stronger synchronizing effect of the environment compared to species with long generation times. Moreover, in birds the effects of synchrony in the environment also depended on movement propensity, with a positive impact for resident and short-distance migration species. In insects, annual population synchrony was affected by species movement propensity and dietary niche breadth, but these traits did not modify the effects of environmental synchrony. Our study provides empirical support for the prediction that spatial correlation in population dynamics is more influenced by environmental stochasticity for life histories with lower mobility and faster pace of life, but only in birds. By quantifying spatial population synchrony across different levels of environmental synchrony and life history traits, our study improves the understanding of the Moran effect as well as factors that drive population persistence in the face of environmental change.
The Bacterial Replicative Helicase Loader DciA is a DNA Condenser
Authors: Marsin Stéphanie , Jeannin Sylvain , Baconnais Sonia , Walbott Hélène , Pehau-Arnaudet Gérard , Noiray Magali , Aumont-Nicaise Magali , Stender Emil GP , Cargemel Claire , Bars Romain Le , Cam Eric Le , Quevillon-Cheruel Sophie 
Published: September 2023

AbstractThe loading of the bacterial replicative helicase is an essential step for genome replication and depends on the assistance of accessory proteins. Several of these proteins have been identified across the bacterial phyla. DciA is the most common loading protein in bacteria, yet the one whose mechanism is the least understood. We have previously shown thatVcDciA fromVibrio cholerae,composed of a globular KH-like domain followed by an unfolded extension, has a strong affinity for DNA. Here, we characterized the droplets formed byVcDciA upon interaction with a short single-stranded substrate. We demonstrate the fluidity of these droplets using light microscopy and address their network organization through electron microscopy, thereby bridging events to conclude on a liquid-liquid phase separation behavior. Additionally, we observe the recruitment ofVcDnaB inside theVcDciA-DNA droplets. We show that DnaC fromEscherichia coliis also competent to form these condensate structures in the presence of ssDNA. Our data open up possibilities for the involvement of DciA in the formation of non-membrane compartments within the bacterium, facilitating the assembly of replication players with the chromosomal DNA.
Multivariate comparison of taxonomic, chemical and technical data from 80 full-scale an-aerobic digester-related systems
Authors: Otto Pascal , Puchol-Royo Roser , Ortega-Legarreta Asier , Tanner Kristie , Tideman Jeroen , de Vries Sjoerd-Jan , Pascual Javier , Porcar Manuel , Latorre-Perez Adriel , Abendroth Christian 
Published: September 2023

AbstractThis study represents one of the most comprehensive characterisations of the anaerobic digestion (AD) microbiome with 80 samples from 45 different large-scale reactors in three coun-tries. Technical, chemical and taxonomic data was thoroughly collected, analyzed and correlated to identify the main drivers of AD processes. Our results showed that MBA03,Proteiniphilum, a member ofDethiobacteraceae, andCaldicoprobacterwere present in all the samples, whileMeth-anosarcinawas the most abundant and prevalent archaea. Two distinct bacterial clusters were iden-tified by correlating microbial abundances. One was correlated with hydrogenotrophic and the other with acetoclastic methanogenesis. Organic acids, ammonia, nitrogen, COD and the trace el-ements Fe, Mo, and the macro nutrient P had the greatest impact on AD microbiomes. Temperature, reactor type and substrate also influenced the formation of a specialized microbial community. Overall, this work sheds light on the microbial key players involved in AD and evaluates how they are affected by technical and chemical parameters.HighlightsGeneration of a holistic dataset of chemical, taxonomic and technical parameters of 80 large-scale anaerobic digestion systems.Identification of a core microbiome comprising MBA03,Proteiniphilum, an uncultured or-ganism from theDethiobacteraceaefamily, and theCaldicoprobacterfamily.Identification of the main influencing parameters that determine the occurrence and non-occurrence of specific genera.Correlation of bacterial taxa with hydrogenotrophic and/or acetoclastic archaea.
The threats to reptiles at global and regional scales
Authors: Farooq Harith , Harfoot Mike , Rahbek Carsten , Geldmann Jonas 
Published: September 2023

AbstractAt least 20% of reptiles are currently threatened with extinction. Due to the lack of comprehensive global assessments of the group, they have been omitted from spatial studies, especially the ones addressing conservation or spatial prioritization. With the recent release of global assessments for reptiles, in this study, we calculate the probability of seven biodiversity threats – logging, pollution, agriculture, invasive species, hunting, climate change and urbanization occurring at a global scale on a 50×50km grid and their impact measured as the probability of finding a threatened species. Despite the global nature of our approach, we compartmented the terrestrial land into 12 regions and conducted separate analyses on each region. We find that despite globally low levels of intensity, climate change and invasive species have the highest impact on reptiles. But when looked at the regional level, various threats have a high impact on biodiversity, even surpassing climate change and invasives. Our study highlights the importance of going beyond measuring the intensity of threats to measure impact and also the importance of subdividing the world into smaller units and testing the impacts separately.