bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Juba, South Sudan: a population-based study
Authors: Wiens Kirsten E. , Mawien Pinyi Nyimol , Rumunu John , Slater Damien , Jones Forrest K. , Moheed Serina , Caflish Andrea , Bior Bior K. , Jacob Iboyi Amanya , Lako Richard Lino Loro , Guyo Argata Guracha , Olu Olushayo Oluseun , Maleghemi Sylvester , Baguma Andrew , Hassen Juma John , Baya Sheila K. , Deng Lul , Lessler Justin , Demby Maya N. , Sanchez Vanessa , Mills Rachel , Fraser Clare , Charles Richelle C. , Harris Jason B. , Azman Andrew S. , Wamala Joseph F. 
Published: March 2021

AbstractBackgroundRelatively few COVID-19 cases and deaths have been reported through much of sub-Saharan Africa, including South Sudan, although the extent of SARS-CoV-2 spread remains unclear due to weak surveillance systems and few population-representative serosurveys.MethodsWe conducted a representative household-based cross-sectional serosurvey in Juba, South Sudan. We quantified IgG antibody responses to SARS-CoV-2 spike protein receptor-binding domain and estimated seroprevalence using a Bayesian regression model accounting for test performance.ResultsWe recruited 2,214 participants from August 10 to September 11, 2020 and 22.3% had anti-SARS-CoV-2 IgG titers above levels in pre-pandemic samples. After accounting for waning antibody levels, age, and sex, we estimated that 38.5% (32.1 - 46.8) of the population had been infected with SARS-CoV-2. For each RT-PCR confirmed COVID-19 case, 104 (87-126) infections were unreported. Background antibody reactivity was higher in pre-pandemic samples from Juba compared to Boston, where the serological test was validated. The estimated proportion of the population infected ranged from 30.1% to 60.6% depending on assumptions about test performance and prevalence of clinically severe infections.ConclusionsSARS-CoV-2 has spread extensively within Juba. Validation of serological tests in sub-Saharan African populations is critical to improve our ability to use serosurveillance to understand and mitigate transmission.
Acceptance and intake of COVID-19 vaccines among older Germans
Authors: Malesza Marta , Wittmann Erich 
Published: March 2021

AbstractThe main aim of this study was to investigate the various factors influencing COVID-19 vaccination acceptance and actual intake among older Germans aged over 75 years old (N = 1037). We found that the intention to get vaccinated or intake of the COVID-19 vaccine were positively related to the perceptions of becoming infected, perceptions of the severity of the potential long-term effects, the vaccine’s efficacy, and the benefits of vaccination. Meanwhile, the intention to get the vaccine or vaccine intake were decreased by perceptions of the negative side-effects and the general impediments to vaccination.
The Induction of Pyrenoid Synthesis by Hyperoxia and its Implications for the Natural Diversity of Photosynthetic Responses inChlamydomonas
Authors: Neofotis Peter , Temple Joshua , Tessmer Oliver L. , Bibik Jacob , Norris Nicole , Poliner Eric , Lucker Ben , Wijetilleke Sarathi , Withrow Alecia , Sears Barbara , Mogos Greg , Frame Melinda , Hall David , Weissman Joseph , Kramer David M. 
Published: March 2021

ABSTRACTIn algae, it is well established that the pyrenoid, a component of the carbon-concentrating mechanism (CCM), is essential for efficient photosynthesis at low CO2. However, the signal that triggers the formation of the pyrenoid has remained elusive. Here, we show that, inChlamydomonas reinhardtii, the pyrenoid is strongly induced by hyperoxia, even at high CO2or bicarbonate levels. These results suggest that the pyrenoid can be induced by a common product of photosynthesis specific to low CO2or hyperoxia. Consistent with this view, the photorespiratory by-product, H2O2, induced the pyrenoid, suggesting that it acts as a signal. Finally, we show evidence for linkages between genetic variations in hyperoxia tolerance, H2O2signaling, and pyrenoid morphologies.
Bayesian Multivariate Growth Mixture Modeling of Longitudinal Data: An Application to Alzheimer’s Disease Study
Authors: Lin Wenyi , Donohue Michael C. , Insel Philip , Schwartzman Armin , Thompson Wesley K. 
Published: March 2021

AbstractAlzheimer’s disease (AD) studies often collect longitudinal biomarker measures of multiple cohorts at different stages of disease and follow these biomarkers with a relatively short period of time. The heterogeneity of the longitudinal patterns of biomarkers can be ubiquitous across both individual trajectories and cognitive domains. We propose a flexible Bayesian multivariate growth mixture model to identify distinct longitudinal patterns of data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) study. A Gibbs sampling is implemented for achieving the Bayesian inference. We perform a simulation study to demonstrate the adequate performance of our proposed approach and apply the model to identify three latent cognitive decline patterns among patients from the ADNI study.
Sequence features around cleavage sites are highly conserved among different species and a critical determinant for RNA cleavage position across eukaryotes
Authors: Ueno Daishin , Yamasaki Shotaro , Sadakiyo Yuta , Teruyama Takumi , Demura Taku , Kato Ko 
Published: March 2021

ABSTRACTRNA degradation is critical for control of gene expression, and endonucleolytic cleavage– dependent RNA degradation is conserved among eukaryotes. Some cleavage sites are secondarily capped in the cytoplasm and identified using the CAGE method. Although uncapped cleavage sites are widespread in eukaryotes, comparatively little information has been obtained about these sites using CAGE-based degradome analysis. Previously, we developed the truncated RNA-end sequencing (TREseq) method in plant species and used it to acquire comprehensive information about uncapped cleavage sites; we observed G-rich sequences near cleavage sites. However, it remains unclear whether this finding is general to other eukaryotes. In this study, we conducted TREseq analyses in fruit flies (Drosophila melanogaster) and budding yeast (Saccharomyces cerevisiae). The results revealed specific sequence features related to RNA cleavage inD. melanogasterandS. cerevisiaethat were similar to sequence patterns inArabidopsis thaliana. Although previous studies suggest that ribosome movements are important for determining cleavage position, feature selection using a random forest classifier showed that sequences around cleavage sites were major determinant for cleaved or uncleaved sites. Together, our results suggest that sequence features around cleavage sites are critical for determining cleavage position, and that sequence-specific endonucleolytic cleavage–dependent RNA degradation is highly conserved across eukaryotes.
Efficient maternofetal transplacental transfer of anti- SARS-CoV-2 spike antibodies after antenatal SARS-CoV-2 BNT162b2 mRNA vaccination
Authors: Rottenstreich Amihai , Zarbiv Gila , Oiknine-Djian Esther , Zigron Roy , Wolf Dana G. , Porat Shay 
Published: March 2021

AbstractBackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during pregnancy and early infancy can result in severe disease. Evaluating the serologic response after maternal vaccination during pregnancy and subsequent transplacental antibody transfer has important implications for maternal care and vaccination strategies.ObjectiveTo assess maternal and neonatal SARS-CoV-2 antibody levels after antenatal mRNA vaccination.Design, Setting, and ParticipantsThis study took place at Hadassah Medical Center in Jerusalem, Israel in February 2021. Maternal and cord blood sera were collected for antibody measurement from mother/newborn dyads following antenatal vaccination.ExposureSARS-CoV-2 BNT162b2 mRNA vaccination.Main outcome and measuresSpike protein (S) and receptor binding domain (RBD) - specific, IgG levels were evaluated in maternal and cord blood sera.ResultsThe study cohort consisted of 20 parturients, with a median maternal age of 32 y ears and a median gestational age of 393/7 weeks at the time of delivery. The median time lapsed from the first and second doses of vaccine administration until delivery was 33 [IQR 30-37] and 11 [IQR 9-15] days, respectively. Of the 20 dyads, all women an d infants were positive for anti S- and anti-RBD-specific IgG. Anti-S and anti-RBD-specific IgG levels in maternal sera were positively correlated to their respective concentrations in cord blood (ρs= 0.72; P<0.001 and ρs= 0.72; P <0.001, respectively). Anti-S and anti-RBD-specific IgG titers in cord blood were directly correlated with time lapsed since the administration of the first vaccine dose (ρs= 0.71; P =0.001 and ρs= 0.63; P=0.004, respectively).Conclusion and RelevanceIn this study, SARS-CoV-2 mRNA vaccine administered during pregnancy induced adequate maternal serologic response with subsequent efficient transplacental transfer. Our findings highlight that vaccination of pregnant women may provide maternal and neonatal protection from SARS-CoV-2 infection.
Measurement of Volatile Compounds for Real-time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt
Authors: Kim Junhyeong , Goldstein Allen H. , Chakraborty Romy , Jardine Kolby , Weber Robert , Sorensen Patrick O. , Wang Shi , Faybishenko Boris , Misztal Pawel K. , Brodie Eoin L. 
Published: March 2021

AbstractSnowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.
The Inflammatory Role of Milk Fat Globule Epidermal Growth Factor VIII in Angiotensin II Induced Arterial Remodeling
Authors: Ni Leng , Liu Lijuan , Zhu Wanqu , Telljohann Richard , Zhang Jing , Monticone Robert E. , McGraw Kimberly R. , Liu Changwei , Morrell Christopher H. , Garrido-Gil Pablo , Labandeira-Garcia Jose Luis , Lakatta Edward G. , Wang Mingyi 
Published: March 2021

AbstractBackgroundAngiotensin II (Ang II) and milk fat globule-epidermal growth factor VIII (MFG-E8) are involved in age-associated arterial remodeling; however, the inflammatory role of MFG-E8 in Ang II associated arterial remodeling with aging remains unknown.Methods and ResultsIn this study, 30-week-old MFG-E8 knock out (KO) and age-matched wild-type (WT) mice were infused with Ang II or saline. After infusion the with Ang II, the aortic molecular, cellular, and structural remodeling were observed in mice and compared to those infused with saline, but these effects were dependent on the expression of MFG-E8: (1) In the WT mice, Ang II infusion substantially increased intimal-medial thickness, elastic lamina degradation, collagen deposition, and the proliferation of VSMCs; in contrast, in the KO mice, these effects were significantly reduced; (2) In the WT mice, Ang II treatment significantly increased the activation and expression of MMP2, TGF-β1, and its downstream signaling molecule p-SMAD2, and collagen type I production, however, in the KO mice, these molecular effects were significantly reduced; (3) In the WT mice, Ang II treatment increased inflammatory p-NF-κB p65, MCP1, TNF-α, ICAM1, and VCAM1 molecular expression, while conversely, in the KO mice, no significant inflammatory changes were found; (4) Importantly, compared to untreated control mice with a wide range of age from 4-96 weeks, Ang II infused “younger” mice produced an “older” arterial inflammatory phenotype, which was alleviated by MFG-E8 deficiency.ConclusionsMFG-E8 mediates Ang II associated arterial inflammatory remodeling. Targeting MFG-E8 is a novel molecular approach to curb adverse arterial remodeling during aging and hypertension.CLINICAL PERSPECTIVEWhat Is New?•Both Ang II and MFG-E8 increases are involved in proinflammatory arterial remodeling mediating the molecular, cellular and tissue events in aging and hypertension.•MFG-E8 is essential for Ang II induced and age-associated adverse arterial remodeling via the increase of proinflammation, intimal medial thickening, elastin fragmentation, collagen deposition, and VSMC proliferation.What Are the Clinical Implications?Since MFG-E8 mediates Ang II induced proinflammation in arterial wall remodeling in aging and hypertension, targeting MFG-E8 is a potential molecular approach to curb inflammatory arterial remodeling, maintaining the health of the vascular system during aging and hypertension.
Chimeric spike mRNA vaccines protect against Sarbecoviruschallenge in mice
Authors: Martinez David R. , Schäfer Alexandra , Leist Sarah R. , De la Cruz Gabriela , West Ande , Atochina-Vasserman Elena N. , Lindesmith Lisa C. , Pardi Norbert , Parks Robert , Barr Maggie , Li Dapeng , Yount Boyd , Saunders Kevin O. , Weissman Drew , Haynes Barton F. , Montgomery Stephanie A. , Baric Ralph S. 
Published: March 2021

AbstractThe emergence of SARS-CoV in 2003 and SARS-CoV-2 in 2019 highlights the need to develop universal vaccination strategies against the broaderSarbecovirussubgenus. Using chimeric spike designs, we demonstrate protection against challenge from SARS-CoV, SARS-CoV-2, SARS-CoV-2 B.1.351, bat CoV (Bt-CoV) RsSHC014, and a heterologous Bt-CoV WIV-1 in vulnerable aged mice. Chimeric spike mRNAs induced high levels of broadly protective neutralizing antibodies against high-risk Sarbecoviruses. In contrast, SARS-CoV-2 mRNA vaccination not only showed a marked reduction in neutralizing titers against heterologous Sarbecoviruses, but SARS-CoV and WIV-1 challenge in mice resulted in breakthrough infection. Chimeric spike mRNA vaccines efficiently neutralized D614G, UK B.1.1.7., mink cluster five, and the South African B.1.351 variant of concern. Thus, multiplexed-chimeric spikes can prevent SARS-like zoonotic coronavirus infections with pandemic potential.SentenceChimerized RBD, NTD, and S2 spike mRNA-LNPs protect mice against epidemic, zoonotic, and pandemic SARS-like viruses
Rapid characterization of complex genomic regions using Cas9 enrichment and Nanopore sequencing
Authors: Bruijnesteijn Jesse , van der Wiel Marit , de Groot Natasja G. , Bontrop Ronald E. 
Published: March 2021

AbstractLong-read sequencing approaches have considerably improved the quality and contiguity of genome assemblies. Such platforms bear the potential to resolve even extremely complex regions, such as multigenic families and repetitive stretches of DNA. Deep sequencing coverage, however, is required to overcome low nucleotide accuracy, especially in regions with high homopolymer density, copy number variation, and sequence similarity, such as theMHCandKIRgene clusters of the immune system. Therefore, we have adapted a targeted enrichment protocol in combination with long-read sequencing to efficiently annotate complex genomic regions. Using Cas9 endonuclease activity, segments of the complexKIRgene cluster were enriched and sequenced on an Oxford Nanopore Technologies platform. This provided sufficient coverage to accurately resolve and phase highly complexKIRhaplotypes. Our strategy facilitates rapid characterization of large and complex multigenic regions, including its epigenetic footprint, in multiple species, even in the absence of a reference genome.
Understanding the Evolution of Nutritive Taste in Animals: Insights from Biological Stoichiometry and Nutritional Geometry
Authors: Demi Lee M. , Taylor Brad W. , Reading Benjamin J. , Tordoff Michael G. , Dunn Robert R. 
Published: March 2021

AbstractA major conceptual gap in taste biology is the lack of a general framework for understanding the evolution of different taste modalities among animal species. We turn to two complementary nutritional frameworks, biological stoichiometry theory and nutritional geometry, to develop hypotheses for the evolution of different taste modalities in animals. We describe how the attractive tastes of Na, Ca, P, N and C containing compounds are consistent with principles of both frameworks based on their shared focus on nutritional imbalances and consumer homeostasis. Specifically, we suggest that the evolution of multiple nutritive taste modalities can be predicted by identifying individual elements that are typically more concentrated in the tissues of animals than plants. Additionally, we discuss how consumer homeostasis can inform our understanding of why some taste compounds (i.e., Na, Ca and P salts) can be either attractive or aversive depending on concentration. We also discuss how these complementary frameworks can help to explain the phylogenetic distribution of different taste modalities and improve our understanding of the mechanisms that lead to loss of taste capabilities in some animal lineages. The ideas presented here will stimulate research that bridges the fields of evolutionary biology, sensory biology and ecology.
Impairing one sensory modality enhances another by reprogramming peptidergic circuits inCaenorhabditis elegans
Authors: Valperga Giulio , Bono Mario de 
Published: March 2021

AbstractAnimals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. To probe these mechanisms, we perform a forward genetic screen for mutants with enhanced O2perception inC. elegans. Multiple mutants exhibiting increased responsiveness to O2concomitantly show defects in other sensory responses. One mutant,qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+responses in the ADL chemosensory neurons. We find that ADL’s responsiveness to pre-synaptic input from O2- sensing neurons is heightened inqui-1and other sensory defective mutants resulting in an enhanced neurosecretion. Expressingqui-1selectively in ADL rescues both thequi-1ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling of ADL neurons indicates its acquired O2-evoked neurosecretion is the result of a transcriptional reprogramming that up-regulates neuropeptide signalling. We show that the conserved neuropeptide receptor NPR-22 is necessary and sufficient in ADL to enhance its neurosecretion levels. Sensory loss can thus confer cross-modal plasticity by re-wiring peptidergic circuits.
A simplified SARS-CoV-2 pseudovirus neutralization assay
Authors: Donofrio Gaetano , Franceschi Valentina , Macchi Francesca , Russo Luca , Rocci Anna , Marchica Valentina , Costa Federica , Giuliani Nicola , Ferrari Carlo , Missale Gabriele 
Published: March 2021

AbstractCOVID-19 is an ongoing pandemic caused by the highly infectious coronavirus SARS-CoV-2 that is engaging worldwide scientific research to find a timely and effective eradication strategy. Great efforts have been put into anti-COVID-19 vaccine generation in an effort to protect the world population and block SARS-CoV-2 spread. To validate the protective efficacy of the vaccination campaign and effectively control the pandemy, it is necessary to quantify the neutralizing antibodies induction by vaccination, since they have been established to be a correlate of protection. In this work a SARS-CoV-2 pseudovirus neutralization assay, based on a replication incompetent lentivirus expressing an adapted form of CoV-2 S protein and an ACE2/TMPRSS2 stably expressing cell line, have been minimized in term of protocol steps without loss of accuracy. The goal of the present simplified neutralization system is to improve SARS-CoV-2 vaccination campaign by means of an easy and accessible approach to be performed in any medical laboratory, maintaining the sensitivity and quantitative reliability of classical serum neutralization assays. Further this assay can be easily adapted to different coronaviruses variants by simply modifying the pseudotyping vector.