bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution of SARS-CoV-2 RNA Signal in a Home with COVID-19 Positive Occupants
Authors: Maestre Juan P. , Jarma David , Yu Cesca , Siegel Jeff , Horner Sharon , Kinney Kerry A. 
Published: December 2020

AbstractAlthough many COVID-19 patients quarantine and recover at home, the dispersal of SARS-CoV-2 onto surfaces and dust within the home environment remains poorly understood. To investigate the distribution and persistence of SARS-CoV-2 in a quarantine home, samples were collected from a household with two confirmed COVID-19 cases (one adult and one child). Home surface swab and dust samples were collected two months after symptom onset (and one month after symptom resolution) in the household. The strength of the SARS-CoV-2 molecular signal in fomites varied as a function of sample location, surface material and cleaning practices. Notably, the SARS-CoV-2 RNA signal was detected at several locations throughout the household although cleaning appears to have attenuated the signal on many surfaces. Of the 24 surfaces sampled, 46% were SARS-CoV-2 positive at the time of sampling. The SARS-CoV-2 concentrations in dust recovered from floor and HVAC filter samples ranged from 104-105 N2 gene copies/g dust. While detection of viral RNA does not imply infectivity, this study confirms that the SARS-CoV-2 RNA signal can be detected at several locations within a COVID-19 quarantine home and can persist after symptoms have resolved. In addition, the concentration of SARS-CoV-2 (normalized per unit mass of dust) recovered in home HVAC filters may prove useful for estimating SARS-CoV-2 airborne levels in homes.
A Net Benefit Approach for the Optimal Allocation of a COVID-19 Vaccine
Authors: Kirwin Erin , Rafferty Ellen , Harback Kate , Round Jeff , McCabe Christopher 
Published: December 2020

AbstractOBJECTIVEWe implement a model-based approach to identify the optimal allocation of a COVID-19 vaccine in the province of Alberta, Canada.METHODSWe develop an epidemiologic model to evaluate allocation strategies defined by age and risk target groups, coverage, effectiveness, and cost of vaccine. The model simulates hypothetical immunization scenarios within a dynamic context, capturing concurrent public health strategies and population behaviour changes.RESULTSIn a scenario with 80% vaccine effectiveness, 40% population coverage, and prioritisation of those over the age of 60 at high-risk of poor outcomes, active cases are reduced by 17% and net monetary benefit increased by $263 million dollars, relative to no vaccine. Concurrent implementation of policies such as school closure and senior contact reductions have similar impacts on incremental net monetary benefit ($352 vs. 292 million, respectively) when there is no prioritisation given to any age or risk group. When older age groups are given priority, the relative benefit of school closures is much larger ($214 vs. 118 million). Results demonstrate that the rank ordering of different prioritisation options varies by prioritisation criteria, vaccine effectiveness and coverage, and concurrently implemented policies.CONCLUSIONSOur results have three implications: (i) optimal vaccine allocation will depend on the public health policies in place at the time of allocation and the impact of those policies on population behaviour; (ii) outcomes of vaccine allocation policies can be greatly supported with interventions targeting contact reduction in critical sub-populations; and (iii) identification of the optimal strategy depends on which outcomes are prioritised.
Dedifferentiation of memory-related brain function as a potential early biomarker of Alzheimer’s disease in asymptomatic older women: Results from the PREVENT-AD Cohort
Authors: Rabipour Sheida , Rajagopal Sricharana , Pasvanis Stamatoula ,   PREVENT-AD Research Group, Rajah M. Natasha 
Published: December 2020

AbstractLate-onset Alzheimer’s disease (AD) disproportionately affects women compared to men. Episodic memory decline is one of the earliest and most pronounced deficits observed in AD. However, it remains unclear whether there are sex differences in episodic memory-related brain function in cognitively intact older adults at risk of developing AD. In the current study, we used task fMRI to test for sex differences in episodic memory-related brain activity and brain activity-behavior correlations in cognitively intact older adults with a family history of AD from the PREVENT-AD cohort study in Montreal, Canada (Mage=63.03±3.78; Meducation=15.41±3.40). Importantly, we tested women and men who were matched in age, body mass index, years of education, and proximity to the age of parental AD onset. We used data-driven task-based multivariate partial least squares (PLS) analysis to identify sex differences in brain activity during the successful encoding and retrieval of objects and their associated spatial context. We used behavior PLS to examine sex differences in the correlations between brain activity and memory performance at encoding and retrieval. Our results suggested no significant sex differences in behavioral performance on the memory task. Yet, we observed sex differences in task-related brain activity and in brain activity-behavior correlations during the encoding of object-location associative memories and object-only item memory, and the retrieval of object only item memories. Specifically, subsequent object-location associative retrieval associated with encoding related activation of caudate, cingulate, and middle occipital cortex in women and, additionally, of temporo-parietal regions in men. We also found male-specific activations in ventrolateral prefrontal cortex (PFC) and insula during associated with the encoding and retrieval of object-only information. Moreover, whereas activity in ventrolateral PFC, posterior cingulate, and inferior parietal regions during encoding supported subsequent performance in women, activity in these regions during retrieval supported object-location associative memory in men. Similarly, we found that activity in ventrolateral PFC, precuneus, parahippocampal, anterior cingulate, and occipital regions during retrieval supported general memory performance in women but object-only retrieval in men. Our findings suggest functional dedifferentiation of episodic memory-related brain activation and performance in women compared to men. Follow up analyses should test for sex differences in the relationship between brain activity patterns and performance longitudinally, in association with risk factors for AD development.
Hierarchical Morphogenesis of Swallowtail Butterfly Wing Scale Nanostructures
Authors: Seah Kwi Shan , Saranathan Vinodkumar 
Published: December 2020

AbstractThe study of color patterns in the animal integument is a fundamental question in biology, with many lepidopteran species being exemplary models in this endeavor due to their relative simplicity and elegance. While significant advances have been made in unravelling the cellular and molecular basis of lepidopteran pigmentary coloration, the morphogenesis of wing scale nanostructures involved in structural color production is not well understood. Contemporary research in this topic largely focuses on a few nymphalid model taxa (e.g.,Bicyclus,Heliconius), despite an overwhelming diversity in the hierarchical nanostructural organization of lepidopteran wing scales. Here, we present a time-resolved, comparative developmental study of hierarchical scale nanostructures inParides eurimedesand five other papilionid species. Our results uphold the putative conserved role of F-actin bundles in acting as spacers between developing ridges, as previously documented in several nymphalid species. Interestingly, while ridges are developing inP. eurimedes, plasma membrane manifests irregular mesh-like crossribs characteristic of Papilionidae, which delineate the accretion of cuticle into rows of planar disks in between ridges. Once the ridges have grown, disintegrating F-actin bundles appear to reorganize into a network that supports the invagination of plasma membrane underlying the disks, subsequently forming an extruded honeycomb lattice. Our results uncover a previously undocumented role for F-actin in the morphogenesis of complex wing scale nanostructures, likely specific to Papilionidae.
Dietary Monoterpenoids As a New Class of Allosteric Human Aryl Hydrocarbon Receptor Antagonists
Authors: Poulíková Karolína , Zůvalová Iveta , Vyhlídalová Barbora , Krasulová Kristýna , Jiskrová Eva , Vrzal Radim , Kortagere Sandhya , Kopečná Martina , Kopečný David , Šebela Marek , Rolfes Katharina Maria , Haarmann-Stemmann Thomas , Mani Sridhar , Dvořák Zdeněk 
Published: December 2020

ABSTRACTCarvones, the constituents of essential oils of dill, caraway, and spearmint, were reported to antagonize the human aryl hydrocarbon receptor (AhR); however, the exact molecular mechanism remains elusive. We show that carvones are non-competitive allosteric antagonists of the AhR that inhibit the induction of AhR target genes in a ligand-selective and cell type-specific manner. Carvones do not displace radiolabeled ligand from binding at the AhR, but they bind allosterically within the bHLH/PAS-A region of the AhR. Carvones did not influence a translocation of ligand-activated AhR into the nucleus. Carvones inhibited the heterodimerization of the AhR with its canonical partner ARNT and subsequent binding of the AhR to the promotor of CYP1A1. Interaction of carvones with potential off-targets, including ARNT and protein kinases, was refuted. This is the first report of a small dietary monoterpenoids as a new class of AhR non-competitive allosteric antagonists with the potential preventive and therapeutic application.
Dynamic cholinergic tone in the basal forebrain reflects reward-seeking and reinforcement during olfactory behavior
Authors: Hanson Elizabeth , Brandel-Ankrapp Katie L , Arenkiel Benjamin R 
Published: December 2020

AbstractSensory perception underlies how we internalize and interact with the external world. In order to adapt to changing circumstances and interpret signals in a variety of contexts, sensation needs to be reliable, but perception of sensory input needs to be flexible. An important mediator of this flexibility is top-down regulation from the cholinergic basal forebrain. Basal forebrain projection neurons serve as pacemakers and gatekeepers for downstream neural networks, modulating circuit activity across diverse neuronal populations. This top-down control is necessary for sensory cue detection, learning, and memory, and is disproportionately disrupted in neurodegenerative diseases associated with cognitive decline. Intriguingly, cholinergic signaling acts locally within the basal forebrain to sculpt the activity of basal forebrain output neurons. To determine how local cholinergic signaling impacts basal forebrain output pathways that participate in top-down regulation, we sought to define the dynamics of cholinergic signaling within the basal forebrain during motivated behavior and learning. Towards this, we utilized fiber photometry and the genetically encoded acetylcholine indicator GAChR2.0 to define temporal patterns of cholinergic signaling in the basal forebrain during olfactory-guided, motivated behaviors and learning. We show that cholinergic signaling reliably increased during reward-seeking behaviors but was strongly suppressed by reward delivery in a go/no-go, olfactory-cued discrimination task. The observed transient reduction in cholinergic tone was mirrored by a suppression in basal forebrain GABAergic neuronal activity. Together, these findings suggest that cholinergic tone in the basal forebrain changes rapidly to reflect rewardseeking behavior and positive reinforcement to impact basal forebrain circuit activity.
Assessment by Matrix-Assisted Laser Desorption – Time of Flight Mass Spectrometry of the Diversity of Endophytes and Rhizobacteria Cultured from the Maize Microbiome
Authors: LaMontagne Michael G. , Tran Phi L. , Benavidez Alexander , Morano Lisa D. 
Published: December 2020

AbstractMany endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be cultured, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption – time of flight (MALDI-TOF) has enabled high throughput “culturomics” studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties ofZea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (> 99%) 16S rRNA gene sequences. Mass spectra were used to successfully train a machine learning algorithm that perfectly classified isolates. The 60 MTUs provided > 70 % coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method.Acidovoraxsp.,Pseudomonassp. andCellulosimicrobiumsp. dominated the library generated from the rhizoplane and the heritage variety contained a relatively high number of MTUs specific to that niche. This suggests a rapid, inexpensive method of describing the types of bacteria cultured from niches within maize microbiomes and the coverage achieved with a cultivation strategy.
Chlamydia gallinacea: genetically armed as a pathogen however a phenotypical commensal?
Authors: Heijne Marloes , Jelocnik Martina , Umanets Alexander , Brouwer Michael S.M. , Dinkla Annemieke , Harders Frank , van Keulen Lucien J.M. , Roest Hendrik Jan , Schaafsma Famke , Velkers Francisca C. , van der Goot Jeanet A. , Pannekoek Yvonne , Koets Ad P. 
Published: December 2020

AbstractChlamydia gallinaceais an obligate intracellular bacterium that has recently been added to the family ofChlamydiaceae.C. gallinaceais genetically diverse, widespread in poultry and a suspected cause of pneumonia in slaughterhouse workers. In poultry,C. gallinaceainfections appear asymptomatic, but studies about the pathogenic potential are limited. In this study two novel sequence types ofC. gallinaceawere isolated from apparently healthy chickens. Both isolates (NL_G47 and NL_F725) were closely related to each other and showed 99.1% DNA sequence identity toC. gallinaceaType strain 08-1274/3. To gain further insight in the pathogenic potential, infection experiments in embryonated chicken eggs and comparative genomics withChlamydia psittaciwere performed.C. psittaciis an ubiquitous zoonotic pathogen of birds and mammals, and infection in poultry can result in severe systemic illness. In experiments with embryonated chicken eggsC. gallinaceainduced mortality was observed, potentially strain dependent but lower compared toC. psittaciinduced mortality. Comparative analyses confirmed all currently availableC. gallinaceagenomes possess the hallmark genes coding for known and potential virulence factors as found inC. psittacialbeit to a reduced number of orthologues or paralogs. The presence of (potential) virulence factors and the observed mortality in embryonated eggs indicatesC. gallinaceashould rather be considered as a (conditional) pathogen than an innocuous commensal.ImportanceChlamydiaceaeare a family of bacteria comprising human and animal pathogens including the recently recognizedChlamydia gallinacea. C. gallinaceais widespread in poultry without causing clinical signs, which raises questions about its pathogenic potential. To assess this potential, two novelC. gallinaceastrains were isolated, tested in infection experiments in embryonated chicken eggs and compared toC. psittaci. C. psittaciinfection in poultry can result in severe systemic illness, depending on the conditions, and infections can be transmitted to humans. In the experimentsC. gallinaceainfection induced mortality of the embryo, but to a lower extent than infection withC. psittaci. Subsequent genome comparisons confirmed bothC. gallinaceastrains possess potential virulence genes typical for chlamydia, but fewer thanC. psittaci. These results indicateC. gallinaceadoes have a pathogenic potential which warrants further research to elucidate its role as a poultry pathogen.
Balancing positive and negative selection:in vivoevolution ofCandida lusitaniae MRR1
Authors: Demers Elora G. , Stajich Jason , Ashare Alix , Occhipinti Patricia , Hogan Deborah A. 
Published: December 2020

AbstractThe evolution of pathogens in response to selective pressures present during chronic infections can influence persistence, virulence, and the outcomes of antimicrobial therapy. Because subpopulations within an infection can be spatially separated and the host environment can fluctuate, an appreciation of the pathways under selection may be most easily revealed through the analysis of numerous isolates from single infections. Here, we continued our analysis of a set of clonally-derivedClavispora (Candida) lusitaniaeisolates from a single chronic lung infection with a striking enrichment in the number of alleles ofMRR1. Genetic and genomic analyses found evidence for repeated acquisition of gain-of-function mutations that conferred constitutive Mrr1 activity. In the same population, there were multiple alleles with both gain-of-function mutations and secondary suppressor mutations that either attenuated or abolished the constitutive activity suggesting the presence of counteracting selective pressures. Our studies demonstrated tradeoffs between high Mrr1 activity, which confers resistance to the antifungal fluconazole, host factors, and bacterial products through its regulation ofMDR1, and resistance to hydrogen peroxide, a reactive oxygen species produced in the neutrophilic environment associated with this infection. This inverse correlation between high Mrr1 activity and hydrogen peroxide resistance was observed in multipleCandidaspecies and in serial analysis of populations from this individual collected over three years. These data lead us to propose that dynamic or variable selective pressures can be reflected in population genomics and that these dynamics can complicate the drug resistance profile of the population.ImportanceUnderstanding microbial evolution within patients is critical for managing chronic infections and understanding host-pathogen interactions. Here, our analysis of multipleMRR1alleles in isolates from a singleClavispora (Candida) lusitaniaeinfection revealed the selection for both high and low Mrr1 activity. Our studies reveal tradeoffs between high Mrr1 activity, which confers resistance to the commonly used antifungal fluconazole, host antimicrobial peptides and bacterial products, and resistance to hydrogen peroxide. This work suggests that spatial or temporal differences within chronic infections can support a large amount of dynamic and parallel evolution, and that Mrr1 activity is under both positive and negative selective pressure to balance different traits that are important for microbial survival.
Early detection of physiological deterioration in post-surgical patients using wearable technology combined with an integrated monitoring system: a pre- and post-interventional study
Authors: Watkinson Peter J , Pimentel Marco AF , Clifton Lei , Clifton David A , Vollam Sarah , Young Duncan , Tarassenko Lionel 
Published: December 2020

ABSTRACTObjectivesLate recognition of physiological deterioration is a frequent problem in hospital wards. We assessed whether ambulatory (wearable) physiological monitoring combined with a system that continuously merges physiological variables into a single “risk” score (VSI), changed care and outcome in patients after major surgery.DesignPre- and post-interventional study.SettingA single centre tertiary referral university hospital upper-gastrointestinal service.ParticipantsPatients who underwent major upper-gastrointestinal surgery.InterventionsPhase-I (pre-intervention phase): Patients received continuous wearable monitoring and standard care, but the VSI score was not available for clinical use. Phase-II (post-intervention phase): Patients received continuous wearable monitoring. In addition to standard care the VSI score was displayed for use in clinical practice.Measurements and Main Results200 participants were monitored in phase-I. 207 participants were monitored in phase-II. Participants were monitored (median, interquartile range, IQR) for 30.2% (13.8-49.2) of available time in phase-I and 58.2% (33.1-75.2) of available time in phase-II.Clinical staff recorded observations more frequently in the 36 hours prior to a major adverse event (death, cardiac arrest or unplanned admission to intensive care) for phase-II participants (median, IQR, time between observations of 1.00, 0.50-2.08 hours) than phase-I participants (1.50, 0.75-2.50 hours, p<0.001). There was no difference in observation frequency between the two phases for participants who did not undergo an adverse event (p=0.129). 6/200 participants died before hospital discharge in phase-I, 1/207 participants died in hospital in phase-II. 20 (10.0%) patients in phase-I and 26 (12.6%) patients in phase-II had an unplanned admission to intensive care. Ward length-of-stay was unaltered (8.91, 6.71-14.02 days in phase-I, vs. 8.97, 5.99-13.85 days in phase-II, p=0.327).ConclusionThe combination of the integrated monitoring system with ambulatory monitoring in high-risk post-surgical patients improved recognition and management of deteriorating patients without increasing the observation rate in those patients who did not deteriorate.
Correcting the Reproduction Number for Time-Varying Tests: a Proposal and an Application to COVID-19 in France*
Authors: Baunez Christelle , Degoulet Mickaël , Luchini Stéphane , Pintus Matteo L. , Pintus Patrick A. , Teschl Miriam 
Published: December 2020

AbstractWe provide a novel way to correct the effective reproduction number for the time-varying amount of tests, using the acceleration index (Baunez et al., 2021) as a simple measure of viral spread dynamics. Not correcting results in the reproduction number being a biased estimate of viral acceleration and we provide a formal decomposition of the resulting bias, involving the useful notions of test and infectivity intensities. When applied to French data for the COVID-19 pandemic (May 13, 2020 - October 26, 2022), our decomposition shows that the reproduction number, when considered alone, characteristically underestimates the resurgence of the pandemic, compared to the acceleration index which accounts for the time-varying volume of tests. Because the acceleration index aggregates all relevant information and captures in real time the sizable time variation featured by viral circulation, it is a more parsimonious indicator to track the dynamics of an infectious disease outbreak in real time, compared to the equivalent alternative which would combine the reproduction number with the test and infectivity intensities.JEL Classification NumbersI18; H12