bluuebunny/crossref_metadata_2025_split huggingface dataset:
High coverage COVID-19 mRNA vaccination rapidly controls SARS-CoV-2 transmission in Long-Term Care Facilities
Authors: De Salazar Pablo M , Link Nicholas , Lamarca Karuna , Santillana Mauricio 
Published: April 2021

AbstractResidents of Long-Term Care Facilities (LTCFs) represent a major share of COVID-19 deaths worldwide. Measuring the vaccine effectiveness among the most vulnerable in these settings is essential to monitor and improve mitigation strategies.We evaluated the early effect of the administration of BNT162b2 mRNA vaccines to individuals older than 64 years residing in LTCFs in Catalonia, a region of Spain. We monitored all the SARS-CoV-2 documented infections and deaths among LTCFs residents from February 6th to March 28th, 2021, the subsequent time period after which 70% of them were fully vaccinated. We developed a modeling framework based on the relation between community and LTFCs transmission during the pre-vaccination period (July -December 2020) and compared the true observations with the counterfactual model predictions. As a measure of vaccine effectiveness, we computed the total reduction in SARS-CoV-2 documented infections and deaths among residents of LTCFs over time, as well as the reduction on the detected transmission for all the LTCFs.We estimated that once more than 70% of the LTCFs population were fully vaccinated, 74% (58%-81%, 90% CI) of COVID-19 deaths and 75% (36%-86%, 90% CI) of all expected documented infections among LTCFs residents were prevented. Further, detectable transmission among LTCFs residents was reduced up to 90% (76-93%, 90%CI) relative to that expected given transmission in the community.Our findings provide evidence that high-coverage vaccination is the most effective intervention to prevent SARS-CoV-2 transmission and death among LTCFs residents. Conditional on key factors such as vaccine roll out, escape and coverage --across age groups--, widespread vaccination could be a feasible avenue to control the COVID-19 pandemic.
ddPCR Reveals SARS-CoV-2 Variants in Florida Wastewater
Authors: Gering Eben , Colbert Jacob , Schmedes Sarah , Duncan George , Lopez Joe , Motes Jessy , Weiss James , Azarian Taj , Tekin Omer , Blanton Jason 
Published: April 2021

AbstractWastewater was screened for the presence of functionally significant mutations in SARS-CoV-2 associated with emerging variants of concern (VOC) by ddPCR, and results accorded with sequencing of clinical samples from the same region. We propose that PCR-based screening of wastewater can provide a powerful tool for rapid and inexpensive screening of large population segments for VOC-associated mutations and can hone complementary sampling and sequencing of direct (human) test material to track emerging VOC.
The PUPPY Study – Protocol for a Longitudinal Mixed Methods Study Exploring Problems Coordinating and Accessing Primary Care for Attached and Unattached Patients Exacerbated During the COVID-19 Pandemic Year
Authors: Marshall Emily Gard , Breton Mylaine , Cossette Benoît , Isenor Jennifer E , Mathews Maria , Ayn Caitlyn , Smithman Mélanie Ann , Stock David , Frymire Eliot , Edwards Lynn , Green Michael 
Published: April 2021

AbstractBackgroundThe COVID-19 pandemic significantly disrupted primary care in Canada, with many walk-in clinics and family practices initially closing or being perceived as inaccessible, pharmacies remaining open with restrictions on patient interactions, rapid uptake of virtual care, and reduced referrals for lab tests, diagnostics, and specialist care. The PUPPY Study (Problems Coordinating and Accessing Primary Care for Attached and Unattached Patients Exacerbated During the COVID-19 Pandemic Year) seeks to understand the impact of COVID-19 across the quadruple aim of primary care, with particular focus on the impacts on patients without attachment to a regular provider and those with chronic health conditions.ObjectiveThe PUPPY Study objective is to understand the impact of COVID-19 across the quadruple aim of primary care.MethodsThe PUPPY study builds on an existing research program exploring patients’ access and attachment to primary care, pivoted to adapt to the emerging COVID-19 context. We will undertake a longitudinal mixed methods study to understand critical gaps in primary care access and coordination, comparing data pre- and post-pandemic in three Canadian provinces (Quebec, Ontario, and Nova Scotia). Multiple data sources will be used including: a policy review; qualitative interviews with primary care policymakers, providers (i.e., family physicians, nurse practitioners, and pharmacists), and patients (N=120); and medication prescribing and healthcare billings. The findings will inform the strengthening of primary care during and beyond the COVID-19 pandemic.ResultsFunding was provided by the Canadian Institutes of Health Research COVID-19 Rapid Funding Opportunity Grant. Ethical approval to conduct this study was granted in Ontario (Queens Health Sciences & Affiliated Teaching Hospitals Research Ethics Board, file number 6028052; Western University Health Sciences Research Ethics Board, project 116591; University of Toronto Health Sciences Research Ethics Board, protocol number 40335), Québec (Centre intégré universitaire de santé et de services sociaux de l’Estrie, project number 2020-3446) and Nova Scotia (Nova Scotia Health Research Ethics Board, file number 1024979).ConclusionsThis is the first study of its kind exploring the impacts of COVID-19 on primary care systems, with particular focus on the issues of patient’s attachment and access to primary care. Through a multi-stakeholder, cross-jurisdictional approach, the PUPPY Study will generate findings and implications for future policy and practice.
Risk factors associated with respiratory infectious disease-related presenteeism: a rapid review
Authors: Daniels Sarah , Wei Hua , Han Yang , Catt Heather , Denning David W. , Hall Ian , Regan Martyn , Verma Arpana , Whitfield Carl A. , van Tongeren Martie 
Published: April 2021

ABSTRACTBackgroundWorkplace transmission is a significant contributor to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks. Previous studies have found that infectious illness presenteeism could contribute to outbreaks in occupational settings and identified multiple occupational and organisational risk factors. Amid the COVID-19 pandemic, it is imperative to investigate presenteeism particularly in relation to respiratory infectious disease (RID). Hence, this rapid review aims to determine the prevalence of RID-related presenteeism, including COVID-19, and examines the reported reasons and associated risk factors.MethodsThe review followed a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) search approach and focused on studies published in English and Chinese. Database searches included MEDLINE, EMBASE, Web of Science, China Knowledge Resource Integrated Database (CNKI) and preprint databases MedRxiv and BioRxiv.ResultsThe search yielded 54 studies, of which four investigated COVID-19-related presenteeism. Prevalence of work presenteeism ranged from 14.1% to 55% for confirmed RID, and 6.6% to 100% for those working with suspected or subclinical RID. The included studies demonstrated that RID-related presenteeism is associated with occupation, sick pay policy, age, gender, health behaviour and perception, vaccination, peer pressure and organisational factors such as presenteeism culture.ConclusionsThis review demonstrates that presenteeism or non-adherence to isolation guidance is a real concern and can contribute to workplace transmissions and outbreaks. Policies which would support workers financially and improve productivity, should include a range of effective non-pharmaceutical inventions such as workplace testing, promoting occupational health services, reviewing pay and bonus schemes and clear messaging to encourage workers to stay at home when ill. Future research should focus on the more vulnerable and precarious occupational groups, and their inter-relationships, to develop comprehensive intervention programs to reduce RID-related presenteeism.
Self-regulation of stress-related large-scale brain network balance using real-time fMRI Neurofeedback
Authors: Krause Florian , Kogias Nikos , Krentz Martin , Lührs Michael , Goebel Rainer , Hermans Erno J. 
Published: April 2021

AbstractIt has recently been shown that acute stress affects the allocation of neural resources between large-scale brain networks, and the balance between the executive control network and the salience network in particular. Maladaptation of this dynamic resource reallocation process is thought to play a major role in stress-related psychopathology, suggesting that stress resilience may be determined by the retained ability to adaptively reallocate neural resources between these two networks. Actively training this ability could hence be a potentially promising way to increase resilience in individuals at risk for developing stress-related symptomatology. Using real-time functional Magnetic Resonance Imaging, the current study investigated whether individuals can learn to self-regulate stress-related large-scale network balance. Participants were engaged in a bidirectional and implicit real-time fMRI neurofeedback paradigm in which they were intermittently provided with a visual representation of the difference signal between the average activation of the salience and executive control networks, and tasked with attempting to self-regulate this signal. Our results show that, given feedback about their performance over three training sessions, participants were able to (1) learn strategies to differentially control the balance between SN and ECN activation on demand, as well as (2) successfully transfer this newly learned skill to a situation where they (a) did not receive any feedback anymore, and (b) were exposed to an acute stressor in form of the prospect of a mild electric stimulation. The current study hence constitutes an important first successful demonstration of neurofeedback training based on stress-related large-scale network balance – a novel approach that has the potential to train control over the central response to stressors in real-life and could build the foundation for future clinical interventions that aim at increasing resilience.HighlightsAcute stress affects the allocation of neural resources between large-scale brain networksWe provide a first successful demonstration of neurofeedback training based on stress-related large-scale brain networksNovel approach has the potential to train control over central response to stressors in real-lifeCould build foundation for future clinical interventions to increase resilience
RNA labelling in live plants reveals single cell transcriptional dynamics: application to phosphate signaling
Authors: Hani Sahar , Cuyas Laura , David Pascale , Secco David , Whelan James , Thibaud Marie-Christine , Merret Rémy , Mueller Florian , Pochon Nathalie , Javot Hélène , Faklaris Orestis , Maréchal Eric , Bertrand Edouard , Nussaume Laurent 
Published: April 2021

AbstractPlants are sessile organisms constantly adapting to ambient fluctuations through spatial and temporal transcriptional responses. Here, we implemented the latest generation RNA imaging system and combined it with microfluidics to visualize transcriptional regulation in living Arabidopsis plants. This enabled quantitative measurements of the transcriptional activity of single loci in single cells, real time and changing environmental conditions. Using phosphate responsive genes as model, we found that active genes displayed high transcription initiation rates (∼3s) and frequently clustered together in endoreplicated cells. We observed gene bursting and large allelic differences in single cells, revealing that at steady-state, intrinsic noise dominated extrinsic variations. Moreover, we established that transcriptional repression triggered in roots by phosphate, a crucial macronutrient limiting plant development, occurred with unexpected fast kinetics (∼minutes) and striking heterogeneity between neighboring cells. Access to single cell RNA polymerase II dynamics within live plants will benefit future studies of signaling processes.
Estimating the age of poorly dated fossil specimens and deposits using a total-evidence approach and the fossilized birth-death process
Authors: Barido-Sottani Joëlle , Żyła Dagmara , Heath Tracy A. 
Published: April 2021

AbstractBayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical datasets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical dataset of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical datasets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits.
Recovery of silver fir (Abies albaMill.) seedlings from ungulate browsing mirrors soil nitrogen availability
Authors: Csilléry Katalin , Buchmann Nina , Brendel Oliver , Gessler Arthur , Glauser Alexandra , Kupferschmid Andrea Doris 
Published: April 2021

AbstractAbies albahas a high potential for mitigating climate change in European mountain forests, yet, its natural regeneration is severely limited by ungulate browsing. Here, we simulated browsing in a common garden experiment to study growth and physiological traits, measured from bulk needles, using a randomized block design with two levels of browsing severity and seedlings originating from 19 populations across Switzerland. Genetic factors explained most variation in growth (on average, 51.5%) and physiological traits (10.2%) under control conditions, while heavy browsing considerably reduced the genetic effects on growth (to 30%), but doubled those on physiological traits related to C storage. While browsing reduced seedling height, it also lowered seedlings’ water use efficiency (decreasedδ13C) and N supply by mycorrhizal fungi as indicated by an increase inδ15N. Different populations reacted differently to browsing stress, and for Height, Starch andδ15N, population differences appeared to be the result of natural selection. We found that the fastest growing populations, originating from the warmest regions, decreased their needle starch level the most as a reaction to heavy browsing, suggesting a potential genetic underpinning for a growth-storage trade-off. Further, we found that seedlings originating from mountain populations growing on steep slopes had a significantly lower N discrimination in the common garden than those originating from flat areas, indicating that they have been selected to grow on N poor, potentially drained, soils. This finding was corroborated by the fact that N concentration in adult needles was lower on steep slopes than on flat ground, strongly indicating that steep slopes are the most N poor environments. Seedlings from these poor environments generally had a low growth rate and high storage, thus might be slower to recover from browsing stress than fast growing provenances from the warm environments with developed soils, such as the Swiss plateau.
Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology
Authors: Griffiths Jessica A. , Yoo Bryan B. , Thuy-Boun Peter , Cantu Victor , Weldon Kelly , Challis Collin , Sweredoski Michael J. , Chan Ken Y. , Thron Taren M. , Sharon Gil , Moradian Annie , Humphrey Gregory , Zhu Qiyun , Shaffer Justin , Wolan Dennis W. , Dorrestein Pieter C. , Knight Rob , Gradinaru Viviana , Mazmanian Sarkis K. 
Published: April 2021

SUMMARYThe gastrointestinal (GI) tract is extensively innervated by intrinsic neurons of the enteric nervous system (ENS) and extrinsic neurons of the central nervous system and peripheral ganglia, which together regulate gut physiology. The GI tract also harbors a diverse microbiome, but interactions between the ENS and the microbiome remain poorly understood. Herein, we activate choline acetyltransferase (ChAT)-expressing or tyrosine hydroxylase (TH)-expressing gut-associated neurons in mice to determine effects on intestinal microbial communities and their metabolites, as well as on host physiology. The resulting multi-omics datasets support broad roles for discrete peripheral neuronal subtypes in shaping microbiome structure, including modulating bile acid profiles and fungal colonization. Physiologically, activation of either ChAT+or TH+neurons increases fecal output, while only ChAT+activation results in increased colonic migrating motor complexes and diarrhea-like fluid secretion. These findings suggest that specific subsets of peripherally-activated ENS neurons differentially regulate the gut microbiome and GI physiology in mice, without involvement of signals from the brain.
Dynamic Causal Modeling of Neural Responses to an Orofacial Pneumotactile Velocity Array
Authors: Wang Yingying , Custead Rebecca , Oh Hyuntaek , Barlow Steven M. 
Published: April 2021

AbstractThe effective connectivity of neuronal networks during orofacial pneumotactile stimulation with different velocities is still unknown. The present study aims to characterize the effectivity connectivity elicited by three different saltatory velocities (5, 25, and 65 cm/s) over the lower face using dynamic causal modeling on functional magnetic resonance imaging data of twenty neurotypical adults. Our results revealed the contralateral SI and SII as the most likely sources of the driving inputs within the sensorimotor network for the pneumotactile stimuli, suggesting parallel processing of the orofacial pneumotactile stimuli. The 25 cm/s pneumotactile stimuli modulated forward interhemispheric connection from the contralateral SII to the ipsilateral SII, suggesting a serial interhemispheric connection between the bilateral SII. Moreover, the velocity pneumotactile stimuli influenced the contralateral M1 through both contralateral SI and SII, indicating that passive pneumotactile stimulation may positively impact motor function rehabilitation. Furthermore, the slow velocity 5 cm/s pneumotactile stimuli modulated both forward and backward connections between the right cerebellar lobule VI and the contralateral left SI, SII, and M1, while the medium velocity 25 cm/s pneumotactile stimuli modulated both forward and backward connections between the right cerebellar lobule VI and the contralateral left SI and M1. Our findings suggest that the right cerebellar lobule VI plays a role in the sensorimotor network through feedforward and feedback neuronal pathways.
Peptidylarginine deiminase IV (PADI4) is not essential for cell-autonomous HSC maintenance and normal haematopoiesis
Authors: Young Christine , Russell John R. , Lawson Hannah , Mapperley Christopher , Kranc Kamil R. , Christophorou Maria A. 
Published: April 2021

AbstractPeptidylarginine deiminases (PADIs, or PADs) are emerging as key regulators of human physiology and pathophysiology. The nuclear deiminase PADI4 regulates embryonic stem cell pluripotency, however its role in adult stem cells is unknown. PADI4 is expressed most highly in the bone marrow (BM), where it is found as part of a self-renewal-associated gene signature and shown to modulate the function of critical transcriptional regulators such as Tal1 and c-Myc, suggesting that it regulates haematopoietic development or regeneration. We investigated the functional significance of PADI4 in haematopoietic stem cell (HSC) biology and normal haematopoiesis. We employed two conditional mouse models of tissue-specificPadi4ablation, wherePadi4was completely deleted either after the emergence of HSCs, or acutely in the BM of adult mice. We found that loss of PADI4 does not significantly affect HSC self-renewal or differentiation potential upon injury or serial transplantation, nor does it lead to exhaustion or premature ageing of HSCs. Thus, surprisingly, PADI4 is dispensable for cell-autonomous HSC maintenance, differentiation and haematopoietic regeneration. This work has important implications for the clinical use of PADI4 inhibitors as therapeutic agents in autoimmunity and cancer.Key PointsPADI4 is dispensable for steady-state and post-transplantation haematopoiesisHSCs do not require intrinsic PADI4 activity to respond to haematopoietic injuryPADI4 deficiency does not lead to premature HSC ageing or exhaustion
Cortical tracking of unheard formant modulations derived from silently presented lip movements and its decline with age
Authors: Suess Nina , Hauswald Anne , Reisinger Patrick , Rösch Sebastian , Keitel Anne , Weisz Nathan 
Published: April 2021

AbstractThe integration of visual and auditory cues is crucial for successful processing of speech, especially under adverse conditions. Recent reports have shown that when participants watch muted videos of speakers, the phonological information about the acoustic speech envelope is tracked by the visual cortex. However, the speech signal also carries much richer acoustic details, e.g. about the fundamental frequency and the resonant frequencies, whose visuo-phonological transformation could aid speech processing. Here, we investigated the neural basis of the visuo-phonological transformation processes of these more fine-grained acoustic details and assessed how they change with ageing. We recorded whole-head magnetoencephalography (MEG) data while participants watched silent intelligible and unintelligible videos of a speaker. We found that the visual cortex is able to track the unheard intelligible modulations of resonant frequencies and the pitch linked to lip movements. Importantly, only the processing of intelligible unheard formants decreases significantly with age in the visual and also in the cingulate cortex. This is not the case for the processing of the unheard speech envelope, the fundamental frequency or the purely visual information carried by lip movements. These results show that unheard spectral fine-details (along with the unheard acoustic envelope) are transformed from a mere visual to a phonological representation. Aging affects especially the ability to derive spectral dynamics at formant frequencies. Since listening in noisy environments should capitalize on the ability to track spectral fine-details, our results provide a novel focus on compensatory processes in such challenging situations.