bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemic dreams: dreaming about health during the COVID-19 pandemic
Authors: Šćepanović Sanja , Aiello Luca Maria , Barrett Deirdre , Quercia Daniele
Published: January 2022

The continuity hypothesis of dreams suggests that the content of dreams is continuous with the dreamer's waking experiences. Given the unprecedented nature of the experiences during COVID-19, we studied the continuity hypothesis in the context of the pandemic. We implemented a deep-learning algorithm that can extract mentions of medical conditions from text and applied it to two datasets collected during the pandemic: 2888 dream reports (dreaming life experiences), and 57 milion tweets (waking life experiences) mentioning the pandemic. The health expressions common to both sets were typical COVID-19 symptoms (e.g. cough, fever and anxiety), suggesting that dreams reflected people's real-world experiences. The health expressions that distinguished the two sets reflected differences in thought processes: expressions in waking life reflected a linear and logical thought process and, as such, described realistic symptoms or related disorders (e.g.
nasal pain, SARS, H1N1
); those in dreaming life reflected a thought process closer to the visual and emotional spheres and, as such, described either conditions unrelated to the virus (e.g.
maggots, deformities, snake bites
), or conditions of surreal nature (e.g.
teeth falling out, body crumbling into sand
). Our results confirm that dream reports represent an understudied yet valuable source of people's health experiences in the real world.
The tainted altruism effect: a successful pre-registered replication
Authors: Alcala Valerie , Johnson Kendra , Steele Caroline , Wu Juanshu , Zhang Donglai , Pashler Harold
Published: January 2022

Newman and Cain (Newman, Cain 2014Psychol. Sci.25, 648–655 (doi:10.1177/0956797613504785)) reported that observers view a person's choices as less ethical when that person has acted in response to both altruistic and selfish (commercial) motivations, as compared with purely selfish interests. The altruistic component reduces the observers' approval rather than raising it. This puzzling phenomenon termed the ‘tainted altruism’ effect, has attracted considerable interest but no direct replications in prior research. We report direct replications of Newman and Cain's Experiments 2 and 3, using a larger sample (n= 501) intended to be fairly representative of the US population. The results confirm the original findings in considerable detail.
V-type H
+
-ATPase in the symbiosome membrane is a conserved mechanism for host control of photosynthesis in anthozoan photosymbioses
Authors: Barott Katie L. , Thies Angus B. , Tresguerres Martin
Published: January 2022

In reef-building corals (order Scleractinia) and giant clams (phylum Molluca), V-type H
+
-ATPase (VHA) in host cells is part of a carbon concentrating mechanism (CCM) that regulates photosynthetic rates of their symbiotic algae. Here, we show that VHA plays a similar role in the sea anemone
Anemonia majano
, a member of the order Actinaria and sister group to the Scleractinia, which in contrast to their colonial calcifying coral relatives is a solitary, soft-bodied taxa. Western blotting and immunofluorescence revealed that VHA was abundantly present in the host-derived symbiosome membrane surrounding the photosymbionts. Pharmacological inhibition of VHA activity in individual anemones resulted in an approximately 80% decrease of photosynthetic O
2
production. These results extend the presence of a host-controlled VHA-dependent CCM to non-calcifying cnidarians of the order Actiniaria, suggesting it is widespread among photosymbiosis between aquatic invertebrates and
Symbiodiniaceae
algae.
An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins
Authors: Sornay Charlotte , Vaur Valentine , Wagner Alain , Chaubet Guilhem
Published: January 2022

The bioconjugation of proteins—that is, the creation of a covalent link between a protein and any other molecule—has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties—they are sensitive and polynucleophilic macromolecules—that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues,vizthe precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity—harnessing the reacting chemical functionality—and site-selectivity—controlling the reacting amino acid residue—most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.
Structural engineering from an inverse problems perspective
Authors: Gallet A. , Rigby S. , Tallman T. N. , Kong X. , Hajirasouliha I. , Liew A. , Liu D. , Chen L. , Hauptmann A. , Smyl D.
Published: January 2022

The field of structural engineering is vast, spanning areas from the design of new infrastructure to the assessment of existing infrastructure. From the onset, traditional entry-level university courses teach students to analyse structural responses given data including external forces, geometry, member sizes, restraint, etc.—characterizing a
forward
problem (structural causalities

→

structural response). Shortly thereafter, junior engineers are introduced to structural design where they aim to, for example, select an appropriate structural form for members based on design criteria, which is the
inverse
of what they previously learned. Similar inverse realizations also hold true in structural health monitoring and a number of structural engineering sub-fields (response

→

structural causalities). In this light, we aim to demonstrate that many structural engineering sub-fields may be fundamentally or partially viewed as
inverse problems
and thus benefit via the rich and established methodologies from the inverse problems community. To this end, we conclude that the future of inverse problems in structural engineering is inexorably linked to engineering education and machine learning developments.
On the transport equation for probability density functions of turbulent vorticity fields
Authors: Li Jiawei , Qian Zhongmin , Zhou Mingrui
Published: January 2022

Vorticity random fields of turbulent flows (modelled over the vorticity equation with random initial data for example) are singled out as the main dynamic variables for the description of turbulence, and the evolution equation of the probability density function (PDF) of the vorticity field has been obtained. This PDF evolution equation is a mixed type partial differential equation (PDE) of second order which depends only on the conditional mean (which is a first-order statistics) of the underlying turbulent flow. This is in contrast with Reynolds mean flow equation which relies on a quadratic statistics. The PDF PDE may provide new closure schemes based on the first-order conditional statistics, and some of them will be described in the paper. We should mention that the PDF equation is interesting by its own and is worthy of study as a PDE of second order.
Challenges in computational fluid dynamics applications for bone tissue engineering
Authors: Pires Tiago , Dunlop John W. C. , Fernandes Paulo Rui , Castro André P. G.
Published: January 2022

Bone injuries or defects that require invasive surgical treatment are a serious clinical issue, particularly when it comes to treatment success and effectiveness. Accordingly, bone tissue engineering (BTE) has been researching the use of computational fluid dynamics (CFD) analysis tools to assist in designing optimal scaffolds that better promote bone growth and repair. This paper aims to offer a comprehensive review of recent studies that use CFD analysis in BTE. The mechanical and fluidic properties of a given scaffold are coupled to each other via the scaffold architecture, meaning an optimization of one may negatively affect the other. For example, designs that improve scaffold permeability normally result in a decreased average wall shear stress. Linked with these findings, it appears there are very few studies in this area that state a specific application for their scaffolds and those that do are focused onin vitrobioreactor environments. Finally, this review also demonstrates a scarcity of studies that combine CFD with optimization methods to improve scaffold design. This highlights an important direction of research for the development of the next generation of BTE scaffolds.
Enhanced attraction between drops carrying fluctuating charge distributions
Authors: Ambaum M. H. P. , Auerswald T. , Eaves R. , Harrison R. G.
Published: January 2022

The electrostatic force between conductive spheres is always attractive at small separations, irrespective of their mean charge, when the charge on the spheres is constant. In many situations, the charge may not be fixed, such as for water drops in the natural atmosphere which vary in size and charge. We show that the attractive force between charged conductive spheres increases with increasing charge variance. The importance of this unrecognized electrostatic effect between water drops is evaluated for its potential to enhance rain formation.
Large mesopelagic fish biomass in the Southern Ocean resolved by acoustic properties
Authors: Dornan Tracey , Fielding Sophie , Saunders Ryan A. , Genner Martin J.
Published: January 2022

The oceanic mesopelagic zone, 200–1000 m below sea level, holds abundant small fishes that play central roles in ecosystem function. Global mesopelagic fish biomass estimates are increasingly derived using active acoustics, where echosounder-generated signals are emitted, reflected by pelagic organisms and detected by transducers on vessels. Previous studies have interpreted a ubiquitous decline in acoustic reflectance towards the Antarctic continent as a reduction in mesopelagic fish biomass. Here, we use empirical data to estimate species-specific acoustic target strength for the dominant mesopelagic fish of the Scotia Sea in the Southern Ocean. We use these data, alongside estimates of fish relative abundance from net surveys, to interpret signals received in acoustic surveys and calculate mesopelagic biomass of the broader Southern Ocean. We estimate the Southern Ocean mesopelagic fish biomass to be approximately 274 million tonnes if Antarctic krill contribute to the acoustic signal, or 570 million tonnes if mesopelagic fish alone are responsible. These quantities are approximately 1.8 and 3.8 times greater than previous net-based biomass estimates. We also show a peak in fish biomass towards the seasonal ice-edge, corresponding to the preferred feeding grounds of penguins and seals, which may be at risk under future climate change scenarios. Our study provides new insights into the abundance and distributions of ecologically significant mesopelagic fish stocks across the Southern Ocean ecosystem.
Endocrine disruption from plastic pollution and warming interact to increase the energetic cost of growth in a fish
Authors: Wu Nicholas C. , Rubin Alexander M. , Seebacher Frank
Published: January 2022

Energetic cost of growth determines how much food-derived energy is needed to produce a given amount of new biomass and thereby influences energy transduction between trophic levels. Growth and development are regulated by hormones and are therefore sensitive to changes in temperature and environmental endocrine disruption. Here, we show that the endocrine disruptor bisphenol A (BPA) at an environmentally relevant concentration (10 µgl
−1
) decreased fish (
Danio rerio
) size at 30°C water temperature. Under the same conditions, it significantly increased metabolic rates and the energetic cost of growth across development. By contrast, BPA decreased the cost of growth at cooler temperatures (24°C). BPA-mediated changes in cost of growth were not associated with mitochondrial efficiency (P/O ratios (i.e. adenosine diphosphate (ADP) used/oxygen consumed) and respiratory control ratios) although BPA did increase mitochondrial proton leak. In females, BPA decreased age at maturity at 24°C but increased it at 30°C, and it decreased the gonadosomatic index suggesting reduced investment into reproduction. Our data reveal a potentially serious emerging problem: increasing water temperatures resulting from climate warming together with endocrine disruption from plastic pollution can impact animal growth efficiency, and hence the dynamics and resilience of animal populations and the services these provide.
Evolution of flexible biting in hyperdiverse parasitoid wasps
Authors: van de Kamp Thomas , Mikó István , Staniczek Arnold H. , Eggs Benjamin , Bajerlein Daria , Faragó Tomáš , Hagelstein Lea , Hamann Elias , Spiecker Rebecca , Baumbach Tilo , Janšta Petr , Krogmann Lars
Published: January 2022

One key event in insect evolution was the development of mandibles with two joints, which allowed powerful biting but restricted their movement to a single degree of freedom. These mandibles define the Dicondylia, which constitute over 99% of all extant insect species. It was common doctrine that the dicondylic articulation of chewing mandibles remained unaltered for more than 400 million years. We report highly modified mandibles overcoming the restrictions of a single degree of freedom and hypothesize their major role in insect diversification. These mandibles are defining features of parasitoid chalcid wasps, one of the most species-rich lineages of insects. The shift from powerful chewing to precise cutting likely facilitated adaptations to parasitize hosts hidden in hard substrates, which pose challenges to the emerging wasps. We reveal a crucial step in insect evolution and highlight the importance of comprehensive studies even of putatively well-known systems.
Over a decade of field physiology reveals life-history specific strategies to drought in garter snakes (
Thamnophis elegans
)
Authors: Holden Kaitlyn G. , Gangloff Eric J. , Miller David A. W. , Hedrick Ashley R. , Dinsmore Carli , Basel Alison , Kutz Greta , Bronikowski Anne M.
Published: January 2022

Changing climates and severe weather events can affect population viability. Individuals need to buffer such negative fitness consequences through physiological plasticity. Whether certain life-history strategies are more conducive to surviving changing climates is unknown, but theory predicts that strategies prioritizing maintenance and survival over current reproduction should be better able to withstand such change. We tested this hypothesis in a meta-population of garter snakes having naturally occurring variation in life-history strategies. We tested whether slow pace-of-life (POL) animals, that prioritize survival over reproduction, are more resilient than fast POL animals as measured by several physiological biomarkers. From 2006 to 2019, which included two multi-year droughts, baseline and stress-induced reactivity of plasma corticosterone and glucose varied annually with directionalities consistent with life-history theory. Slow POL animals exhibited higher baseline corticosterone and lower baseline glucose, relative to fast POL animals. These patterns were also observed in stress-induced measures; thus, reactivity was equivalent between ecotypes. However, in drought years, measures of corticosterone did not differ between different life histories. Immune cell distribution showed annual variation independent of drought or life history. These persistent physiological patterns form a backdrop to several extirpations of fast POL populations, suggesting a limited physiological toolkit to surviving periods of extreme drought.
Long-distance dependencies in birdsong syntax
Authors: Searcy William A. , Soha Jill , Peters Susan , Nowicki Stephen
Published: January 2022

Songbird syntax is generally thought to be simple, in particular lacking long-distance dependencies in which one element affects choice of another occurring considerably later in the sequence. Here, we test for long-distance dependencies in the sequences of songs produced by song sparrows (
Melospiza melodia
). Song sparrows sing with eventual variety, repeating each song type in a consecutive series termed a ‘bout'. We show that in switching between song types, song sparrows follow a ‘cycling rule', cycling through their repertoires in close to the minimum possible number of bouts. Song sparrows do not cycle in a set order but rather vary the order of song types from cycle to cycle. Cycling in a variable order strongly implies long-distance dependencies, in which choice of the next type depends on the song types sung over the past cycle, in the range of 9–10 bouts. Song sparrows also follow a ‘bout length rule', whereby the number of repetitions of a song type in a bout is positively associated with the length of the interval until that type recurs. This rule requires even longer distance dependencies that cross one another; such dependencies are characteristic of more complex levels of syntax than previously attributed to non-human animals.
Interindividual variation in the use of social information during learning in honeybees
Authors: Tait Catherine , Naug Dhruba
Published: January 2022

Slow–fast differences in cognition among individuals have been proposed to be an outcome of the speed–accuracy trade-off in decision-making. Based on the different costs associated with acquiring information via individual and social learning, we hypothesized that slow–fast cognitive differences would also be tied to the adoption of these different learning modes. Since foragers in honeybee colonies likely have both these information acquisition modes available to them, we chose to test them for interindividual differences in individual and social learning. By measuring performance on a learning task with and without a social cue and quantifying learning rate and maximum accuracy in these two tasks, our results show the existence of a speed–accuracy trade-off in both the individual and the social learning contexts. However, the trade-off is steeper during individual learning, which was slower than social learning but led to higher accuracy. Most importantly, our results also show that bees that attained high accuracy on the individual learning task had low accuracy on the social learning task andvice versa. We discuss how these two information acquisition strategies tie to slow–fast differences in cognitive phenotypes and how they might contribute to division of labour and social behaviour.
Beaked whales and state-dependent decision-making: how does body condition affect the trade-off between foraging and predator avoidance?
Authors: Siegal Eilidh , Hooker Sascha K. , Isojunno Saana , Miller Patrick J. O.
Published: January 2022

Body condition is central to how animals balance foraging with predator avoidance—a trade-off that fundamentally affects animal fitness. Animals in poor condition may accept greater predation risk to satisfy current foraging ‘needs’, while those in good condition may be more risk averse to protect future ‘assets’. These state-dependent behavioural predictions can help interpret responses to human activities, but are little explored in marine animals. This study investigates the influence of body condition on how beaked whales trade-off foraging and predator avoidance. Body density (indicating lipid-energy stores) was estimated for 15 foraging northern bottlenose whales tagged near Jan Mayen, Norway. Composite indices of foraging (diving and echolocation clicks) and anti-predation (long ascents, non-foraging dives and silent periods reducing predator eavesdropping) were negatively related. Experimental sonar exposures led to decreased foraging and increased risk aversion, confirming a foraging/perceived safety trade-off. However, lower lipid stores were not related to a decrease in predator avoidance versus foraging, i.e. worse condition animals did not prioritize foraging. Individual differences (personalities) or reproductive context could offer alternative explanations for the observed state-behaviour relationships. This study provides evidence of foraging/predator-avoidance trade-offs in a marine top predator and demonstrates that animals in worse condition might not always take more risks.
The McGill Approach to Core Stabilization in the Treatment of Chronic Low Back Pain: A Review
Authors: Laurin Erica , Minerbi Amir , Besemann LCol Markus , Courchesne Captain Isabel , Gupta Gaurav
Published: January 2022

Introduction

Low back pain (LBP) is a major cause of disability and is progressively becoming worse on a global scale. [1,2] The prevention and rehabilitation of LBP lacks clarity in part due to the heterogeneity of the exercise programs prescribed to treat low back pain. Some authors have proposed stabilizing exercises for lower back pain which exert minimal loads on the spine. [3,4,5] Despite a multitude of existing exercise therapies, McGill has introduced three exercises for rehabilitating lower back pain, termed the McGill Big Three (MGB3). [6,7,8,9,10] These include the curl-up, side plank and bird-dog. The purpose of this review is to investigate the clinical outcomes from prescribing the MGB3 to individuals with chronic LBP.

Methods

Inclusion criteria were randomized control trials that involved an intervention with MGB3 core stabilization exercises for patients with chronic low back pain. The research included articles published during any period in full English text. Studies were critically reviewed by two authors EL and GG independently and collaboratively.

Results

In total, four randomized control trials were included in this review. Multiple cohorts, with varying age, demographics and occupation were studied. Outcomes studied included various pain scores, patient reported functional and performance measures.

Discussion

Controlled clinical trials employing this method in low back pain treatment showed low quality data with mixed statistical significance, and little to no clinical significance irrespective of the measure used or even when compared to baseline. Limitations of these trials are detailed herein.

Conclusion

Currently there is limited data supporting the clinical benefit of the McGill approach for the treatment of low back pain based on the available randomized clinical trials. More study is required prior to widespread adoption into clinical practice.
COVID-19 vaccination recruits and matures cross-reactive antibodies to conserved epitopes in endemic coronavirus Spike proteins
Authors: Elko Evan A , Nelson Georgia A , Mead Heather L , Kelley Erin J , Verche Virginia Le , Cardoso Angelo A , Ely Jennifer L , Boyle Annalee S , Piña Alejandra , Henson Sierra N , Rahee Fatima , Keim Paul S , Celona Kimberly R , Yi Jinhee , Settles Erik W , Yu George C , Morris Sheldon R , Zaia John A , Ladner Jason T , Altin John A
Published: January 2022

The COVID-19 pandemic has triggered the first widespread vaccination campaign against a coronavirus. Most vaccinated subjects are naïve to SARS-CoV-2, however almost all have previously encountered other coronaviruses (CoVs) and the role of this immunity in shaping the vaccine response remains uncharacterized. Here we use longitudinal samples and highly-multiplexed serology to identify mRNA-1273 vaccine-induced antibody responses against a range of CoV Spike epitopes and in both phylogenetically conserved and non-conserved regions. Whereas reactivity to SARS-CoV-2 epitopes showed a delayed but progressive increase following vaccination, we observed distinct kinetics for the endemic CoV homologs at two conserved sites in Spike S2: these became detectable sooner, and decayed at later timepoints. Using homolog-specific depletion and alanine-substitution experiments, we show that these distinctly-evolving specificities result from cross-reactive antibodies as they mature against rare, polymorphic residues within these epitopes. Our results reveal mechanisms for the formation of antibodies with broad reactivity against CoVs.
Projection of Healthcare Demand in Germany and Switzerland Urged by Omicron Wave (January-March 2022)
Authors: Gorji Hossein , Stauffer Noé , Lunati Ivan , Caduff Alexa , Bühler Martin , Engel Doortje , Chung Ho Ryun , Loukas Orestis , Feig Sabine , Renz Harald
Published: January 2022

After the implementation of broad vaccination programs, there is an urgent need to understand how the population immunity affects the dynamics of the COVID-19 pandemic in presence of the protection waning and of the emergence of new vari-ants of concern. In the current Omicron wave that is propagating across Europe, assessing the risk of saturation of the healthcare systems is crucial for pandemic management, as it allows us to support the transition towards the endemic course of SARS-CoV-2 and implement more refined mitigation strategies that shield the most vulnerable groups and protect the healthcare systems. We investigated the current pandemic dynamics by means of compartmental models that describe the age-stratified social-mixing, and consider vaccination status, vaccine types, and their waning efficacy. Our goal is to provide insight into the plausible scenarios that are likely to be seen in Switzerland and Germany in the coming weeks and help take informed decisions. Despite the huge numbers of new positive cases, our results suggest that the current wave is unlikely to create an overwhelming health-care demand: owing to the lower hospitalization rate of the novel variant and the effectiveness of the vaccines. Our findings are robust with respect to the plausible variability of the main parameters that govern the severity and the progression of the Omicron infection. In a broader context, our framework can be applied also to future endemic scenarios, offering quantitative support for refined public health interventions in response to recurring COVID-19 waves.
Gasdermin-D activation by SARS-CoV-2 trigger NET and mediate COVID-19 immunopathology
Authors: Silva Camila Meirelles , Wanderley Carlos Wagner S , Veras Flavio Protasio , Gonçalves Augusto Veloso , Lima Mikhael Haruo Fernandes , Toller Kawahisa Juliana E. , Gomes Giovanni Freitas , Nascimento Daniele Carvalho , Silva Monteiro Valter V. , Paiva Isadora Marques , Almeida Cícero José Luíz Ramos , Caetité Diego Brito , Silva Juliana da Costa , Lopes Maria Isabel Fernandes , Bonjorno Letícia Pastorelli , Giannini Marcela Cavichioli , Amaral Natalia Brasil , Benatti Maíra Nilson , Damasceno Luis Eduardo Alves , Silva Bruna Manuella Souza , Schneider Ayda Henriques , Castro Icaro Maia Santos , Silva Juan Carlo Santos , Vasconcelos Amanda Pereira , Gonçalves Tiago Tomazini , Batah Sabrina Setembre , Rodrigues Tamara Silva , Costa Victor Ferreira , Pontelli Marjorie Cornejo , Martins Ronaldo B , Martins Timna Varela , Espósito Danillo Lucas Alves , Cebinelli Guilherme Cesar Martelossi , da Fonseca Benedito Antônio Lopes , Leiria Luiz Osório Silveira , Cunha Larissa Dias , Arruda Eurico , Nakaia Helder I , Fabro Alexandre Todorovic , Oliveira Renê D , Zamboni Dario S , Junior Paulo Louzada , Cunha Thiago Mattar , Alves Filho José Carlos Farias , Cunha Fernando de Queiroz
Published: January 2022

The release of neutrophil extracellular traps (NETs) is associated with inflammation, coagulopathy, and organ damage found in severe cases of COVID-19. However, the molecular mechanisms underlying the release of NETs in COVID-19 remain unclear. Using a single-cell transcriptome analysis we observed that the expression of GSDMD and inflammasome-related genes were increased in neutrophils from COVID-19 patients. Furthermore, high expression of GSDMD was found associated with NETs structures in the lung tissue of COVID-19 patients. The activation of GSDMD in neutrophils requires live SARS-CoV-2 and occurs after neutrophil infection via ACE2 receptors and serine protease TMPRSS2. In a mouse model of SARS-CoV-2 infection, the treatment with GSDMD inhibitor (disulfiram) reduced NETs release and organ damage. These results demonstrated that GSDMD-dependent NETosis plays a critical role in COVID-19 immunopathology, and suggests that GSDMD inhibitors, can be useful to COVID-19 treatment.

In Brief

Here, we showed that the activation of the Gasdermin-D (GSDMD) pathway in neutrophils controls NET release during COVID-19. The inhibition of GSDMD with disulfiram, abrogated NET formation reducing lung inflammation and tissue damage. These findings suggest GSDMD as a target for improving the COVID-19 therapy.
Who Develops Pandemic Fatigue?
Authors: Taylor Steven , Rachor Geoffrey S. , Asmundson Gordon J. G.
Published: January 2022

According to the World Health Organization, pandemic fatigue poses a serious threat for managing COVID-19. The cardinal feature of pandemic fatigue is a progressive decline in adherence to social distancing (SDIS) guidelines, which is associated with pandemic-related emotional burnout. Little is known about the nature of pandemic fatigue; for example, it is unclear who is most likely to develop pandemic fatigue. We sought to evaluate this issue based on data from 5,812 American and Canadian adults recruited during the second year of the COVID-19 pandemic. Past-year decline in adherence to SDIS had a categorical latent structure according to Latent Class Analysis, consisting of an SDIS adherent group (Class 1: 92% of the sample) and a group reporting a progressive decline in adherence to SDIS (i.e., pandemic fatigue; Class 2: 8% of the sample). Class 2, compared to Class 1, was associated with greater pandemic-related burnout, pessimism, and apathy about the COVID-19 pandemic. They also tended to be younger, perceived themselves to be more affluent, tended to have greater levels of narcissism, entitlement, and gregariousness, and were more likely to report having been previously infected with SARSCOV2, which they regarded as an exaggerated threat. People in Class 2 also self-reported higher levels of pandemic-related stress, anxiety, and depression, and described making active efforts at coping with SDIS restrictions that they perceived as unnecessary and stressful. People in Class 1 generally reported that they engaged in SDIS for the benefit of themselves and their community, although 35% of this class also feared they would be publicly shamed if they did not comply with SDIS guidelines. The findings suggest that pandemic fatigue affects a substantial minority of people and even many SDIS-adherent people experience emotionally adverse effects (i.e., fear of being shamed). Implications for the future of SDIS are discussed.
Human NLRP1 is activated by ZAKɑ-driven ribotoxic stress response
Authors: Robinson Kim S. , Toh Gee Ann , Rozario Pritisha , Bayat Shima , Sun Zijin , Bauernfried Stefan , Nadkarni Rhea , Harapas Cassandra R. , Lim Chrissie K. , Chu Werncui , Tan Kiat Yi , Bonnard Carine , Sobota Radoslaw , Connolly John E. , Masters Seth L. , Chen Kaiwen W. , Ho Lena , Hornung Veit , Zhong Franklin L.
Published: January 2022

Human NLRP1 is a multifunctional inflammasome sensor predominantly expressed in skin and airway epithelium; however its function in skin-specific immunity and its mechanisms of activation are not fully understood. Here we report that human NLRP1 is specifically activated by the ZAKɑ- driven ribotoxic stress response pathway (RSR) induced by ultraviolet B (UVB) irradiation or select microbial ribotoxins. Biochemically, RSR-triggered NLRP1 activation requires ZAKɑ- dependent hyperphosphorylation of a human-specific linker region of NLRP1 (NLRP1DR), leading to the ‘functional degradation’ of the auto-inhibitory NLRP1 N-terminal fragment. Additionally, we show that fusing NLRP1DRto the signaling domains of CARD8, which in itself is insensitive to RSR, creates a minimal inflammasome sensor for UVB and ribotoxins. In summary, these discoveries resolve the mechanisms of UVB sensing by human NLRP1, identify ZAKɑ-activating toxins as novel human NLRP1 activators, and establish NLRP1 inflammasome-dependent pyroptosis as an integral component of the ribotoxic stress response in primary human cells.

UVB-induced NLRP1 activation in human keratinocytes involves a nuclear DNA-independent stress response involving photodamaged RNA

ZAKɑ kinase is required for UVB-triggered, but not VbP- or dsRNA-induced human NLRP1 activation

ZAKɑ-activating microbial ribotoxins specifically activate the NLRP1 inflammasome in multiple primary human cell types

Hyperphosphorylation of a linker region (NLRP1DR) is required for RSR-dependent human NLRP1 activation
Transcriptional, post-transcriptional, and post-translational mechanisms rewrite the tubulin code during cardiac hypertrophy and failure
Authors: Phyo Sai Aung , Uchida Keita , Chen Christina Yingxian , Caporizzo Matthew A. , Bedi Kenneth , Griffin Joanna , Margulies Kenneth , Prosser Benjamin L.
Published: January 2022

A proliferated and post-translationally modified microtubule network underlies cellular growth in cardiac hypertrophy and contributes to contractile dysfunction in heart failure. Yet how the heart achieves this modified network is poorly understood. Determining how the “tubulin code” – the permutations of tubulin isoforms and post-translational modifications - is rewritten upon cardiac stress may provide new targets to modulate cardiac remodeling. Further, while tubulin can autoregulate its own expression, it is unknown if autoregulation is operant in the heart or tuned in response to stress. Here we use heart failure patient samples and murine models of cardiac remodeling to interrogate transcriptional, autoregulatory, and post-translational mechanisms that contribute to microtubule network remodeling at different stages of heart disease. We find that autoregulation is operant across tubulin isoforms in the heart and leads to an apparent disconnect in tubulin mRNA and protein levels in heart failure. We also find that within 4 hours of a hypertrophic stimulus and prior to cardiac growth, microtubule detyrosination is rapidly induced to help stabilize the network. This occurs concomitant with rapid transcriptional and autoregulatory activation of specific tubulin isoforms and microtubule motors. Upon continued hypertrophic stimulation, there is an increase in post-translationally modified microtubule tracks and anterograde motors to support cardiac growth, while total tubulin content increases through progressive transcriptional and autoregulatory induction of tubulin isoforms. Our work provides a new model for how the tubulin code is rapidly rewritten to establish a proliferated, stable microtubule network that drives cardiac remodeling, and provides the first evidence of tunable tubulin autoregulation during pathological progression.
The Existence of At Least Three Genomic Signature Patterns and At Least Seven Subtypes of COVID-19 and the End of the Disease
Authors: Zhang Zhengjun
Published: January 2022

Hoping to find genomic clues linked to COVID-19 and end the pandemic has driven scientists’ tremendous efforts to try all kinds of research. Signs of progress have been achieved but are still limited. This paper intends to prove the existence of at least three genomic signature patterns and at least seven subtypes of COVID-19 driven by five critical genes (the smallest subset of genes). These signatures and subtypes provide crucial genomic information in COVID-19 diagnosis (including ICU patients), research focuses, and treatment methods. Unlike existing approaches focused on gene fold-changes and pathways, gene-gene nonlinear and competing interactions are the driving forces in finding the signature patterns and subtypes. Furthermore, the method leads to 100% accuracy, which shows biological and mathematical equivalences between COVID-19 status and the signature patterns and a methodological advantage over other existing methods that cannot lead to 100% accuracy. As a result, as new biomarkers, the new findings can be much more informative than other findings for interpreting biological mechanisms, developing the second (third) generation of vaccines, antiviral drugs, and treatment methods, and eventually bringing new hopes to an end of the pandemic.
Similarity bias from consensus perturbational signatures from the L1000 Connectivity Map
Authors: Smith Ian , Scott Katy , Haibe-Kains Benjamin
Published: January 2022

The Next Generation L1000 Connectivity Map (L1000) is a massive, high-throughput dataset measuring transcriptional changes - or signatures - in cancer cell lines due to chemical and genetic perturbation. Zhu et al recently presented Deep Learning-Based Efficacy Prediction System (DLEPS), a method that models averages of many signatures (CTPs or meta-signatures) of the same compound across conditions. However, our analysis shows that averaging increasing numbers of signatures from L1000 results in a substantial positive increase in signature similarities even among entirely unrelated perturbations, drastically shifting the baseline threshold for similarity. Consequently, DLEPS overstates how informative the model is about each compound, highlighting the need to account for this similarity bias in any L1000 Connectivity Map analysis.
Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern
Authors: Kim Seonghan , Liu Yi , Ziarnik Matthew , Cao Yiwei , Zhang X. Frank , Im Wonpil
Published: January 2022

The 2019 coronavirus disease (COVID-19) pandemic has had devastating impacts on our global health. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has continued to mutate and spread worldwide despite global vaccination efforts. In particular, the Omicron variant, first identified in South Africa in late November 2021, has now overtaken the Delta variant and become the dominant strain worldwide. Compared to the original strain identified in Wuhan, Omicron features 50 genetic mutations, with 15 mutations in the receptor-binding domain (RBD) of the spike protein, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor for viral entry. However, it is not completely understood how these mutations alter the interaction and binding strength between the Omicron RBD and ACE2. In this study, we used a combined steered molecular dynamics (SMD) simulation and experimental microscale thermophoresis (MST) approach to quantify the interaction between Omicron RBD and ACE2. We report that the Omicron brings an enhanced RBD-ACE2 interface through N501Y, Q493K/R, and T478K mutations; the changes further lead to unique interaction patterns, reminiscing the features of previously dominated variants, Alpha (N501Y) and Delta (L452R and T478K). Our MST data confirmed that the Omicron mutations in RBD are associated with a five-fold higher binding affinity to ACE2 compared to the RBD of the original strain. In conclusion, our result could help explain the Omicron variant’s prevalence in human populations, as higher interaction forces or affinity for ACE2 likely promote greater viral binding and internalization, leading to increased infectivity.

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Nonsynonymous mutations in fepR are associated with Listeria adaptation to low concentrations of benzalkonium chloride, but not increased survival in use level concentrations of benzalkonium chloride
Authors: Bolten Samantha , Harrand Anna Sophia , Skeens Jordan , Wiedmann Martin
Published: January 2022

Presence of and selection for Listeria spp. and Listeria monocytogenes that are less effectively inactivated by quaternary ammonium compounds (such as benzalkonium chloride [BC]) is a food safety concern, including in fresh produce environments. An initial MIC assay on 67 produce-associated Listeria strains showed that strains carrying BC resistance genes bcrABC (n=10) and qacH (n=1) showed higher MIC (4-6 mg/L BC) compared to strains lacking these genes (MIC of 1-2 mg/L BC). Serial passaging experiments that exposed the 67 strains to increasing BC concentrations revealed that 62/67 strains showed growth in BC concentrations above their parent MIC (range of 4-20 mg/L). Two serially passaged isolates were obtained for each parent strain and substreaked onto BHI agar in the absence of BC for seven rounds; 105/134 substreaked isolates showed higher substreaked MIC (range of 4 – 6 mg/L) compared to parent MIC. These results suggested isolates acquired genetic adaptations that confer BC resistance. Substreaked isolates were characterized by a combination of whole genome sequencing and Sanger sequencing of fepR, a local repressor of the MATE family efflux pump FepA. These data identified nonsynonymous fepR mutations in 48/67 isolates including 24 missense, 16 nonsense, and 8 frameshift mutations. The mean inactivation of substreaked isolates after exposure to use level concentrations of BC (300 mg/L) was 4.48 log, which was not significantly different from inactivation observed in parent strains. Serial passage experiments performed on cocultures of Listeria strains containing bcrABC or qacH did not yield growth at higher BC concentrations than monoculture experiments.

IMPORTANCE

Listeria resistance to quaternary ammonium compounds has been raised as a concern with regards to Listeria persistence in food environments, which can increase risk of product contamination, food recalls and foodborne illness outbreaks. Findings from our study show that individual Listeria strains can acquire genetic adaptations that confer resistance to low concentrations of benzalkonium chloride, but these genetic adaptations don’t increase Listeria survival when exposed to concentrations of benzalkonium chloride used for food contact surface sanitation (300 mg/L). Our study also suggests that there is limited risk of benzalkonium chloride resistance genes bcrABC and qacH spreading through horizontal gene transfer and conferring enhanced resistance of L. monocytogenes to benzalkonium chloride. Overall, our study suggests that emergence of benzalkonium chloride resistant Listeria strains in food processing environments is of limited concern, as even strains adapted to gain higher MIC in vitro maintain full sensitivity to use level concentrations of benzalkonium chloride.
TNFα-producing CD4+ T cells dominate the SARS-CoV-2-specific T cell response in COVID-19 outpatients and are associated with durable antibodies
Authors: van der Ploeg Kattria , Kirosingh Adam S. , Mori Diego A. M. , Chakraborty Saborni , Hu Zicheng , Seivers Benjamin L. , Jacobson Karen B. , Bonilla Hector , Parsonnet Julie , Andrews Jason R. , Press Kathleen D. , Ty Maureen C. , Ruiz-Betancourt Daniel R. , de la Parte Lauren , Tan Gene S. , Blish Catherine A. , Takahashi Saki , Rodriguez-Barraquer Isabel , Greenhouse Bryan , Singh Upinder , Wang Taia T. , Jagannathan Prasanna
Published: January 2022

SARS-CoV-2-specific CD4+ T cells are likely important in immunity against COVID-19, but our understanding of CD4+ longitudinal dynamics following infection and specific features that correlate with the maintenance of neutralizing antibodies remains limited. We characterized SARS-CoV-2-specific CD4+ T cells in a longitudinal cohort of 109 COVID-19 outpatients. The quality of the SARS-CoV-2-specific CD4+ response shifted from cells producing IFNγ to TNFα+ from five days to four months post-enrollment, with IFNγ-IL21-TNFα+ CD4+ T cells the predominant population detected at later timepoints. Greater percentages of IFNγ-IL21-TNFα+ CD4+ T cells on day 28 correlated with SARS-CoV-2 neutralizing antibodies measured seven months post-infection (ρ=0.4, P=0.01). mRNA vaccination following SARS-CoV-2 infection boosted both IFNγ and TNFα producing, spike protein-specific CD4+ T cells. These data suggest that SARS-CoV-2-specific, TNFα-producing CD4+ T cells may play an important role in antibody maintenance following COVID-19.
Use of magnetic resonance imaging in neuroprognostication after pediatric cardiac arrest: Survey of current practices
Authors: Piantino Juan A. , Ruzas Christopher M. , Press Craig A. , Subramanian Subramanian , Balakrishnan Binod , Panigrahy Ashok , Pettersson David , Maloney John A. , Vossough Arastoo , Topjian Alexis , Kirschen Matthew P , Doughty Lesley , Chung Melissa G. , Maloney David , Haller Tamara , Fabio Anthony , Fink Ericka L. ,   the POCCA Investigators
Published: January 2022

Background

Use of MRI as a tool to aid in neuroprognostication after cardiac arrest (CA) has been described, yet details of specific indications, timing, and sequences are unknown. We aim to define the current practices in use of brain MRI in prognostication after pediatric cardiac arrest.

METHODS

A survey was distributed to pediatric institutions participating in three international studies. Survey questions related to center demographics, clinical practice patterns of MRI after CA, neuroimaging resources, and details regarding MRI decision support.

RESULTS

Response rate was 31% (44/143). Thirty-four percent (15/44) of centers have a clinical pathway informing the use of MRI after CA. Fifty percent (22/44) of respondents reported that an MRI is obtained in nearly all CA patients and 32% (14/44) obtain an MRI in those who did not return to baseline neurological status. Sixty-four percent of centers (28/44) obtain an MRI greater than 72 hours after return of spontaneous circulation. Poor neurologic exam was reported as the most common factor (91% [40/44]) determining the timing of the MRI. Conventional sequences (T1, T2, FLAIR, and diffusion weighted imaging/apparent diffusion coefficient) are widely used. Advanced imaging techniques, such as MR spectroscopy, diffusion tensor imaging and resting state functional MRI are less commonly used.

CONCLUSIONS

Conventional brain MRI is a common practice for prognostication after CA. Advanced imaging techniques, are used infrequently. The lack of standardized clinical pathways and variability in reported practices support a need for higher-quality evidence regarding the indications, timing, and acquisition protocols of clinical MRI studies.
Exploring the application of behaviour change technique taxonomies in childhood obesity prevention interventions: A systematic scoping review
Authors: Chakraborty Debapriya , Bailey Bronwyn A , Seidler Anna Lene , Yoong Serene , Hunter Kylie E , Hodder Rebecca K , Webster Angela C , Johnson Brittany J
Published: January 2022

Behaviour change technique (BCT) taxonomies provide one approach to unpack the complexity of childhood obesity prevention interventions. This scoping review sought to examine how BCT taxonomies have been applied to understand childhood obesity prevention interventions targeting children aged 12 years or under and/or their caregivers. A systematic search was conducted in Medline, Embase, PsycINFO, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, CINAHL and PROSPERO. Eligible studies included any study design that applied a BCT taxonomy and evaluated behavioural childhood obesity prevention interventions targeting children aged 12 years or under and/or their parents or caregivers. Sixty-three records, describing 54 discrete studies were included; 32 applied a BCT taxonomy prospectively (i.e., to design interventions) and 23 retrospectively (i.e., to assess interventions), 1 study did both. There was substantial variation in the methods used to apply BCT taxonomies and to report BCT-related methods and results. There was a paucity of detail reported in how BCTs were selected in studies applying BCT taxonomies prospectively. Our review provides important insight into the application of BCT taxonomies in childhood obesity prevention and several ongoing challenges, pointing to the need for best practice reporting guidance.