bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk and mitigation of aerosolisation from lung function testing: results from the AERATOR study
Authors: Sheikh S , Hamilton F , Nava GW , Gregson F , Arnold D , Riley C , Brown J ,   AERATOR group, Bzdek B , Reid J , Maskell N , Dodd JW
Published: March 2021

Introduction

Lung function tests are fundamental diagnostic and monitoring tools for patients with respiratory symptoms. There is significant uncertainty around whether potentially infectious aerosol is produced during different lung function testing modalities; and limited data on possible mitigation strategies to reduce risk to staff and limit fallow time.

Methods

Healthy volunteers were recruited in an ultraclean, laminar flow theatre and had standardised spirometry as per ERS/ATS guidance, as well as peak flow measurement and FENO assessment of airway inflammation. Aerosol emission was sampled minimum once each second using both an Aerodynamic Particle Sizer (APS) and Optical Particle Sizer (OPS), and compared to breathing, speaking and coughing. Mitigation strategies such as a peak flow viral filter and a CPET facemask (to mitigate induced coughing) were tested.

Results

33 healthy volunteers were recruited. Aerosol emission was highest in cough (1.61 particles/cm3/sample), followed by unfiltered peak flow (0.76 particles/cm3/sample). Filtered spirometry produced lower peak aerosol emission (0.11 particles/ cm3/sample) than that of a voluntary cough, and addition of a viral filter to the mouthpiece reduced peak flow aerosol emission to similar levels. The filter made little difference to recorded FEV peak flow values. Peak aerosol FENO measurement produced negligible aerosol. Reusable CPET masks with filter reduced aerosol emission when breathing, speaking, and coughing significantly.

Conclusions

Compared to voluntary coughing, all lung function testing produced fewer aerosol particles. Filtered spirometry produces lower peak aerosol emission than peak voluntary coughing, and should not be deemed an aerosol generating procedure. The use of viral filters reduces aerosol emission in peak flow by > 10 times, and has little impact on recorded peak flow values. CPET masks are a useful option to reduce aerosol emission from induced coughing while performing spirometry.
Value-based pricing of a COVID-19 vaccine
Authors: Gandjour Afschin
Published: March 2021

Aim

The purpose of this study is to determine the value-based price of a COVID-19 vaccine from a societal perspective in Germany.

Methods

A decision model was constructed using, e.g., information on age-specific fatality rates, intensive care unit (ICU) costs and outcomes, and herd protection threshold. Three strategies were analysed: vaccination (with 95% and 50% efficacy), a mitigation strategy, and no intervention. The base-case time horizon was 5 years. The value of a vaccine included savings from avoiding COVID-19 mitigation measures and health benefits from avoiding COVID-19 related mortality. The value of an additional life year was borrowed from new, innovative oncological drugs, as cancer reflects a condition with a similar morbidity and mortality burden in the general population in the short term as COVID-19.

Results

A vaccine with a 95% efficacy dominates the mitigation strategy strictly. The value-based price (€1494) is thus determined by the comparison between vaccination and no intervention. This price is particularly sensitive to the probability of ICU admission and the herd protection threshold. In contrast, the value of a vaccine with 50% efficacy is more ambiguous.

Conclusion

This study yields a value-based price for a COVID-19 vaccine with 95% efficacy, which is more than 50 times greater than the purchasing price.
An AI-assisted Online Tool for Cognitive Impairment Detection Using Images from the Clock Drawing Test
Authors: Amini Samad , Zhang Lifu , Hao Boran , Gupta Aman , Song Mengting , Karjadi Cody , Lin Honghuang , Kolachalama Vijaya B. , Au Rhoda , Paschalidis Ioannis Ch.
Published: March 2021

Background

Widespread early dementia detection could drastically increase clinical trial candidates and enable early interventions. Since the Clock Drawing Test (CDT) can be potentially used for diagnosing dementia related diseases, it can be leveraged to devise a computer-aided screening tool.

Objective

This work aims to develop an online screening tool by leveraging Artificial Intelligence and the CDT.

Methods

Images of an analog clock drawn by 3, 263 cognitively intact and 160 impaired subjects were used. First, we processed the images from the CDT by a deep learning algorithm to obtain dementia scores. Then, individuals were classified as belonging to either category by combining CDT image scores with the participant’s age.

Results

We have evaluated the performance of the developed models by applying 5-fold cross validation on 20% of the dataset. The deep learning model generates dementia scores for the CDT images with an Area Under the ROC Curve (AUC) of 81.3% ± 4.3%. A composite logistic regression model using age and the generated dementia scores, yielded an average AUC and average weighted F1 score of 92% ± 0.8% and 94.4% ± 0.7%, respectively.

Discussion

CDT images were subjected to distortion consistent with an image drawn on paper and photographed by a cell phone. The model offers a cost-effective and easily deployable mechanism for detecting cognitive impairment online, without the need to visit a clinic.
A 1 to 1000 SARS-CoV-2 reinfection proportion in members of a large healthcare provider in Israel: a preliminary report
Authors: Perez Galit , Banon Tamar , Gazit Sivan , Moshe Shay Ben , Wortsman Joshua , Grupel Daniel , Peretz Asaf , Tov Amir Ben , Chodick Gabriel , Mizrahi-Reuveni Miri , Patalon Tal
Published: March 2021

With more than 100 million confirmed COVID-19 cases as of March 2021, reinfection is still considered to be rare. In light of increasing reports of reinfected COVID-19 patients, the need to better understand the real risk for reinfection is critical, with potential effects on public health policies aimed at containing the spread of SARS-CoV-2. In this descriptive preliminary report, we conducted a large-scale assessment on the country level of the possible occurrence of COVID-19 reinfection within the members of a large healthcare provider in Israel. Out of 149,735 individuals with a documented positive PCR test between March 2020 and January 2021, 154 had two positive PCR tests at least 100 days apart, reflecting a reinfection proportion of 1 per 1000. Given our strict inclusion criteria, we believe these numbers represent true reinfection incidence in MHS and should be clinically regarded as such.
Low Dose Regimens of BNT162b2 mRNA Vaccine Exceed SARS-Cov-2 Correlate of Protection Estimates for Symptomatic Infection, in those 19-55 Years of Age
Authors: Jurgens Graham
Published: March 2021

Background

An exact correlate of protection (CoP) is not yet known for symptomatic COVID-19. However, it is still possible to show a new vaccine regimen exceeds an unknown CoP, provided the regimen shows an equivalent or greater immunological response in all measured indicators relative to the immunological response elicited by a clinically proven vaccine regimen. The principle of comparing immunogenicity between regimens is what the FDA, EMA, and Access Consortium use to authorize modifications to the vaccines for VOC, without requiring clinical efficacy studies before implementation. It is logical to apply the same principle to modifying vaccine doses if the data is available to do so. A two dose 30ug regimen of BNT162b2 has strong clinical evidence of efficacy, as does a single dose 30 ug regimen. The immunological markers for these regimens have been profiled in detail in Phase 1 and 2 trial data.

Methods

The immunological profile (including binding antibodies, viral neutralization, cytokine profiles, and CD4 and 8 expansion) of the 2 dose 30ug BNT162b2 vaccine is examined, referred to as a highly conservative CoP estimate. The single dose 30 ug BNT162b2 immunological profile is also examined, a tenable CoP estimate. Data from the phase 1 and 2 trials are examined to see if alternate regimens meet or exceed the level of each immune marker measured, relative to the regimens listed above that have proven clinical efficacy.

Results

For adults aged 19-55, a 2 dose 10ug BNT162b2 regimen elicits a comparable response to the standard 30 ug dose for each immune indicator, with viral neutralization nearly an order of magnitude greater than the tenable CoP estimate. Similarly, a single dose 10ug BNT 162b2 regimen or a two dose 1ug BNT 162b2 regimen equals or exceeds the immunogenicity of a single 30 ug dose.

Conclusion

If it is reasonable for the FDA, EMA, and Access Consortium to approve vaccine modifications without a clinical trial based on immunogenicity data, three alternate low dose regimens were identified that meet the requirements of having comparable immunogenicity relative to a protocol that has proven clinical efficacy. Immediate implementation of these lower dose regimens should be considered as they have major implications in alleviating vaccine supply, as well as improving vaccine side effect profile, and lowering total cost of vaccination.
A Kiosk Station for the Assessment of Multiple Cognitive Domains and Enrichment of Monkeys
Authors: Womelsdorf Thilo , Thomas Christopher , Neumann Adam , Watson Marcus , Boroujeni Kianoush Banaie , Hassani Seyed A. , Parker Jeremy M. , Hoffman Kari L.
Published: March 2021

Background

Nonhuman primates (NHPs) are self-motivated to perform cognitive tasks on touchscreens in their animal housing setting. To leverage this ability, fully integrated hardware and software solutions are needed, that work within housing and husbandry routines while also spanning cognitive task constructs of the Research Domain Criteria (RDoC).

New Method

We describe a Kiosk Station (KS-1) that provides robust hardware and software solutions for running cognitive tasks in cage-housed NHPs. KS-1 consists of a frame for mounting flexibly on housing cages, a touchscreen animal interface with mounts for receptables, reward pumps and cameras, and a compact computer cabinet with an interface for controlling behavior. Behavioral control is achieved with a unity3D program that is virtual-reality capable, allowing semi-naturalistic visual tasks to assess multiple cognitive domains.

Results

KS-1 is fully integrated into the regular housing routines of monkeys. A single person can operate multiple KS-1s. Monkeys engage with KS-1 at high motivation and cognitive performance levels at high intra-individual consistency.

Comparison with Existing Methods

KS-1 is optimized for flexible mounting onto standard apartment cage systems. KS-1 has a robust animal interface with options for gaze/reach monitoring. It has an integrated user interface for controlling multiple cognitive task using a common naturalistic object space designed to enhance task engagement. All custom KS-1 components are open-sourced.

Conclusions

KS-1 is a versatile tool for cognitive profiling and enrichment of cage-housed monkeys. It reliably measures multiple cognitive domains which promises to advance our understanding of animal cognition, inter-individual differences and underlying neurobiology in refined, ethologically meaningful behavioral foraging contexts.
Computationally reconstructed interactome ofBradyrhizobium diazoefficiensUSDA110 reveals novel functional modules and protein hubs for symbiotic nitrogen fixation
Authors: Ma Jun-Xiao , Yang Yi , Li Guang , Ma Bin-Guang
Published: March 2021

Symbiotic nitrogen fixation is an important part of the nitrogen biogeochemical cycles and the main nitrogen source of the biosphere. As a classical model system for symbiotic nitrogen fixation, rhizobium-legume systems have been studied elaborately for decades. Detailed panorama about the molecular mechanism of the communication and coordination between rhizobia and host plants is becoming clearer. For more systematic insights, there is an increasing demand on new studies integrating multi-omics information. Here we present a comprehensive computational framework, integrating the reconstructed protein interactome ofB. diazoefficiensUSDA110 with its transcriptome and proteome data, to study the complex protein-protein interaction (PPI) network involved in the symbiosis system. We reconstructed the interactome ofB. diazoefficiensUSDA110 by computational approaches. Based on the comparison of interactomes betweenB. diazoefficiensUSDA110 and other rhizobia, we inferred that the slow growth ofB. diazoefficiensUSDA110 may owe to the requirement of more protein modifications and further identified 36 conserved functional PPI modules. Integrated with transcriptome and proteome data, interactomes representing free-living cell and symbiotic nitrogen-fixing (SNF) bacteroid were obtained. Based on the SNF interactome, a core-sub-PPI-network for symbiotic nitrogen fixation was determined and 9 novel functional modules and 11 key protein hubs playing key roles for symbiosis were identified. The reconstructed interactome ofB. diazoefficiensUSDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.
Minimal interplay between explicit knowledge, dynamics of learning and temporal expectations in different, complex uni- and multisensory contexts
Authors: Ball Felix , Spuerck Inga , Noesselt Toemme
Published: March 2021

While temporal expectations (TE) generally improve reactions to temporally predictable events, it remains unknown how temporal rule learning and explicit knowledge about temporal rules contribute to performance improvements and whether any contributions generalise across modalities. Here, participants discriminated the frequency of diverging auditory, visual or audiovisual targets embedded in auditory, visual or audiovisual distractor sequences. Temporal regularities were manipulated run-wise (early vs. late target within sequence). Behavioural performance (accuracy, RT) plus measures from a computational learning model all suggest that temporal rule learning occurred but did not generalise across modalities, that dynamics of learning (size of TE effect across runs) and explicit knowledge have little to no effect on the strength of TE, and that explicit knowledge affects performance – if at all – in a context dependent manner: only under complex task regimes (unknown target modality) might it partially help to resolve response conflict while it is lowering performance in less complex environments..
Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion
Authors: Jensen Matthew , Tyryshkina Anastasia , Pizzo Lucilla , Smolen Corrine , Das Maitreya , Huber Emily , Krishnan Arjun , Girirajan Santhosh
Published: March 2021

Background

Recent studies have suggested that individual variants do not sufficiently explain the variable expressivity of phenotypes observed in complex disorders. For example, the 16p12.1 deletion is associated with developmental delay and neuropsychiatric features in affected individuals, but is inherited in >90% of cases from a mildly-affected parent. While children with the deletion are more likely to carry additional “second-hit” variants than their parents, the mechanisms for how these variants contribute to phenotypic variability are unknown.

Methods

We performed detailed clinical assessments, whole-genome sequencing, and RNA sequencing of lymphoblastoid cell lines for 32 individuals in five large families with multiple members carrying the 16p12.1 deletion. We identified contributions of the 16p12.1 deletion and “second-hit” variants towards a range of expression changes in deletion carriers and their family members, including differential expression, outlier expression, alternative splicing, allele-specific expression, and expression-quantitative trait loci analyses.

Results

We found that the deletion dysregulates multiple autism and brain development genes such asFOXP1,ANK3, andMEF2. Carrier children also showed an average of 5,323 gene expression changes compared with one or both parents, which matched with 33/39 observed developmental phenotypes. We identified significant enrichments for 13/25 classes of “second-hit” variants in genes with expression changes, where 4/25 variant classes were only enriched when inherited from the non-carrier parent, including loss-of-function SNVs and large duplications. In 11 instances, including forZEB2andSYNJ1, gene expression was synergistically altered by both the deletion and inherited “second-hits” in carrier children. Finally, brain-specific interaction network analysis showed strong connectivity between genes carrying “second-hits” and genes with transcriptome alterations in deletion carriers.

Conclusions

Our results suggest a potential mechanism for how “second-hit” variants modulate expressivity of complex disorders such as the 16p12.1 deletion through transcriptomic perturbation of gene networks important for early development. Our work further shows that family-based assessments of transcriptome data are highly relevant towards understanding the genetic mechanisms associated with complex disorders.
Spontaneously Hypertensive Rat substrains show differences in premorbid addiction vulnerability traits and cocaine self-administration: Implications for a novel rat reduced complexity cross
Authors: Kantak Kathleen M. , Stots Carissa , Mathieson Elon , Bryant Camron D.
Published: March 2021

Forward genetic mapping of F2 crosses between closely related substrains of inbred rodents - referred to as a reduced complexity cross (RCC) - is a relatively new strategy for accelerating the pace of gene discovery for complex traits, such as drug addiction. RCCs to date were generated in mice, but rats are thought to be optimal for addiction genetic studies. Based on past literature, one inbred Spontaneously Hypertensive Rat substrain, SHR/NCrl, is predicted to exhibit a distinct behavioral profile as it relates to cocaine vulnerability traits relative to another substrain, SHR/NHsd. Direct substrain comparisons are a necessary first step before implementing an RCC. We evaluated a number of premorbid addiction vulnerability traits and cocaine self-administration behaviors using a longitudinal within-subjects design. Trait impulsivity and compulsivity were greater in SHR/NCrl than SHR/NHsd, as were reactivity to sucrose reward, sensitivity to acute psychostimulant effects of cocaine, and cocaine abuse liability studied under fixed-ratio and chained schedules of cocaine self-administration. Trait compulsivity correlated with the acute psychostimulant effects of cocaine, which in turn correlated with cocaine taking under the chained schedule. Trait compulsivity also was the best predictor of cocaine seeking responses. Heritability estimates indicated that 22%-40% of the variances for the above phenotypes can be explained by additive genetic factors, providing sufficient genetic variance to conduct genetic mapping in F2 crosses of SHR/NCrl and SHR/NHsd. These results provide compelling support for using an RCC approach in SHR substrains to uncover candidate genes and variants that are of relevance to cocaine use disorders.

Highlights

Closely related SHR substrains have distinct cocaine vulnerability traits

Inhibitory control was poorer in SHR/NCrl than SHR/NHsd

SHR/NCrl were more sucrose reactive and sensitive to acute cocaine than SHR/NHsd

Cocaine abuse liability was greater in SHR/NCrl than SHR/NHsd

SHR substrains can be used in an RCC to uncover cocaine vulnerability genes & variants
Experimental susceptibility of North American raccoons (Procyon lotor) and striped skunks (Mephitis mephitis) to SARS-CoV-2
Authors: Francisco Raquel , Hernandez Sonia M. , Mead Daniel G. , Adcock Kayla G. , Burke Sydney C. , Nemeth Nicole M. , Yabsley Michael J.
Published: March 2021

Skunks and raccoons were intranasally inoculated or indirectly exposed to SARS-CoV-2. Both species are susceptible to infection; however, the lack of, and low quantity of infectious virus shed by raccoons and skunks, respectively, and lack of cage mate transmission in both species, suggest that neither species are competent SARS-CoV-2 reservoirs.

Article Summary Line

Experimental SARS-CoV-2 inoculation of North American raccoons and striped skunks showed susceptibility to infection, but transient, low-level shedding suggests that neither species is likely to be a competent natural reservoir.
COVID-19 vaccine response in pregnant and lactating women: a cohort study
Authors: Gray Kathryn J. , Bordt Evan A. , Atyeo Caroline , Deriso Elizabeth , Akinwunmi Babatunde , Young Nicola , Baez Aranxta Medina , Shook Lydia L. , Cvrk Dana , James Kaitlyn , De Guzman Rose M. , Brigida Sara , Diouf Khady , Goldfarb Ilona , Bebell Lisa M. , Yonker Lael M. , Fasano Alessio , Rabi Sayed A. , Elovitz Michal A. , Alter Galit , Edlow Andrea G.
Published: March 2021

Background

Pregnant and lactating women were excluded from initial COVID-19 vaccine trials; thus, data to guide vaccine decision-making are lacking. We sought to evaluate the immunogenicity and reactogenicity of COVID-19 mRNA vaccination in pregnant and lactating women.

Methods

131 reproductive-age vaccine recipients (84 pregnant, 31 lactating, and 16 non-pregnant) were enrolled in a prospective cohort study at two academic medical centers. Titers of SARS-CoV-2 Spike and RBD IgG, IgA and IgM were quantified in participant sera (N=131), umbilical cord sera (N=10), and breastmilk (N=31) at baseline, 2nd vaccine dose, 2-6 weeks post 2nd vaccine, and delivery by Luminex, and confirmed by ELISA. Titers were compared to pregnant women 4-12 weeks from native infection (N=37). Post-vaccination symptoms were assessed. Kruskal-Wallis tests and a mixed effects model, with correction for multiple comparisons, were used to assess differences between groups.

Results

Vaccine-induced immune responses were equivalent in pregnant and lactating vs non-pregnant women. All titers were higher than those induced by SARS-CoV-2 infection during pregnancy. Vaccine-generated antibodies were present in all umbilical cord blood and breastmilk samples. SARS-CoV-2 specific IgG, but not IgA, increased in maternal blood and breastmilk with vaccine boost. No differences were noted in reactogenicity across the groups.

Conclusions

COVID-19 mRNA vaccines generated robust humoral immunity in pregnant and lactating women, with immunogenicity and reactogenicity similar to that observed in non-pregnant women. Vaccine-induced immune responses were significantly greater than the response to natural infection. Immune transfer to neonates occurred via placental and breastmilk.
Adaptive evolution ofMoniliophthoraPR-1 proteins towards its pathogenic lifestyle
Authors: Vasconcelos Adrielle A. , José Juliana , Filho Paulo M. Tokimatu , Camargo Antonio P. , Teixeira Paulo J. P. L. , Thomazella Daniela P. T. , do Prado Paula F. V. , Fiorin Gabriel L. , Costa Juliana L. , Figueira Antonio , Carazzolle Marcelo F. , Pereira Gonçalo A. G. , Baroni Renata M.
Published: March 2021

Moniliophthora perniciosaandMoniliophthora roreriare hemibiotrophic fungi that harbor a large number of Pathogenesis-Related 1 genes, many of which are induced in the biotrophic interaction withTheobroma cacao.Here, we provide evidence that the evolution of PR-1 inMoniliophthorawas adaptive and potentially related to the emergence of the parasitic lifestyle in this genus. Phylogenetic analysis revealed conserved PR-1 genes, shared by many Agaricales saprotrophic species, that have diversified in new PR-1 genes putatively related to pathogenicity inMoniliophthora, as well as in recent specialization cases within both species. PR-1 families inMoniliophthorawith higher evolutionary rates exhibit induced expression in the biotrophic interaction and positive selection clues, supporting the hypothesis that these proteins accumulated adaptive changes in response to host-pathogen arm race. Furthermore, we show that the highly diversifiedMpPR-1genes are not induced by two phytoalexins, suggesting detoxification might not be their main function as proposed before.
Lung organoids and microplastic fibers: a new exposure model for emerging contaminants
Authors: Winkler Anna , Santo Nadia , Madaschi Laura , Cherubini Alessandro , Rusconi Francesco , Rosso Lorenzo , Tremolada Paolo , Lazzari Lorenza , Bacchetta Renato
Published: March 2021

Background

Three-dimensional (3D) structured organoids are the most advancedin vitromodels for studying human health effects, but they have been applied only once to evaluate the biological effects associated with microplastic exposure. Fibers from synthetic clothes and fabrics are a major source of airborne microplastics, and their release from dryer machines is still poorly understood.

Objectives

In this study, we aimed to establish anin vitroorganoid model of human lung epithelial cells to evaluate its suitability for studying the effects of airborne microplastic contamination on humans. Furthermore, we aimed to characterize the microplastic fibers (MPFs) released in the exhaust filter of a household dryer and to test their interactions and inflammatory effects on the established lung organoids.

Methods

The polyester fibers emitted from the drying of synthetic fabrics were collected. Morphological characterization of the fibers released into the air filter was performed by optical microscopy and scanning electron microscopy (SEM)/energy dispersive x-ray spectroscopy (EDS). The organoids were exposed to various MPF concentrations (1, 10, and 50 mg L−1) and analyzed by optical microscopy, SEM, and confocal microscopy. Gene expression analysis of lung-specific genes, inflammatory cytokines, and oxidative stress-related genes was achieved by quantitative reverse transcription–polymerase chain reaction (qRT-PCR).

Results

We successfully cultured organoids with lung-specific genes. The presence of MPFs did not inhibit organoid growth, but polarized cell growth was observed along the fibers. Moreover, the MPFs did not cause inflammation or oxidative stress. Interestingly, the MPFs were coated with a cellular layer, resulting in the inclusion of fibers in the organoid.

Discussion

This work could have potential long-term implications regarding lung epithelial cells undergoing repair. This preliminary exposure study using human lung organoids could form the basis for further research regarding the toxicological assessment of emerging contaminants such as micro- or nanoplastics.
Genetic inactivation of SARM1 axon degeneration pathway improves outcome trajectory after experimental traumatic brain injury based on pathological, radiological, and functional measures
Authors: Bradshaw Donald V. , Knutsen Andrew K. , Korotcov Alexandru , Sullivan Genevieve M. , Radomski Kryslaine L. , Dardzinski Bernard J. , Zi Xiaomei , McDaniel Dennis P. , Armstrong Regina C.
Published: March 2021

Traumatic brain injury (TBI) causes chronic symptoms and increased risk of neurodegeneration. Axons in white matter tracts, such as the corpus callosum (CC), are critical components of neural circuits and particularly vulnerable to TBI. Treatments are needed to protect axons from traumatic injury and mitigate post-traumatic neurodegeneration. TheSarm1gene is a central driver of axon degeneration through a conserved molecular pathway.Sarm1-/- mice with knockout (KO) of theSarm1gene enable genetic proof-of-concept testing ofSarm1inactivation as a therapeutic target. We evaluatedSarm1deletion effects after TBI using a concussive model that causes traumatic axonal injury and progresses to CC atrophy at 10 weeks, indicating post-traumatic neurodegeneration.Sarm1wild-type (WT) mice developed significant CC atrophy that was reduced inSarm1KO mice. Using electron microscopy to quantify individual axons demonstrated thatSarm1KO preserved more intact axons and reduced damaged or demyelinated axons. MRI in live mice identified significantly reduced CC volume after TBI inSarm1WT mice that was attenuated inSarm1KO mice. MR diffusion tensor imaging detected reduced fractional anisotropy in both genotypes while axial diffusivity remained higher inSarm1KO mice. Immunohistochemistry revealed significant attenuation of CC atrophy, myelin loss, and neuroinflammation inSarm1KO mice after TBI. Functionally, TBI resulted in late-stage motor learning and sleep deficits that were ameliorated inSarm1KO mice. Based on these findings,Sarm1inactivation can protect axons and white matter tracts to improve translational outcomes associated with CC atrophy and post-traumatic neurodegeneration.
Single cell analysis of the aging female hypothalamus
Authors: Hajdarovic Kaitlyn H. , Yu Doudou , Hassell Lexi-Amber , Evans Shane , Packer Sarah , Neretti Nicola , Webb Ashley E.
Published: March 2021

Alterations in metabolism, sleep patterns, body composition, and hormone status are all key features of aging. The hypothalamus is a well-conserved brain region that controls these homeostatic and survival-related behaviors. Despite the importance of this brain region in healthy aging, little is known about the intrinsic features of hypothalamic aging. Here, we utilize single nuclei RNA-sequencing to assess the transcriptomes of 40,064 hypothalamic nuclei from young and aged female mice. We identify cell type-specific signatures of aging in neurons, astrocytes, and microglia, as well as among the diverse collection of neuronal subtypes in this region. We uncover key changes in cell types critical for metabolic regulation and body composition, as well as in an area of the hypothalamus linked to cognition. In addition, our analysis reveals an unexpected female-specific feature of hypothalamic aging. Specifically, we discover that the master regulator of X-inactivation,Xist, is elevated with age, particularly in hypothalamic neurons. Moreover, using machine learning, we show that levels of X-chromosome genes, andXistitself, are the best predictors of cellular age. Together, this study identifies critical cell-specific changes of the aging hypothalamus in mammals, and uncovers a novel marker of neuronal aging in females.
Discrete dynamic model of the mammalian sperm acrosome reaction: the influence of acrosomal pH and biochemical heterogeneity
Authors: Aldana Andrés , Carneiro Jorge , Martínez-Mekler Gustavo , Darszon Alberto
Published: March 2021

The acrosome reaction (AR) is an exocytotic process essential for mammalian fertilization. It involves diverse biochemical and physiological changes that culminate in the release of the acrosomal content to the extracellular medium as well as a reorganization of the plasma membrane (PM) that allows sperm to interact and fuse with the egg. In spite of many efforts, there are still important pending questions regarding the molecular mechanism regulating the AR. Particularly, the contribution of acrosomal alkalinization to AR triggering in physiological conditions is not well understood. Also, the dependence of the proportion of sperm capable of undergoing AR on the biochemical heterogeneity within a sperm population has not been studied. Here we present a discrete mathematical model for the human sperm AR, based on the biophysical and biochemical interactions among some of the main components of this complex exocytotic process. We show that this model can qualitatively reproduce diverse experimental results, and that it can be used to analyze how acrosomal pH (pHa) and cell heterogeneity regulate AR. Our results confirm that pHaincrease can on its own trigger AR in a subpopulation of sperm, and furthermore, it indicates that this is a necessary step to trigger acrosomal exocytosis through progesterone, a known physiological inducer of AR. Most importantly, we show that the proportion of sperm undergoing AR is directly related to the detailed structure of the population biochemical heterogeneity.
Nanoscale organization of Actin Filaments in the Red Blood Cell Membrane Skeleton
Authors: Nowak Roberta B. , Alimohamadi Haleh , Pestonjamasp Kersi , Rangamani Padmini , Fowler Velia M.
Published: March 2021

Red blood cell (RBC) shape and deformability are supported by a planar network of short actin filament (F-actin) nodes interconnected by long spectrin molecules at the inner surface of the plasma membrane. Spectrin-F-actin network structure underlies quantitative modelling of forces controlling RBC shape, membrane curvature and deformation, yet the nanoscale organization of F-actin nodes in the networkin situis not understood. Here, we examined F-actin distribution in RBCs using fluorescent-phalloidin labeling of F-actin imaged by multiple microscopy modalities. Total internal reflection fluorescence (TIRF) and Zeiss Airyscan confocal microscopy demonstrate that F-actin is concentrated in multiple brightly stained F-actin foci ∼200-300 nm apart interspersed with dimmer F-actin staining regions. Live cell imaging reveals dynamic lateral movements, appearance and disappearance of F-actin foci. Single molecule STORM imaging and computational cluster analysis of experimental and synthetic data sets indicate that individual filaments are non-randomly distributed, with the majority as multiple filaments, and the remainder sparsely distributed as single filaments. These data indicate that F-actin nodes are non-uniformly distributed in the spectrin-F-actin network and necessitate reconsideration of current models of forces accounting for RBC shape and membrane deformability, predicated upon uniform distribution of F-actin nodes and associated proteins across the micron-scale RBC membrane.
Post discharge persistent symptoms after COVID-19 in rheumatic and musculoskeletal diseases
Authors: Leon Leticia , Perez-Sancristobal Ines , Garcia Alfredo Madrid , Pedraza Leticia Lopez , Colomer Jose Ignacio , Lara Sergio Lerma , Bermejo Pia Lois , Mucientes Arkaitz , Rodriguez-Rodriguez Luis , Fernandez-Gutierrez Benjamin , Abasolo Lydia
Published: March 2021

OBJECTIVES

To describe persistent symptoms and consequences in Rheumatic and Musculoskeletal diseases (RMD) discharged from the hospital after Covid-19; to assess the roll of autoimmune rheumatic diseases (ARD) compared to and non-autoimmune rheumatic and musculoskeletal diseases (NARD) on persistent symptoms and consequences.

METHODS

We performed a cross-sectional observational study. RMD attended at a rheumatology outpatient clinic in Madrid with Covid-19 that required hospital admission were included. The main outcomes were persistence of symptoms and health consequences related to Covid19 after discharge. Independent variable was RMD group (ARD and NARD) and covariates were sociodemographic, clinical, and treatments. We ran a multivariable logistic regression model to assess the risk by RMD group on main outcomes.

RESULTS

We included 105 patients and 51.5% had ARD. 68.57% reported at least one persistent symptom. The most frequent were dyspnea, fatigue, and chest pain. 31 patients had consequences. Lung damage was found in 11.4% of the patients, 18% had blood test abnormalities (10% lymphopenia), two died, one developed central retinal vein occlusion and one patient developed optic neuritis. 11 patients required readmission due to Covid-19 problems (16.7% ARD vs 3.9% NARD; p=0.053). No statistically significant differences by RMD groups were found in the final models.

CONCLUSION

Many RMD patients have persistent symptoms, similar to other populations. This study also highlights that lung damage is the most frequent consequence. ARD compared to NARD does not seem to differ in terms of persistent symptoms or consequences, although ARD might have a greater number of readmissions due to Covid-19.
Ameliorating Emotional Attention through Modulation of Neural Oscillations with Transcranial Alternating Current Stimulation
Authors: Liu Shuang , He Yuchen , Guo Dongyue , Liu Xiaoya , Hao Xinyu , Hu Pengchong , Ming Dong
Published: March 2021

Background

Numerous clinical reports suggest that psychopathy like schizophrenia, anxiety and depressive disorder is accompanied by early attentional abnormalities in emotional information processing. In the past decade, the efficacy of transcranial alternating current stimulation (tACS) in changing emotional functioning has been repeatedly observed and has demonstrated a causal relationship between endogenous oscillations and emotional processing. However, tACS effects on emotional attention have not yet been tested.

Methods

A total of 53 healthy participants were randomized to 2 groups, and they were subjected to active or sham tACS at individual alpha frequency (IAF) in the bilaterally dorsolateral prefrontal cortex (dlPFC). Participants and received this treatment for 20 min durations daily for 7 consecutive days. On days 1 and 7, electroencephalogram (EEG) recording of 8 minute resting with eyes open and closed. Responses to a facial emotion identification task were also recorded to measure alpha changes and event-related potential (ERP) alterations.

Results

On day 7 after tACS, the active group showed a more clear elevation in alpha power at rest, especially in open state around stimulation area, compared to the sham group. ERPs revealed a significant larger P200 amplitude after active stimulation (p< 0.05), indicating attentional improvement in facial emotion processing. Additionally, a notable positive correlation (p< 0.05) between alpha power and P200 amplitude was found, providing an electrophysiological interpretation regarding the role of tACS in emotional attention modulation. In addition, the IAF-tACS showed an obvious advantage in alpha entrainment compared to an additional 10 Hz-tACS.

Conclusions

These results support a seminal outcome for the effect of IAF-tACS on emotional attention modulation, demonstrating a feasible and individual-specific therapy for neuropsychiatric disorders related to emotion processing, especially regarding oscillatory disturbances.
Systematic exploration ofEscherichia coliphage-host interactions with the BASEL phage collection
Authors: Maffei Enea , Shaidullina Aisylu , Burkolter Marco , Druelle Valentin , Willi Luc , Estermann Fabienne , Michaelis Sarah , Hilbi Hubert , Thaler David S. , Harms Alexander
Published: March 2021

Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 66 newly isolated phages infecting the model organismEscherichia colithat we share with the community as the BASEL collection (BActeriophage SElection for your Laboratory). This collection is largely representative of naturalE. coliphage diversity and was intensively characterized phenotypically and genomically alongside ten well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to eleven defense systems across different layers of bacterial immunity, and matched these results to the phages’ host range across a panel of pathogenic enterobacterial strains. Our results reveal clear patterns in the distribution of phage phenotypes and genomic features that highlight systematic differences in the potency of different immunity systems and point towards the molecular basis of receptor specificity in several phage groups. Strong trade-offs were detected between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.
Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization
Authors: Wang Yuhan , Eddison Mark , Fleishman Greg , Weigert Martin , Xu Shengjin , Henry Fredrick E. , Wang Tim , Lemire Andrew L. , Schmidt Uwe , Yang Hui , Rokicki Konrad , Goina Cristian , Svoboda Karel , Myers Eugene W. , Saalfeld Stephan , Korff Wyatt , Sternson Scott M. , Tillberg Paul W.
Published: March 2021

Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developedExpansion-Assisted IterativeFluorescenceInSituHybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 µm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine novel spatially and molecularly defined subregions. EASI-FISH also facilitates iterative re-analysis of scRNA-Seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.

Highlights

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EASI-FISH enables robust gene expression profiling in thick brain slices

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A turnkey analysis pipeline for facile analysis of large EASI-FISH image datasets

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EASI-FISH reveals novel subregions of the lateral hypothalamus

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Identification of rare cell types based on morphological and spatial heterogeneity
Spatial patterns in functional brain connectomes reflect acute and chronic cannabis use
Authors: Ramaekers JG , Mason NL , Toennes SW , Theunissen EL , Amico E
Published: March 2021

Resting state fMRI has been employed to identify alterations in functional connectivity within or between brain regions following acute and chronic exposure to Δ9-tetrahydrocannabinol (THC), the psychoactive component in cannabis. Most studies focused a priori on a limited number of local brain areas or circuits, without considering the impact of cannabis on wholebrain network organization. The present study attempted to identify changes in the wholebrain human functional connectome as assessed with ultra-high field (7T) resting state scans of occasional (N=12) and chronic cannabis users (N=14) during placebo and following vaporization of cannabis. Two distinct data-driven methodologies, i.e. network-based statistics (NBS) and connICA, were used to identify changes in functional connectomes associated with acute cannabis intoxication and chronic cannabis use. Both methodologies revealed a broad state of hyperconnectivity within the entire range of major brain networks in chronic cannabis users compared to occasional cannabis users, which might be reflective of an adaptive network reorganization following prolonged cannabis exposure. The connICA methodology also extracted a distinct spatial connectivity pattern of hypoconnectivity involving the dorsal attention, limbic, subcortical and cerebellum networks and of hyperconnectivity between the default mode and ventral attention network, that was associated with the feeling of subjective high during THC intoxication across both user groups. Whole-brain network approaches identified spatial patterns in functional brain connectomes that distinguished acute from chronic cannabis use, and offer an important utility for probing the interplay between short and long-term alterations in functional brain dynamics when progressing from occasional to chronic use of cannabis.
Cyclodextrins increase membrane tension and are universal activators of mechanosensitive channels
Authors: Cox Charles D , Zhang Yixiao , Zhou Zijing , Walz Thomas , Martinac Boris
Published: March 2021

The bacterial mechanosensitive channel of small conductance, MscS, has been extensively studied to understand how mechanical forces are converted into the conformational changes that underlie mechanosensitive (MS) channel gating. We showed that lipid removal by β-cyclodextrin can mimic membrane tension. Here, we show that all cyclodextrins (CDs) can activate reconstitutedE. coliMscS, that MscS activation by CDs depends on CD-mediated lipid removal, and that the CD amount required to gate MscS scales with the channel’s sensitivity to membrane tension. CD-mediated lipid removal ultimately causes MscS desensitization, which we show is affected by the lipid environment. CDs can also activate the structurally unrelated MscL. While many MS channels respond to membrane forces, generalized by the ‘force-from-lipids’ principle, their different molecular architectures suggest that they use unique ways to convert mechanical forces into conformational changes. CDs emerge as a universal tool for the structural and functional characterization of unrelated MS channels.
An unusually long 5’UTR of ATP dependent cold shock DEAD-box RNA helicase genecsdAnegatively regulates its own expression inEscherichia coli
Authors: Jana Soma , Datta Partha P.
Published: March 2021

Cold-shockDEAD-box proteinA(CsdA) is an ATP dependant cold shock DEAD-box RNA helicase. It is a major cold shock protein needed for the cold adaptation inEscherichia coli. Although the CsdA has been studied at the protein level, further studies are necessary to understand its mechanisms of gene regulations. In this regard, we have constructed a promoter less vector with the ORF of a GFP reporter and found that the promoter of thecsdAgene resides far upstream (more than 800 bases) of its coding region. Furthermore, ourin vivodeletion experiment has confirmed the existence of this extraordinarily long 5’UTR. Our results show that it represses its own expression. In addition, the short peptide encoding (26 aa)yrbNgene resides within this 5’UTR as an operon with 8 overlapping nucleotides with thecsdAcoding region. Besides, we observed that thecsdAgene expression may also occur along with immediate upstream (180 nucleotides)nlpIgene both at 37°C and 15°C and from thepnpgene (1173 nucleotides upstream) only during cold. In conclusion,csdAgene has operon feature like prokaryotes, in contrast, it also contains an extraordinarily long 5’UTR, found in eukaryotes.