bluuebunny/crossref_metadata_2025 huggingface dataset:
A Systematic Review: The Dimensions utilized in the Performance Evaluation of Healthcare- An Implication during the COVID-19 Pandemic
Authors: Amer Faten , Hammoud Sahar , Khatatbeh Haitham , Lohner Szimonetta , Boncz Imre , Endrei Dóra
Published: June 2021

Background

The balanced scorecard (BSC) has been implemented to evaluate the performance of health care organizations (HCOs). BSC proved to be effective in improving financial performance and patient satisfaction.

Aim

This systematic review aims to identify key performance indicators (KPIs) and dimensions that are vital and most frequently used by health care managers in BSC implementations. Additionally, it attempts to analyze the resulting dimensions during the COVID-19 era.

Methods

This systematic review adheres to PRISMA guidelines. The PubMed, Embase, Cochrane, and Google Scholar databases and Google search engine were inspected to find all implementations of BSC at HCO. The risk of bias was assessed using the nonrandomized intervention studies (ROBINS-I) tool to evaluate the quality of observational and quasi- experimental studies and the Cochrane (RoB 2) tool for randomized controlled trials (RCTs).

Results

There were 33 eligible studies, of which we identified 36 BSC implementations. The categorization and regrouping of the 797 KPIs resulted in 46 subdimensions. The reassembly of these subdimensions resulted in 13 major dimensions: financial, efficiency and effectiveness, availability and quality of supplies and services, managerial tasks, health care workers (HCW) scientific development error-free and safety, time, HCW-centeredness, patient-centeredness, technology, and information systems, community care and reputation, HCO building, and communication. On the other hand, this review detected that BSC design modification to include external and managerial perspectives was necessary for many BSC implementations.

Conclusion

This review solves the KPI categorization dilemma. It also guides researchers and health care managers in choosing dimensions for future BSC implementations and performance evaluations in general. Consequently, dimension uniformity will improve the data sharing and comparability among studies. Additionally, despite the pandemic negatively influencing many dimensions, the researchers observed a lack of comprehensive HCO performance evaluations. In the same vein, although some resulting dimensions were assessed separately during the pandemic, other dimensions still lack investigation. Lastly, BSC dimensions may play an essential role in tackling the COVID-19 pandemic. However, further research is required to investigate the BSC implementation effect in mitigating the pandemic consequences on HCO.
Discharge prediction of critical patients with spinal cord injury: a machine learning study with 1485 cases
Authors: Fan Guoxin , Liu Huaqing , Yang Sheng , Luo Libo , Wang Lunji , Pang Mao , Liu Bin , Zhang Liangming , Han Lanqing , Rong Limin
Published: June 2021

Objectives

Prognostication of spinal cord injury (SCI) is vital, especially for critical patients who need intensive care. The study aims to develop machine-learning (ML) classifiers for discharge prediction of SCI patients in the intensive care unit (ICU).

Methods

Clinical data of patients diagnosed with SCI were extracted from the publicly available ICU database. A total of 105 ML classifiers were initially developed to predict the discharge destination (dead, further medical care, home), and then the top 3 classifiers with the best performance were stacked into an ensemble classifier (Esb-Clf). To balance the accuracy and the feasibility, the complete Esb-Clf was finally simplified with top 10 features (simplified Esb-Clf). The micro-average area under the curve (AUC) was used to compare the prediction performance of difference ML classifiers and 6 doctors’ artificial prediction.

Results

A total of 1485 SCI patients were used for the early and the recent prediction of discharge destination. In the early prediction, the micro-average AUC of the Esb-Clf and the simplified Esb-Clf was 0.846 and 0.835 during the independent testing, respectively. While in the recent prediction, the micro-average AUC of the Esb-Clf and the simplified Esb-Clf was 0.898 and 0.892. Performance of both the Esb-Clf and the simplified Esb-Clf were superior to the doctors’ in the early and the recent prediction.

Conclusions

ML classifiers can discriminate the discharge destination of SCI patients with high accuracy, feasibility and interpretability. Whether the simplified Esb-Clf as an online predictive tool is applicable to guiding clinical management needs further verification.
The COVID-19 Yorkshire Rehabilitation Scale (C19-YRS): application and psychometric analysis in a post-COVID-19 syndrome cohort
Authors: Preston Nick , Parkin Amy , Makower Sophie , Ross Denise H , Gee Jeremy , Halpin Stephen J , Horton Mike C , O’Connor Rory J , Sivan Manoj
Published: June 2021

Background

As our understanding of the nature and prevalence of Post-COVID-19 syndrome (PCS) is increasing, a measure of the impact of COVID-19 could provide valuable insights into patients’ perceptions in clinical trials and epidemiological studies, as well as routine clinical practice.

Objective

To evaluate the clinical usefulness and psychometric properties of the COVID-19 Yorkshire Rehabilitation Scale (C19-YRS) in patients with PCS.

Design

A prospective, observational study of 187 consecutive patients attending a post-COVID-19 rehabilitation clinic. The C19-YRS was used to record patients’ symptoms, functioning and disability. A global health question was used to measure the overall impact of PCS on health. Classical psychometric methods (data quality, scaling assumptions, targeting, reliability and validity) were used to assess the C19-YRS.

Results

For the overall scale, missing data were low, scaling and targeting assumptions were satisfied, and internal consistency was high (Cronbach’s alpha = 0.891). Relationships between perception of health and patients’ reports of symptoms, functioning and disability demonstrated good concordance.

Conclusions

This is the first study to examine the psychometric properties of an outcome measure in patients with PCS. In this sample of patients, the C19-YRS was clinically useful and satisfied standard psychometric criteria, providing preliminary evidence of its suitability as a measure of PCS.
Diverse soil RNA viral communities have the potential to influence grassland ecosystems across multiple trophic levels
Authors: Hillary Luke S. , Adriaenssens Evelien M. , Jones David L. , McDonald James E.
Published: June 2021

Grassland ecosystems form 30-40%1 of total land cover and provide essential ecosystem services, including food production, flood mitigation and carbon storage2. Their productivity is closely related to soil microbial communities3, yet the role of viruses within these critical ecosystems is currently undercharacterised4 and in particular, our knowledge of soil RNA viruses is significantly limited5. Here, we applied viromics6 to characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3,462 viral operational taxonomic units (vOTUs) and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited showed minimal similarity in viral community composition, but with >10-fold more vOTUs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses of viral sequences predicted broad host ranges including bacteria, plants, fungi, vertebrates and invertebrates, contrasting with soil DNA viromes which are typically dominated by bacteriophages7. RNA viral communities therefore likely have the ability to influence soil ecosystems across multiple trophic levels. Our study represents an important step towards the characterisation of terrestrial RNA viral communities and the intricate interactions with their hosts, which will provide a more holistic view of the biology of economically and ecologically important terrestrial ecosystems.
Brain histone beta-hydroxy-butyrylation couples metabolism with gene expression
Authors: Cornuti Sara , Chen Siwei , Lupori Leonardo , Finamore Francesco , Samad Muntaha , Raimondi Francesco , Mazziotti Raffaele , Magnan Christophe , Rocchiccioli Silvia , Baldi Pierre , Tognini Paola
Published: June 2021

Little is known about the impact of metabolic stimuli on brain tissue at a molecular level. The ketone body beta-hydroxybutyrate (BHB) can be a signaling molecule regulating gene transcription. Thus, we assessed lysine beta-hydroxybutyrylation (K-bhb) levels in proteins extracted from the cerebral cortex of mice undergoing a ketogenic metabolic challenge (48 hrs fasting). We found that fasting enhanced K-bhb in a variety of proteins including histone H3. ChIP-seq experiments showed that K9 beta-hydroxybutyrylation of H3 (H3K9-bhb) was significantly enriched by fasting on more than 8000 DNA loci. Transcriptomic analysis showed that H3K9-bhb on enhancers and promoters correlated with active gene expression. One of the most enriched functional annotations both at the epigenetic and transcriptional level was “circadian rhythms’’. Indeed, we found that the diurnal oscillation of specific transcripts was modulated by fasting at distinct zeitgebers both in the cortex and suprachiasmatic nucleus. Moreover, specific changes in locomotor activity daily features were observed during re-feeding after 48-hour fasting.

Thus, our results suggest that fasting dramatically impinges on the cerebral cortex transcriptional and epigenetic landscape, and BHB acts as a powerful epigenetic molecule in the brain through direct and specific histone marks remodeling in neural tissue cells.
Brain signaling dynamics after vagus nerve stimulation
Authors: Teckentrup Vanessa , Krylova Marina , Jamalabadi Hamidreza , Neubert Sandra , Neuser Monja P. , Hartig Renée , Fallgatter Andreas J. , Walter Martin , Kroemer Nils B.
Published: June 2021

The vagus nerve projects to a well-defined neural circuit via the nucleus tractus solitarii (NTS) and its stimulation elicits a wide range of metabolic, neuromodulatory, and behavioral effects. Transcutaneous vagus nerve stimulation (tVNS) has been established as a promising technique to non-invasively alter brain function. However, the precise dynamics elicited by tVNS in humans are still largely unknown. Here, we performed fMRI with concurrent right-sided tVNS (vs. sham) following a randomized cross-over design (N=40). First, to unravel the temporal profile of tVNS-induced changes in the NTS, we compared fMRI time series to canonical profiles for stimulation ON and OFF cycles. Model comparisons indicated that NTS time series were best fit by block-wise shifts in signal amplitude with stimulation ON and OFF estimates being highly correlated. Therefore, we compared stimulation (ON + OFF) versus baseline phases and found that tVNS increased fMRI BOLD activation in the NTS, but this effect was dependent on sufficient temporal signal-to-noise ratio (tSNR) in the mask. Second, to identify the spatiotemporal evolution of tVNS-induced changes in the brain, we examined lagged co-activation patterns and phase coherence. In contrast to our hypothesis, tVNS did not alter dynamic functional connectivity after correction for multiple comparisons. Third, to establish a positive control for future research, we measured changes in gastric myoelectrical frequency via an electrogastrogram. Again, in contrast to our hypothesis, tVNS induced no changes in gastric frequency. Collectively, our study provides evidence that tVNS can perturb brain signaling in the NTS, but these effects are dependent on tSNR and require precise localization. In light of an absence of acute tVNS-induced effects on dynamic functional connectivity and gastric motility, we discuss which steps are necessary to advance future research on afferent and efferent effects of tVNS.
Human engineered heart tissue transplantation in a guinea pig chronic injury model
Authors: von Bibra Constantin , Shibamiya Aya , Geertz Birgit , Querdel Eva , Köhne Maria , Stuedemann Tim , Starbatty Jutta , Hansen Arne , Hiebl Bernhard , Eschenhagen Thomas , Weinberger Florian
Published: June 2021

Abstract

Myocardial injury leads to an irreversible loss of cardiomyocytes (CM). The implantation of human engineered heart tissue (EHT) has become a promising regenerative approach. Previous studies exhibited beneficial, dose-dependent effects of human induced pluripotent stem cell (hiPSC)–derived EHT patch transplantation in a guinea pig model in the subacute phase of myocardial injury. Yet, advanced heart failure often results from a chronic remodeling process. Therefore, from a clinical standpoint it is worthwhile to explore the ability to repair the chronically injured heart. In this study human EHT patches were generated from hiPSC–derived CMs (15×106 cells) and implanted epicardially four weeks after injury in a guinea-pig cryo-injury model. Cardiac function was evaluated by echocardiography after a follow-up period of four weeks. Hearts revealed large transmural myocardial injuries amounting to 27% of the left ventricle. EHT recipient hearts demonstrated compact muscle islands of human origin in the scar region, as indicated by a positive staining for human Ku80 and dystrophin, remuscularizing 5% of the scar area. Echocardiographic analysis demonstrated no significant difference between animals that received EHT patches and animals in the control group (fractional area change 36% vs. 34%). Thus, EHT patches engrafted in the chronically injured heart but in contrast to the subacute model, grafts were smaller and EHT patch transplantation did not improve left ventricular function, highlighting the difficulties for a regenerative approach.
Delayed effects of climate on vital rates lead to demographic divergence in Amazonian forest fragments
Authors: Scott Eric R. , Uriarte María , Bruna Emilio M.
Published: June 2021

Deforestation often results in landscapes where remaining forest habitat is highly fragmented, with remnants of different sizes embedded in an often highly contrasting matrix. Local extinction of species from individual fragments is common, but the demographic mechanisms underlying these extinctions are poorly understood. It is often hypothesized that altered environmental conditions in fragments drive declines in reproduction, recruitment, or survivorship. The Amazon basin, in addition to experiencing continuing fragmentation, is experiencing climate change related increases in the frequency and intensity of droughts and unusually wet periods. Whether plant populations in tropical forest fragments are particularly susceptible to extremes in precipitation remains unclear. Most studies of plants in fragments are relatively short (1–6 years), focus on a single life-history stage, and often do not compare to populations in continuous forest. Even fewer studies consider delayed effects of climate on demographic vital rates despite the importance of delayed effects in studies that consider them. Using a decade of demographic and climate data from an experimentally fragmented landscape in the Central Amazon, we assess the effects of climate on populations of an understory herb (Heliconia acuminata, Heliconiaceae). We used distributed lag non-linear models to understand the delayed effects of climate (measured as standardized precipitation evapotranspiration index, SPEI) on survival, growth, and flowering. We detected delayed effects of climate up to 36 months. Extremes in SPEI in the previous year reduced survival, drought in the wet season 8–11 months prior to the February census increased growth, and drought two dry seasons prior increased flowering probability. Effects of extremes in precipitation on survival and growth were more pronounced in forest fragments compared to continuous forest. The complex delayed effects of climate and habitat fragmentation in our study point to the importance of long-term demography experiments in understanding the effects of anthropogenic change on plant populations.
Laminin-binding Integrins Regulate Angiogenesis by Distinct and Overlapping Mechanisms in Organotypic Cell Culture Models
Authors: Xu Hao , LaFlamme Susan E.
Published: June 2021

Endothelial cells engage extracellular matrix and basement membrane components through integrin-mediated adhesion to promote angiogenesis. Our previous studies demonstrated that endothelial expression of laminin-411 and laminin-511 as well as α6 integrins is required for endothelial sprouting and tube formation in organotypic angiogenesis assays. These studies demonstrated that α6 integrins promote migration and regulate the expression of ANGPT2 and CXCR4 and that α6-dependent regulation of CXCR4 contributes to endothelial morphogenesis in our assays. However, these studies did not identify specific roles for the α6β1, α6β4, or α3β1 laminin-binding integrins. Here, we employ RNAi technology to parse the contributions of these integrins. We demonstrate that α6β4 promotes migration, sprouting, and tube formation, and also positively regulates the expression of ANGPT2, but does not promote CXCR4 expression, suggesting that α6β1 functions in this regulation. Additionally, we show that α3β1 regulates endothelial sprouting and tube formation, but is not required for migration in our assays or for the expression of ANGPT2 or CXCR4. Integrin α3β1 promotes the expression of NRP1 and ID1 RNAs, both of which are known to promote angiogenesis. Taken together, our results indicate that laminin-binding integrins play distinct roles during endothelial morphogenesis and do not compensate for one another in organotypic culture.

Summary Statement

The laminin-binding integrins α3β1, α6β1, and α6β4 contribute to endothelial sprouting and tube formation in organotypic angiogenesis assays.
Actin force generation in vesicle formation: mechanistic insights from cryo-electron tomography
Authors: Serwas Daniel , Akamatsu Matthew , Moayed Amir , Vegesna Karthik , Vasan Ritvik , Hill Jennifer M , Schöneberg Johannes , Davies Karen M , Rangamani Padmini , Drubin David G
Published: June 2021

Actin assembly provides force for a multitude of cellular processes. Compared to actin assembly- based force production during cell migration, relatively little is understood about how actin assembly generates pulling forces for vesicle formation. Here, cryo-electron tomography revealed actin filament number, organization, and orientation during clathrin-mediated endocytosis in human cells, showing that force generation is robust despite variance in network organization. Actin dynamics simulations incorporating a measured branch angle indicate that sufficient force to drive membrane internalization is generated through polymerization, and that assembly is triggered from ∼4 founding “mother” filaments, consistent with tomography data. Hip1R actin filament anchoring points are present along the entire endocytic invagination, where simulations show that it is key to pulling force generation, and along the neck, where it targets filament growth and makes internalization more robust. Actin cytoskeleton organization described here allowed direct translation of structure to mechanism with broad implications for other actin-driven processes.

Highlights

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Filament anchorage points are key to pulling force generation and efficiency.

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Native state description of CME-associated actin force-producing networks.

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Branched actin filament assembly is triggered from multiple mother filaments.

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Actin force production is robust despite considerable network variability.
Capsid-E2 interactions rescue core assembly in viruses that cannot form cytoplasmic nucleocapsid cores
Authors: Button Julie M. , Mukhopadhyay Suchetana
Published: June 2021

Alphavirus capsid proteins (CPs) have two domains: the N-terminal domain (NTD) that interacts with the viral RNA, and the C-terminal domain (CTD) that forms CP-CP inter-actions and interacts with the cytoplasmic domain of the E2 spike protein (cdE2). In this study, we examine how mutations in the CP NTD affect CP CTD interactions with cdE2. We changed the length and/or charge of the NTD of Ross River virus CP and found that changing the charge of the NTD has a greater impact on core and virion assembly than changing the length of the NTD. The NTD CP insertion mutants are unable to form cyto-plasmic cores during infection but they do form cores or core-like structures in virions. Our results are consistent with cdE2 having a role in core maturation during virion assembly and rescuing core formation when cytoplasmic cores are not assembled. We go on to find that the isolated cores from some mutant virions are now assembly competent in that they can be disassembled and reassembled back into cores. These results show how the two domains of CP may have distinct yet coordinated roles.

IMPORTANCE

Structural viral proteins have multiple roles during entry and assembly. The capsid protein (CP) of alphaviruses has one domain that interacts with the viral genome and another domain that interacts with the E2 spike protein. In this work we determine that the length and/or charge of the CP affects cytoplasmic core formation. However, defects in cytoplasmic core formation can be overcome by E2-CP interactions, thus assembling a core or core-like complex in the virion. In the absence of both cytoplasmic cores and CP-E2 interactions, CP is not even packaged in the released virions, but some infectious particles are still released presumably as RNA packaged in a glycoprotein containing membrane shell. This suggests that the virus has multiple mechanisms in place to ensure the viral genome is surrounded by a capsid core during its lifecycle.
Survival mechanism of a novel marine multistress-tolerant Meyerozyma guilliermondii GXDK6 under high NaCl stress as revealed by integrative omics analysis
Authors: Cai Xinghua , Sun Huijie , Bai Huashan , Chen Yanyi , Kashif Muhammad , Bu Ru , Mo Xueyan , Su Guijiao , Ou Qian , Yan Bing , Jiang Chengjian
Published: June 2021

A novel strain named Meyerozyma guilliermondii GXDK6 was provided in this work, which was confirmed to survive independently under high salt stress (12% NaCl) or co-stress condition of strong acid (pH 3.0) and high salts (10% NaCl) without sterilization. Its survival mechanism under high salt stress was revealed by integrated omics for the first time. Whole-genome analysis showed that 14 genes (e.g., GPD1 and FPS1) of GXDK6 relevant to salt tolerance were annotated and known to belong to various salt-resistant mechanisms (e.g., regulation of cell signal transduction and glycerol metabolism controls). Transcriptome sequencing results indicated that 1220 genes (accounting for 10.15%) of GXDK6 were differentially transcribed (p < 0.05) when GXDK6 growth was under 10% stress for 16 h, including important novel salt-tolerant-related genes (e.g., RTM1 and YHB1). Proteomics analysis demonstrated that 1005 proteins (accounting for 27.26%) of GXDK6 were differentially expressed (p < 0.05) when GXDK6 was stressed by 10% NaCl. Some of the differentially expressed proteins were defined as the novel salt-tolerant related proteins (e.g., sugar transporter STL1 and NADPH-dependent methylglyoxal reductase). Metabolomic analysis results showed that 63 types of metabolites (e.g., D-mannose, glycerol and inositol phosphate) of GXDK6 were up- or downregulated when stressed by 10% NaCl. Among them, D-mannose is one of the important metabolites that could enhance the salt-tolerance survival of GXDK6.

IMPORTANCE

Microbial contamination is a huge obstacle in industrial fermentation. The emergence of multistress-tolerant microorganism is expected to realize industrial fermentation without sterilization by controlling specific conditions. However, microorganisms eligible for non-sterile fermentation are required to survive independently under the selected special conditions for the fermentation conditions to be controlled to avoid microbial contamination. Here, a novel marine Meyerozyma guilliermondii was presented, which is able to survive well under high salt stress, its survival mechanism was systematically revealed by integrated omics technology. In addition, finding that NaCl stress could also stimulate the biosynthesis of functional metabolites from GXDK6 (e.g., calcitriol and didemnin B). Among the functional metabolites, calcitriol biosynthesis via microbial method was rarely reported. Thus, its biosynthetic mechanism was further revealed. The findings in this study contributed to understanding the survival mechanism of M. guilliermondii under high salt stress, and the development of new molecular drugs from M. guilliermondii GXDK6.

Graphic abstract
Relating in vitro neutralisation level and protection in the CVnCoV (CUREVAC) trial
Authors: Cromer Deborah , Reynaldi Arnold , Steain Megan , Triccas James A , Davenport Miles P , Khoury David S
Published: June 2021

A recent study analysed the relationship between neutralising antibody response and protection from SARS-CoV-2 infection across eight vaccine platforms1. The efficacy results from a phase 2b/3 trial of a ninth vaccine candidate, CVnCoV (CUREVAC), was announced on 16 June 20212. The low efficacy of this new mRNA vaccine, which showed only 47% protection from symptomatic SARS-CoV-2 infection, was surprising given the high efficacy of two previous mRNA-based vaccines3,4. A number of factors have been suggested to play a role in the low efficacy in the CVnCoV study, particularly around the dose and immunogenicity of the vaccine (which uses an unmodified mRNA construct5,6) and the potential role of infection with SARS-CoV-2 variants (which were the dominant strains observed in the CVnCoV trial)2.
Raloxifene reduces sex- and age-related intervertebral disc degeneration in mice by estrogen signaling
Authors: Bhadouria Neharika , Niziolek Paul , El Jordi Omar , Berman Alycia G. , McKinzie David , Wallace Joseph M. , Holguin Nilsson
Published: June 2021

Estrogen agonist raloxifene is an FDA-approved treatment for osteoporosis in postmenopausal women that may also be a promising prophylactic for painful intervertebral disc (IVD) degeneration. Here, we hypothesized that raloxifene would augment IVD structure and reduce neurokinin-1 (substance P) in young and old mice by stimulating estrogen signaling. 2.5 month (male and female) and 22.5 month (female) C57Bl/6J mice were subcutaneously injected with raloxifene hydrochloride (5x/week, 6week, n=7-9/grp). Next, to determine the impact of estrogen-deficiency to IVD structure and substance P, female mice were ovariectomized (OVX) at 4mo and tissues from OVX and sham-operated mice were harvested at 6mo (n=5-6/grp). First, compared to male IVD, female IVD expressed less col2 and osterix transcription, early markers of IVD degeneration. Irrespective of sex, raloxifene increased the transcriptional expression for extracellular matrix anabolism, proliferation, notochordal cells (vs chondrocyte-like cells) and estrogen signaling in young IVD. Next, we determined that biological sex and aging each induced structural features of lumbar IVD degeneration. Therapeutically, injection of raloxifene countered these features by increasing IVD height in young mice, preventing mild sex-related IVD degeneration in young female mice and partially reversing age-related IVD degeneration in old female mice. Further, estrogen agonist raloxifene upregulated er-α protein and downregulated substance P protein in young and old IVD. By contrast, estrogen-deficiency by OVX increased IVD degeneration and substance P protein in IVD cells. Similarly, substance P protein in vertebral osteocytes was upregulated in females relative to males and by estrogen-deficiency and downregulated by raloxifene. Overall, raloxifene augmented IVD structure and reduced substance P expression in young and old female murine IVD, whereas estrogen-deficiency increased substance P in the spine. These data suggest that raloxifene may potentially relieve painful IVD degeneration in postmenopausal women induced by biological sex, estrogen-deficiency and advanced age.

Abstract Figure

Graphical Abstract

Injection of raloxifene promotes IVD health by engaging estrogen and Wnt signaling to promote cell proliferation and IVD structure. Differential estrogen signaling by raloxifene and ovariectomy regulated nerve signaling protein substance P in the spine. Raloxifene may also bind water to collagen to promote hydration. Acan: aggrecan, AF: annulus fibrosus, NC: notochordal cell, NP: nucleus pulposus
Mechanical Stimulation via Muscle Activity is Necessary for the Maturation of Tendon Multiscale Mechanics during Embryonic Development
Authors: Peterson Benjamin E. , Rolfe Rebecca A. , Kunselman Allen , Murphy Paula , Szczesny Spencer E.
Published: June 2021

During embryonic development, tendons transform into a hypocellular tissue with robust tensile load-bearing capabilities. Previous work suggests that this mechanical transformation is due to increases in collagen fibril length and is dependent on mechanical stimulation via muscle activity. However, the relationship between changes in the microscale tissue structure and changes in macroscale tendon mechanics is still unclear. Additionally, the specific effect of mechanical stimulation on the multiscale structure-function relationships of developing tendons is also unknown. Therefore, the objective of this study was to measure the changes in tendon mechanics and structure at multiple length scales during embryonic development with and without skeletal muscle paralysis. Tensile testing of tendons from chicken embryos was performed to determine the macroscale tensile modulus as well as the magnitude of the fibril strains and interfibrillar sliding with applied tissue strain. Embryos were also treated with either decamethonium bromide or pancuronium bromide to produce rigid or flaccid paralysis. Histology was performed to assess changes in tendon size, spacing between tendon subunits, and collagen fiber diameter. We found that the increase in the macroscale modulus observed with development is accompanied by an increase in the fibril:tissue strain ratio, which is consistent with an increase in collagen fibril length. Additionally, we found that flaccid paralysis reduced the macroscale tendon modulus and the fibril:tissue strain ratio, whereas less pronounced effects that were not statistically significant were observed with rigid paralysis. Finally, skeletal paralysis also reduced the size of collagen fibril bundles (i.e., fibers). Together, these data suggest that more of the applied tissue strain is transmitted to the collagen fibrils at later embryonic ages, which leads in an increase the tendon macroscale tensile mechanics. Furthermore, our data suggest that mechanical stimulation during development is necessary to induce structural and mechanical changes at multiple physical length scales. This information provides valuable insight into the multiscale structure-function relationships of developing tendons and the importance of mechanical stimulation in producing a robust tensile load-bearing soft tissue.
Distinct epicardial gene regulatory programmes drive development and regeneration of the zebrafish heart
Authors: Weinberger Michael , Simões Filipa C. , Sauka-Spengler Tatjana , Riley Paul R.
Published: June 2021

Unlike the adult mammalian heart, which has limited regenerative capacity, the zebrafish heart can fully regenerate following injury. Reactivation of cardiac developmental programmes is considered key to successfully regenerating the heart, yet the regulatory elements underlying the response triggered upon injury and during development remain elusive. Organ-wide activation of the epicardium is essential for zebrafish heart regeneration and is considered a potential regenerative source to target in the mammalian heart. Here we compared the transcriptome and epigenome of the developing and regenerating zebrafish epicardium by integrating gene expression profiles with open chromatin ATAC-seq data. By generating gene regulatory networks associated with epicardial development and regeneration, we inferred genetic programmes driving each of these processes, which were largely distinct. We identified wt1a, wt1b, and the AP-1 subunits junbb, fosab and fosb as central regulators of the developing network, whereas hif1ab, zbtb7a, tbx2b and nrf1 featured as putative central regulators of the regenerating epicardial network. By interrogating developmental gene regulatory networks that drive cell-specific transcriptional heterogeneity, we tested novel subpopulation-related epicardial enhancers in vivo. Taken together, our work revealed striking differences between the regulatory blueprint deployed during epicardial development and regeneration. These findings challenge the dogma that heart regeneration is essentially a reactivation of developmental programmes, and provide important insights into epicardial regulation that can assist in developing therapeutic approaches to enable tissue regeneration in the adult mammalian heart.
Persistence of Hippocampal and Striatal Multivoxel Patterns During Awake Rest after Motor Sequence Learning
Authors: King Bradley R. , Gann Mareike A. , Mantini Dante , Doyon Julien , Albouy Geneviève
Published: June 2021

Memory consolidation, the process by which newly encoded and fragile memories become more robust, is thought to be supported by the reactivation of brain regions - including the hippocampus - during post-learning rest. While hippocampal reactivations have been demonstrated in humans in the declarative memory domain, it remains unknown whether such a process takes place after motor learning. Using multivariate analyses of task-related and resting state fMRI data, here we show that patterns of brain activity within both the hippocampus and striatum elicited during motor learning persist into post-learning rest, indicative of reactivation of learning-related neural activity patterns. Moreover, results indicate that hippocampal reactivation reflects the spatial representation of the learned motor sequence. These results thus provide insights into the functional significance of neural reactivation after motor sequence learning.
Substrate access mechanism in a novel membrane-bound phospholipase A of Pseudomonas aeruginosa concordant with specificity and regioselectivity
Authors: Ahmad Sabahuddin , Strunk Christoph Heinrich , Schott-Verdugo Stephan N. , Jaeger Karl-Erich , Kovacic Filip , Gohlke Holger
Published: June 2021

PlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates has remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by fatty acid-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.
The ACF chromatin remodeling complex is essential for Polycomb repression
Authors: Wiles Elizabeth T. , Mumford Colleen C. , McNaught Kevin J. , Tanizawa Hideki , Selker Eric U.
Published: June 2021

Establishing and maintaining appropriate gene repression is critical for the health and development of multicellular organisms. Histone H3 lysine 27 (H3K27) methylation is a chromatin modification associated with repressed facultative heterochromatin, but the mechanism of this repression remains unclear. We used a forward genetic approach to identify genes involved in transcriptional silencing of H3K27-methylated chromatin in the filamentous fungus Neurospora crassa. We found that the N. crassa homologs of ISWI (NCU03875) and ACF (NCU00164) are required for repression of a subset of H3K27-methylated genes and that they form an ACF chromatin remodeling complex. This N. crassa ACF complex interacts with chromatin throughout the genome, yet association with facultative heterochromatin is specifically promoted by the H3K27 methyltransferase, SET-7. H3K27-methylated genes that are upregulated when iswi or acf1 are deleted show a downstream shift of the +1 nucleosome, suggesting that proper nucleosome positioning is critical for repression of facultative heterochromatin. Our findings support a direct role for the ACF complex in Polycomb repression.
The MuvB Complex Binds and Stabilizes Nucleosomes Downstream of the Transcription Start Site of Cell-Cycle Dependent Genes
Authors: Asthana Anushweta , Ramanan Parameshwaran , Hirschi Alexander , Guiley Keelan Z. , Wijeratne Tilini U. , Shelansky Robert , Doody Michael J. , Narasimhan Haritha , Boeger Hinrich , Tripathi Sarvind , Müller Gerd A. , Rubin Seth M.
Published: June 2021

The chromatin architecture in promoters is thought to regulate gene expression, but it remains uncertain how most transcription factors (TFs) impact nucleosome position. The MuvB TF complex regulates cell-cycle dependent gene-expression and is critical for differentiation and proliferation during development and cancer. MuvB can both positively and negatively regulate expression, but the structure of MuvB and its biochemical function are poorly understood. Here we determine the overall architecture of MuvB assembly and the crystal structure of a subcomplex critical for MuvB function in gene repression. We find that the MuvB subunits LIN9 and LIN37 function as scaffolding proteins that arrange the other subunits LIN52, LIN54 and RBAP48 for TF, DNA, and histone binding, respectively. Biochemical and structural data demonstrate that MuvB binds nucleosomes through an interface that is distinct from LIN54-DNA consensus site recognition and that MuvB increases nucleosome occupancy in a reconstituted promoter. We find in arrested cells that MuvB primarily associates with a tightly positioned +1 nucleosome near the transcription start site (TSS) of MuvB-regulated genes. These results support a model that MuvB binds and stabilizes nucleosomes just downstream of the TSS on its target promoters to repress gene-expression.
Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain
Authors: Cerutti Gabriele , Guo Yicheng , Wang Pengfei , Nair Manoj S. , Huang Yaoxing , Yu Jian , Liu Lihong , Katsamba Phinikoula S. , Bahna Fabiana , Reddem Eswar R. , Kwong Peter D. , Ho David D. , Sheng Zizhang , Shapiro Lawrence
Published: June 2021

Antibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or the N-terminal domain (NTD). Over a dozen potently neutralizing NTD-directed antibodies have been studied structurally, and all target a single antigenic supersite in NTD (site 1). Here we report the 3.7 Å resolution cryo-EM structure of a potent NTD-directed neutralizing antibody 5-7, which recognizes a site distinct from other potently neutralizing antibodies, inserting a binding loop into an exposed hydrophobic pocket between the two sheets of the NTD β-sandwich. Interestingly, this pocket has been previously identified as the binding site for hydrophobic molecules including heme metabolites, but we observe their presence to not substantially impede 5-7 recognition. Mirroring its distinctive binding, antibody 5-7 retains a distinctive neutralization potency with variants of concern (VOC). Overall, we reveal a hydrophobic pocket in NTD proposed for immune evasion can actually be used by the immune system for recognition.

Highlights

Cryo-EM structure of neutralizing antibody 5-7 in complex with SARS CoV-2 spike

5-7 recognizes NTD outside of the previously identified antigenic supersite

5-7 binds to a site known to accommodate numerous hydrophobic ligands

Structural basis of 5-7 neutralization tolerance to some variants of concern
AUTS2 controls neuronal lineage choice through a novel PRC1-independent complex and BMP inhibition
Authors: Geng Zhuangzhuang , Wang Qiang , Miao Weili , Wolf Trevor , Chavez Jessenia , Giddings Emily , Hobbs Ryan , DeGraff David J. , Wang Yinsheng , Stafford James , Gao Zhonghua
Published: June 2021

Despite a prominent risk factor for Neurodevelopmental disorders (NDD), it remains unclear how Autism Susceptibility Candidate 2 (AUTS2) controls the neurodevelopmental program. Our studies investigated the role of AUTS2 in neuronal differentiation and discovered that AUTS2, together with WDR68 and SKI, forms a novel protein complex (AWS) specifically in neuronal progenitors and promotes neuronal differentiation through inhibiting BMP signaling. Genomic and biochemical analyses demonstrated that the AWS complex achieves this effect by recruiting the CUL4 E3 ubiquitin ligase complex to mediate poly-ubiquitination and subsequent proteasomal degradation of phosphorylated SMAD1/5/9. Furthermore, using primary cortical neurons, we observed aberrant BMP signaling and dysregulated expression of neuronal genes upon manipulating the AWS complex, indicating that the AWS-CUL4-BMP axis plays a role in regulating neuronal lineage specification in vivo. Thus, our findings uncover a sophisticated cellular signaling network mobilized by a prominent NDD risk factor, presenting multiple potential therapeutic targets for NDD.
Simultaneous Binding of the N- and C-terminal Cytoplasmic Domains of Aquaporin 4 to Calmodulin May Contribute to Vesicular Trafficking
Authors: Ishida Hiroaki , Vogel Hans J. , Conner Alex C. , Kitchen Philip , Bill Roslyn M. , MacDonald Justin A.
Published: June 2021

Aquaporin 4 (AQP4) is a water transporting, transmembrane channel protein that has important regulatory roles in maintaining cellular water homeostasis. Several other AQP proteins exhibit calmodulin (CaM)-binding properties, and CaM has recently been implicated in the cell surface localization of AQP4 that occurs in response to osmotically-driven changes in cell swelling in the central nervous system. The objective of the present study was to assess the CaM-binding properties of AQP4 in detail. Inspection of AQP4 revealed two putative CaM-binding domains (CBDs) in the cytoplasmic N- and C-terminal regions, respectively. The Ca2+-dependent CaM-binding properties of synthetic and recombinant AQP4 CBD peptides were assessed using fluorescence spectroscopy, isothermal titration calorimetry, and two-dimensional 1H, 15N-HSQC NMR with 15N-labeled CaM. The N-terminal CBD peptide of AQP4 predominantly interacted with the N-lobe of CaM with a 1:1 binding ratio and a Kd of 3.4 μM. CaM bound two C-terminal AQP4 peptides with interactions observed for both the C- and N-lobes of CaM (Kd1: 3.6 μM, Kd2: 113.6 μM, respectively). A recombinant AQP4 protein domain (rAQP4ct, containing the entire cytosolic C-terminal domain sequence) bound CaM in a 1:1 binding mode with a Kd of 6.1 μM. A ternary bridging complex could be generated with the N- and C-lobes of CaM interacting simultaneously with the N- and C-terminal CBD peptides. These data suggest that this unique adapter protein binding mode of CaM and AQP4 may be an important regulatory mechanism for the vesicular trafficking of AQP4.
Synthesis and characterization of 5-(2-fluoro-4-[11C]methoxyphenyl)-2,2-dimethyl-3,4-dihydro-2H-pyrano[2,3-b]pyridine-7-carboxamide as a PET imaging ligand for metabotropic glutamate receptor 2
Authors: Yuan Gengyang , Dhaynaut Maeva , Lan Yu , Guehl Nicolas J. , Huynh Dalena , Iyengar Suhasini , Afshar Sepideh , Wang Hao , Moon Sung-Hyun , Ondrechen Mary Jo , Wang Changning , Shoup Timothy , El Fakhri Georges , Normandin Marc D. , Brownell Anna-Liisa
Published: June 2021

Metabotropic glutamate receptor 2 (mGluR2) is a therapeutic target for the treatment of several neuropsychiatric disorders and conditions. The role of mGluR2 function in etiology could be unveiled byin vivoimaging using positron emission tomography (PET). In this regard, 5-(2- fluoro-4-[11C]methoxyphenyl)-2,2-dimethyl-3,4-dihydro-2H-pyrano[2,3-b]pyridine-7- carboxamide ([11C]13), a potent negative allosteric modulator (NAM), was developed to support this endeavor. Radioligand [11C]13was synthesized via theO-[11C]methylation of phenol24with a high molar activity of 212 ± 76 GBq/µmol (n = 5) and excellent radiochemical purity (> 99%). PET imaging of [11C]13in rats demonstrated its superior brain heterogeneity, particularly in the regions of striatum, thalamus, hippocampus, and cortex. Accumulation of [11C]13in these regions of interest (ROIs) was reduced with pretreatment of mGluR2 NAMs, VU6001966 (9) and MNI-137 (26), the extent of which revealed a time-dependent drug effect of the blocking agents. In a nonhuman primate, [11C]13selectively accumulated in mGluR2-rich regions, especially in different cortical areas, putamen, thalamus, and hippocampus, and resulted in high-contrast brain images. The regional total volume of distribution (VT) estimates of [11C]13decreased by 14% after the pretreatment with9. Therefore, [11C]13is a potential candidate for translational PET imaging studies of mGluR2 function.
Prefrontal cortical connectivity mediates locus coeruleus noradrenergic regulation of inhibitory control in older adults
Authors: Tomassini Alessandro , Hezemans Frank H. , Ye Rong , Cam-CAN  , Tsvetanov Kamen A. , Wolpe Noham , Rowe James B.
Published: June 2021

Response inhibition is a core executive function enabling adaptive behaviour in dynamic environments. Human and animal models indicate that inhibitory control and control networks are modulated by noradrenaline, arising from the locus coeruleus. The integrity (i.e., cellular density) of the locus coeruleus noradrenergic system can be estimated from magnetization transfer sensitive magnetic resonance imaging, in view of neuromelanin present in noradrenergic neurons of older adults. Noradrenergic psychopharmacological studies indicate noradrenergic modulation of prefrontal and frontostriatal stopping-circuits in association with behavioural change. Here we test the noradrenergic hypothesis of inhibitory control, in healthy adults. We predicted that locus coeruleus integrity is associated with age-adjusted variance in response inhibition, mediated by changes in connectivity between frontal inhibitory control regions. In a preregistered analysis, we used magnetization transfer MRI images from N=63 healthy adults aged above 50 years who performed a stop-signal task, with atlas-based measurement of locus coeruleus contrast. We confirm that better response inhibition is correlated with locus coeruleus integrity and stronger connectivity between pre-supplementary motor area and right inferior frontal gyrus, but not volumes of the cortical regions. We confirmed a significant role of prefrontal connectivity in mediating the effect of individual differences in the locus coeruleus on behaviour, whereby this effect was moderated by age, over and above adjustment for the mean effects of age. Our results support the hypothesis that in normal populations, as in clinical settings, the locus coeruleus noradrenergic system regulates inhibitory control.