bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell Geometry Distinguishes Migration-Associated Heterogeneity in Two-Dimensional Systems
Authors: Varankar Sagar S , Hari Kishore , Bapat Sharmila A , Jolly Mohit Kumar 
Published: December 2021

AbstractBackgroundIn vitromigration assays are a cornerstone of cell biology and have found extensive utility in research. Over the past decade, several variations of the two-dimensional (2D) migration assay have improved our understanding of this fundamental process. However, the ability of these approaches to capture the functional heterogeneity during migration and their accessibility to inexperienced users has been limited.MethodsWe downloaded published time-lapse 2D cell migration datasets and subjected them to feature extraction with the Fiji software. We used the ‘Analyze Particles’ tool to extract ten cell geometry features (CGFs), which were grouped into ‘shape’, ‘size’ and ‘position’ descriptors. Next, we defined the migratory status of cells using the ‘MTrack2’ plugin. All data obtained from Fiji were further subjected to rigorous statistical analysis with R version 4.0.2.ResultsWe observed consistent associative trends between size and shape descriptors and validated the robustness of our observations across four independent datasets. We used these descriptors to resolve the functional heterogeneity during migration by identifying and characterizing ‘non-migrators (NM)’ and ‘migrators (M)’. Statistical analysis allowed us to identify considerable heterogeneity in the NM subset, that has not been previously reported. Interestingly, differences in 2D-packing appeared to affect CGF trends and heterogeneity of the migratory subsets for the datasets under investigation.ConclusionWe developed an analytical pipeline using open source tools, to identify and morphologically characterize functional migratory subsets from label-free, time-lapse migration data. Our quantitative approach identified a previously unappreciated heterogeneity of non-migratory cells and predicted the influence of 2D-packing on migration.
Accelerating manufacturing to enable large-scale supply of a new adenovirus-vectored vaccine within 100 days
Authors: Joe Carina C D , Segireddy Rameswara R , Oliveira Cathy , Berg Adam , Li Yuanyuan , Doultsinos Dimitrios , Chopra Nitin , Scholze Steffi , Ahmad Asma , Nestola Piergiuseppe , Niemann Julia , Douglas Alexander D 
Published: December 2021

AbstractThe Coalition for Epidemic Preparedness Innovations’ ‘100-day moonshot’ aspires to launch a new vaccine within 100 days of pathogen identification. Here, we describe work to optimize adenovirus vector manufacturing for rapid response, by minimizing time to clinical trial and first large-scale supply, and maximizing the output from the available manufacturing footprint.We describe a rapid viral seed expansion workflow that allows vaccine release to clinical trials within 60 days of antigen sequence identification, followed by vaccine release from globally distributed sites within a further 40 days. We also describe a new perfusion-based upstream production process, designed to maximize output while retaining simplicity and suitability for existing manufacturing facilities. This improves upstream volumetric productivity of ChAdOx1 nCoV-19 by around four-fold and remains compatible with the existing downstream process, yielding drug substance sufficient for 10000 doses from each liter of bioreactor capacity.Transition to a new production process across a large manufacturing network is a major task. In the short term, the rapid seed generation workflow could be used with the existing production process. We also use techno-economic modelling to show that, if linear scale-up were achieved, a single cleanroom containing two 2000 L bioreactors running our new perfusion-based process could supply bulk drug substance for around 120 million doses each month, costing <0.20 EUR/dose. We estimate that a manufacturing network with 32000 L of bioreactor capacity could release around 1 billion doses of a new vaccine within 130 days of genomic sequencing of a new pathogen, in a hypothetical ‘surge campaign’ with suitable prior preparation and resources, including adequate fill-and-finish capacity.This accelerated manufacturing process, along with other advantages such as thermal stability, supports the ongoing value of adenovirus-vectored vaccines as a rapidly adaptable and deployable platform for emergency response.
A spatiotemporal steroidogenic regulatory network in human fetal adrenal glands and gonads
Authors: Wang Yifu , Guo Bingqian , Guo Yajie , Qi Nana , Lv Yufang , Ye Yu , Huang Yan , Long Xinyang , Chen Hongfei , Su Cheng , Zhang Liying , Zhang Qingyun , Li Minxi , Liao Jingling , Yan Yunkun , Mao Xingning , Zeng Yanyu , Jiang Jinghang , Chen Zhongyuan , Guo Yi , Gao Shuai , Cheng Jiwen , Jiang Yonghua , Mo Zengnan 
Published: December 2021

AbstractHuman fetal adrenal glands produce substantial amounts of dehydroepiandrosterone (DHEA), which is one of the most important precursors of sex hormones. However, the underlying biological mechanism remains largely unknown. Herein, we sequenced human fetal adrenal glands and gonads from 7 to 14 GW via the 10× Genomics single-cell transcriptome techniques and reconstructed their location information by Spatial Transcriptome, conducted COOL-seq for the MC2R+ inner zone steroidogenic cells during the time window of sex differentiation (8-12GW). We found that relative to gonads, adrenal glands begin to synthesize steroids early. The coordination among steroidogenic cells and multiple nonsteroidogenic cells promotes adrenal cortex construction and steroid synthesis. Notably, during the time window of sex differentiation (8–12 GW), key enzyme gene expression shifts to accelerate DHEA synthesis in males and cortisol synthesis in females. Furthermore, high SST+ expressions in the adrenal gland and testis amplify androgen synthesis in males. Our research highlights the robustness of the action of fetal adrenal glands on gonads to modify the process of sexual differentiation.
Influential factors of saliva microbiota composition
Authors: Wells Philippa M. , Sprockett Daniel D. , Bowyer Ruth C E , Kurushima Yuko , Relman David A. , Williams Frances M.K. , Steves Claire J. 
Published: December 2021

AbstractBackgroundThe oral microbiota is emerging as an influential factor of host physiology and disease state. Factors influencing oral microbiota composition have not been well characterised. In particular, there is a lack of population-based studies. We undertook a large hypothesis-free study of the saliva microbiota, considering potential influential factors of host health (frailty; diet; periodontal disease), demographics (age; sex; BMI) and sample processing (storage time), in a sample (n=679) of the TwinsUK cohort of adult twins.ResultsAlpha and beta diversity of the saliva microbiota was associated most strongly with frailty (alpha diversity: Q = 0.003, Observed; Q=0.002, Shannon; Q=0.003, Simpson; Beta diversity: Q = 0.002, Bray Curtis dissimilarity) and age (alpha diversity: Q=0.006, Shannon; Q=0.003, Simpson; beta diversity: Q=0.002, Bray Curtis dissimilarity; Q= 0.032, Weighted UniFrac) in multivariate models including age, frailty, sex, BMI, frailty and diet, and adjustment for multiple testing. Those with a more advanced age were more likely to be dissimilar in the saliva microbiota composition than younger participants (P = 5.125e-06, ANOVA). In subsample analyses, including consideration of periodontal disease (total n=138, periodontal disease n=66), the association with frailty remained for alpha diversity (Q=0.002, Observed ASVs; Q= 0.04 Shannon Index), but not beta diversity, whilst age was not demonstrated to associate with alpha or beta diversity in this subsample, potentially due to insufficient statistical power. Length of time that samples were stored prior to sequencing was associated with beta diversity (Q = 0.002, Bray Curtis dissimilarity). Six bacterial taxa were associated with age after adjustment for frailty and diet.ConclusionsFrailty and age emerged as the most influential factors of saliva microbiota composition. Whilst frailty and age are correlates, the associations were independent of each other, suggesting that both biological and chronological ageing are key drivers of saliva microbiota composition.
Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants : Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability
Authors: Verkhivker Gennady 
Published: December 2021

AbstractThe experimental and computational studies of the SARS-CoV-2 spike protein variants revealed an important role of the D614G mutation that is shared across variants of concern(VOCs), linking the effect of this mutation with the enhanced virus infectivity and transmissibility. The recent structural and biophysical studies characterized the closed and open states of the B.1.1.7 (B.1.1.7) and B.1.351 (Beta) spike variants allowing for a more detailed atomistic characterization of the conformational landscapes and functional changes. In this study, we employed coarse-grained simulations of the SARS-CoV-2 spike variant trimers together with the ensemble-based mutational frustration analysis to characterize the dynamics signatures of the conformational landscapes. By combining the local frustration analysis of the conformational ensembles with collective dynamics and residue-based mutational scanning of protein stability, we determine protein stability hotspots and identify potential energetic drivers favoring the receptor-accessible open spike states for the B.1.1.7 and B.1.351 spike variants. Through mutational scanning of protein stability changes we quantify mutational adaptability of the S-G614, S-B.1.1.7 and S-B.1.351 variants in different functional forms. Using this analysis, we found a significant conformational and mutational plasticity of the open states for all studied variants. The results of this study suggest that modulation of the energetic frustration at the inter-protomer interfaces can serve as a mechanism for allosteric couplings between mutational sites, the inter-protomer hinges of functional motions and motions of the receptor-binding domain required for binding of the host cell receptor. The proposed mechanism of mutation-induced energetic frustration may result in the greater adaptability and the emergence of multiple conformational substates in the open form. This study also suggested functional relationships between mutation-induced modulation of protein dynamics, local frustration and allosteric regulation of the SARS-CoV-2 spike protein.
Growth-limiting drought stress induces time-of-day dependent transcriptome and physiological responses in hybrid poplar
Authors: Robertson Sean M. , Sakariyahu Solihu Kayode , Bolaji Ayooluwa J. , Belmonte Mark F. , Wilkins Olivia 
Published: December 2021

AbstractDrought stress negatively impacts the health of long-lived trees. Understanding the genetic mechanisms that underpin response to drought stress is requisite for selecting or enhancing climate change resilience. We aimed to determine how hybrid poplars respond to prolonged and uniform exposure to drought; how responses to moderate and more severe growth-limiting drought stresses differed; and, how drought responses change throughout the day. We established hybrid poplar trees (Populus x ‘Okanese’) from unrooted stem cutting with abundant soil moisture for six weeks. We then withheld water to establish well-watered, moderate, and severe growth-limiting drought conditions. These conditions were maintained for three weeks during which growth was monitored. We then measured photosynthetic rates and transcriptomes of leaves that had developed during the drought treatments at two times of day. The moderate and severe drought treatments elicited distinct changes in growth and development, photosynthetic rates, and global transcriptome profiles. Notably, the time of day of sampling produced the strongest signal in the transcriptome data. The moderate drought treatment elicited global transcriptome changes that were intermediate to the severe and well-watered treatments in the early evening, but did not elicit a strong drought response in the morning, emphasizing the complex nature of drought regulation in long-lived trees.HighlightPoplar drought transcriptome is defined by the time of day of sampling and by the extent of water deficit.
Regulation of KHNYN antiviral activity by the extended di-KH domain and nucleo-cytoplasmic trafficking
Authors: Lista María José , Galão Rui Pedro , Ficarelli Mattia , Kmiec Dorota , Wilson Harry , Winstone Helena , Morris Elizabeth R , Mischo Hannah E , Wanford Joseph , Youle Rebecca , Odendall Charlotte , Taylor Ian A , Neil Stuart J D , Swanson Chad M 
Published: December 2021

ABSTRACTThe zinc finger antiviral protein (ZAP) restricts a broad range of viruses by binding CpG dinucleotides in viral RNA to target it for degradation and inhibit its translation. KHNYN was recently identified as an antiviral protein required for ZAP to inhibit retroviral replication, though little is known about its functional determinants. KHNYN contains an N-terminal extended di-KH-like domain, a PIN endoribonuclease domain and a C-terminal CUBAN domain that binds NEDD8 and ubiquitin. We show that deletion of the extended di-KH domain reduces its antiviral activity. However, despite its similarity to RNA binding KH domains, the extended di-KH domain in KHNYN does not appear to bind RNA. Mutation of residues in the CUBAN domain that bind NEDD8 increase KHNYN abundance but do not alter its antiviral activity, suggesting that this interaction regulates KHNYN homeostatic turnover. In contrast, a CRM1-dependent nuclear export signal (NES) at the C-terminus of the CUBAN domain is required for antiviral activity. Deletion of this signal retains KHNYN in the nucleus and inhibits its interaction with ZAP. Interestingly, this NES appeared in the KHNYN lineage at a similar time as when ZAP evolved in tetrapods, indicating that these proteins may have co-evolved to restrict viral replication.AUTHOR SUMMARYAntiviral proteins restrict viral replication in many different ways, including inhibiting viral gene expression. ZAP is an antiviral RNA binding protein that must interact with other cellular proteins to inhibit viral protein synthesis. KHNYN is a ZAP cofactor that is required for it to inhibit retroviral replication. Because little is known about how KHNYN functions in this role, we have analyzed how two of its domains regulate its antiviral activity. We first show that the extended di-KH domain in KHNYN is required for its antiviral activity. While it is related to di-KH domains in RNA binding proteins, it appears to have lost its ability to bind RNA and KHNYN likely acts in the restriction pathway after ZAP binds a target viral RNA. Second, we show that the KHNYN CUBAN domain regulates both its protein abundance and trafficking within the cell. The CUBAN domain contains a nuclear export signal and, when this signal is mutated, KHNYN is sequestered in the nucleus, has substantially reduced antiviral activity and does not interact with ZAP. Overall, we show that the extended di-KH and CUBAN domains in KHNYN are required for it to act as a cofactor for ZAP to restrict viral replication.
TROPONIN IS INDEPENDENTLY ASSOCIATED WITH DEATH IN PATIENTS WITH COVID: A RETROSPECTIVE STUDY
Authors: Shyam-Sundar Vijay , Stein Dan , Spazzapan Martina , Sullivan Andrew , Qin Cathy , Voon Victor 
Published: December 2021

AbstractObjectiveWe performed a single-centre retrospective observational study investigating the association between troponin positivity in patients hospitalised with COVID-19 and increased mortality in the short term.MethodsAll adults admitted with swab-proven RT-PCR COVID-19 to Homerton University Hospital (HUH) from 04.02.20 to 30.04.20 were eligible for inclusion.We retrospectively analysed demographic and biochemical data collected from the physical and electronic patient records according to the primary outcome of death at 28 days during hospital admission.Troponin positivity was defined above the upper limit of normal according to our local laboratory assay (>15.5ng/l for females, >34 ng/l for males). Univariate and multivariate logistical regression analyses were performed to evaluate the link between troponin positivity and death.ResultsMean length of stay for all 402 hospitalised COVID-19 patients at HUH was 9.1 days (SD 12.0). Mean age was 65.3 years for men compared to 63.8 years for women. A chi-squared test showed that survival of COVID-19 patients was significantly higher in those with a negative troponin (p = 3.23 ×10−10) compared to those with a positive troponin. In the multivariate logistical regression, lung disease, age, troponin positivity and CPAP were all significantly associated with death, with an AUC of 0.8872, sensitivity of 0.9004 and specificity of 0.6292 for the model. Within this model, troponin positivity was independently associated with short term mortality (OR 3.23, 95% CI 1.53-7.16, p=0.00278).ConclusionsWe demonstrated an independent association between troponin positivity and increased short-term mortality in COVID-19 in a London district general hospital.Key QuestionsWhat is already known about this subject?An elevated Troponin is associated with increased mortality. Troponin is known to be elevated in some patients who test positive for COVID-19 infection.What does this study add?This study shows an association between an elevated troponin in hospitalised COVID-19 patients and increased short-term mortality.How might this impact on clinical practice?Troponin is a readily available, easy to measure biomarker which can be used to predict the severity of COVID-19 illness and could aid prognostication in hospital.
Dynamics of immune recall following SARS-CoV-2 vaccination or breakthrough infection
Authors: Koutsakos Marios , Lee Wen Shi , Reynaldi Arnold , Tan Hyon-Xhi , Gare Grace , Kinsella Paul , Liew Kwee Chin , Williamson Deborah A. , Kent Helen E. , Stadler Eva , Cromer Deborah , Khoury David S. , Wheatley Adam K. , Juno Jennifer A. , Davenport Miles P. , Kent Stephen J. 
Published: December 2021

AbstractVaccination against SARS-CoV-2 results in protection from acquisition of infection as well as improved clinical outcomes even if infection occurs, likely reflecting a combination of residual vaccine-elicited immunity and the recall of immunological memory. Here, we define the early kinetics of spike-specific humoral and T cell immunity after vaccination of seropositive individuals, and after breakthrough infection in vaccinated individuals. Intensive and early longitudinal sampling reveals the timing and magnitude of recall, with the phenotypic activation of B cells preceding an increase in neutralizing antibody titres. In breakthrough infections, the delayed kinetics of humoral immune recall provides a mechanism for the lack of early control of viral replication but likely underpins accelerated viral clearance and the protective effects of vaccination against severe COVID-19.
Exploration of attitudes regarding uptake of COVID-19 vaccines among vaccine hesitant adults in the UK: A qualitative analysis
Authors: Denford Sarah , Mowbray Fiona , Towler Lauren , Wehling Helena , Lasseter Gemma , Amlôt Richard , Oliver Isabel , Yardley Lucy , Hickman Mathew 
Published: December 2021

AbstractBackgroundThe aim of this work was to explore barriers and facilitators to uptake of COVID-19 vaccines and to explore views and reactions to efforts to improve vaccine uptake among those who were vaccine hesitant.MethodsSemi-structured interviews were conducted with people between the age of 18-29 years who had not had a COVID-19 vaccine, and those between 30-49 years who had not received a second dose of a COVID-19 vaccine (more than 12 weeks after receiving a first).ResultsA total of 70 participants took part in the study, 35 participants had received one dose of the vaccine, and 35 had not received any vaccine.Participants described a possible willingness to be vaccinated to keep themselves and those around them safe, and to avoid restrictions and return to normal. Barriers to uptake included: 1) perceived lack of need for COVID-19 vaccinations, 2) concerns about the efficacy of vaccinations, 3) concerns about safety, and 4) access issues. Uptake appeared to be influenced by the age and health status of the individual, trust in government and knowledge and understanding of science. Introduction of vaccine passes may provide a motive for having a vaccine but may also be viewed as coercive.ConclusionParticipants were hesitant, rather than opposed, and had questions about their need for, and the safety and efficacy of the vaccine. Young people did not consider themselves to be at risk of becoming ill from COVID-19, did not think the vaccination was effective in preventing infection and transmission, and did not think sufficient research had been conducted with regard to the possible long-term side-effects. These concerns were exacerbated by a lack of trust in the government, and misunderstanding of science. In order to promote uptake, public health campaigns should focus on the provision of information from trusted sources that carefully explains the benefits of vaccination and addresses safety concerns more effectively. To overcome inertia in people with low levels of motivation to be vaccinated, appointments must be easily accessible.
Conserved angio-immune subtypes of the cancer microenvironment predict response to immune checkpoint blockade therapy
Authors: Subramanian Madhav , Kabir Ashraf Ul , Barisas Derek A.G. , Krchma Karen , Choi Kyunghee 
Published: December 2021

ABSTRACTTumor microenvironment (TME) shapes the tumor progression and therapy outcome. Particularly, tumor angiogenesis and immunity impact the effect of immune checkpoint blockade (ICB) therapy. Here, we analyzed the transcriptome from 11,069 patients from The Cancer Genome Atlas (TCGA) to assess 91 functional gene sets corresponding to endothelial and T-cell activity. Intriguingly, TME across 30 non-hematological tumors can be classified into three distinct conserved angio-immune subtypes: high angiogenesis with low immune activity, low angiogenesis with high immune activity, and the one in-between. Remarkably, patients displaying TME with poor angiogenic activity with corresponding high immune activity show the most significant responses to ICB therapy in many cancer types. Notably, re-evaluation of the Javelin Renal 101, renal cell carcinoma clinical trial, provided compelling evidence that the baseline angiogenic state is critical in determining responses to checkpoint blockade. This study offers a clear rationale for incorporating baseline angiogenic state for ICB treatment decision-making.