bluuebunny/crossref_metadata_2025_split huggingface dataset:
The High Transmission of SARS-CoV-2 Omicron (B.1.1.529) Variant is Not Only Due to Its hACE2 binding: A Free Energy of Perturbation Study
Authors: Fratev Filip 
Published: December 2021

AbstractThe mutations in the spike protein of SARS-CoV-2 Omicron variant (B.1.1.529 lineage) gave rise to questions, but the data on the mechanism of action at the molecular level is limited. In this study, we present the Free energy of perturbation (FEP) data about the RBD-hACE2 binding of this new variant.We identified two groups of mutations located close to the most contributing substitutions Q498R and Q493R, which altered significantly the RBD-hACE2 interactions. The Q498R, Y505H and G496S mutations, in addition to N501Y, highly increased the binding to hACE2. They enhanced the binding by 98, 14 and 13 folds, respectively, which transforms the S1-RBD to a picomolar binder. However, in contrast to the case in mice the Q493R/K mutations, in a combination with K417N and T478K, dramatically reduced the S1 RBD binding by over 100 folds. The N440K, G446S and T478K substitutions had lesser contribution. Thus, the total effect of these nine mutations located on the interaction surface of RBD-hACE2 turns out to be similar to that observed in the Alpha variant. In a special circumstances it could be further altered by the E484A and S477N mutations and even lower binding capacity is likely to be detected. Finally, we provide a structural basis of the observed changes in the interactions.These data may explain only partially the observed in South Africa extremely high Omicron spread and is in support to the hypothesis for multiple mechanisms of actions involved in the transmission.Graphical abstract
Waning antibody levels after vaccination with mRNA BNT162b2 and inactivated CoronaVac COVID-19 vaccines in Hong Kong blood donors
Authors: Kwok Shirley LL , Cheng Samuel MS , Leung Jennifer NS , Leung Kathy , Lee Cheuk-Kwong , Peiris JS Malik , Wu Joseph T 
Published: December 2021

AbstractBoth inactivated vaccine (CoronaVac; Sinovac) and mRNA vaccine (Comirnaty/BNT162b2; Fosun-Pharma/BioNTech) are available in Hong Kong’s COVID-19 Vaccination Programme. We reported waning antibody levels by enzyme-linked immunosorbent assays (ELISA) and surrogate virus neutralization test (sVNT) among 850 fully vaccinated blood donors (i.e., received two doses). The BNT162b2 group’s antibody levels remain over the 50% protection threshold within six months, and the CoronaVac’s group’s median antibody levels begin to fall below the 50% protection threshold two months after vaccination.
Sleep Dependent Changes of Lactate Concentration in Human Brain
Authors: Yildiz Selda , Lim Miranda M. , Sammi Manoj K. , Powers Katherine , Murchison Charles F. , Iliff Jeffrey J. , Rooney William D. 
Published: December 2021

AbstractLactate is an important cellular metabolite that is present at high concentrations in the brain, both within cells and in the extracellular space between cells. Small animal studies demonstrated high extracellular concentrations of lactate during wakefulness with reductions during sleep and/or anesthesia with a recent study suggesting the glymphatic activity as the mechanism for the reduction of lactate concentrations. We have recently developed a rigorous non-invasive imaging approach combining simultaneous magnetic resonance spectroscopy (MRS) and polysomnography (PSG) measurements, and here, we present the first in-vivo evaluation of brain lactate levels during sleep-wake cycles in young healthy humans. First, we collected single voxel proton MRS (1H-MRS) data at the posterior cingulate with high temporal resolution (every 7.5 sec), and simultaneously recorded PSG data while temporally registering with 1H-MRS time-series. Second, we evaluated PSG data in 30 s epochs, and classified into four stages Wake (W), Non-REM sleep stage 1 (N1), Non-REM sleep stage 2 (N2), and Non-REM sleep stage 3 (N3). Third, we determined lactate signal intensity from each 7.5-s spectrum, normalized to corresponding water signal, and averaged over 30-s for each PSG epoch. In examinations of nine healthy participants (four females, five males; mean age 24.2 (±2; SD) years; age range: 21-27 years) undergoing up to 3-hour simultaneous MRS/PSG recordings, we observed a group mean reduction of [4.9 ± 4.9] % in N1, [10.4 ± 5.2] % in N2, and [24.0 ± 5.8] % in N3 when compared to W. Our finding is consistent with more than 70 years of invasive lactate measurements from small animal studies. In addition, reduced brain lactate was accompanied by a significant reduction the apparent diffusion coefficient of brain lactate. Taken together, these findings are consistent with the loss of lactate from the extracellular space during sleep while suggesting lactate metabolism is altered and/or lactate clearance via glymphatic exchange is increased during sleep.Significance StatementThis study describes a non-invasive magnetic resonance spectroscopy/polysomnography technique that allows rigorous measurement of brain metabolite levels together with simultaneous characterization of brain arousal state as either wakeful or one of the several sleep states. The results provide the first in-vivo demonstration of reductions in brain lactate concentration and diffusivity during sleep versus wakefulness in young healthy human brain. These findings are consistent with invasive small-animal studies showing the loss of extracellular lactate during sleep, and support the notion of altered lactate metabolism and/or increased glymphatic activity in sleeping human brain.
A zebrafish model of COVID-19-associated cytokine storm syndrome reveals differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern
Authors: Tyrkalska Sylwia D. , Martínez-López Alicia , Arroyo Ana B. , Martínez-Morcillo Francisco J. , Candel Sergio , García-Moreno Diana , Mesa-del-Castillo Pablo , Cayuela María L. , Mulero Victoriano 
Published: December 2021

AbstractThe sudden and unexpected appearance of the COVID-19 pandemic turned the whole world upside down in a very short time. One of the main challenges faced has been to understand COVID-19 patient heterogeneity, as a minority develop life-threatening hyperinflammation, the so-called cytokine storm syndrome (CSS). Using the unique advantages of the zebrafish model we report here the proinflammatory role of Spike (S) proteins from different SARS-CoV-2 variants of concern after injection into the hindbrain ventricle, a cavity filled with cerebrospinal fluid to which immune cells can be easily recruited and that mimics the alveolar environment of the human lung. We found that wild type/Wuhan variant S1 (S1WT) protein promoted neutrophil and macrophage recruitment, local and systemic hyperinflammation, emergency myelopoiesis, and hemorrhages. In addition, S1γ protein was more proinflammatory and S1δ was less proinflammatory than S1WT and, strikingly, S1β promoted delayed and long-lasting inflammation. Pharmacological inhibition of the canonical inflammasome robustly alleviated S1 protein-induced inflammation and emergency myelopoiesis. In contrast, genetic inhibition of angiotensin-converting enzyme 2 strengthened the proinflammatory activity of S1, and the administration of angiopoietin (1-7) fully rescued S1-induced hyperinflammation and hemorrhages. These results shed light into the mechanisms orchestrating the COVID-19-associated CSS and the host immune response to different SARS-CoV-2 S protein variants.HighlightsS proteins of SARS-CoV-2 promote hyperinflammation, neutrophilia, monocytosis and hemorrhages in zebrafish.S protein effects in zebrafish are mediated via the canonical inflammasome and the Ace2/Angiopoietin (1-7) axis.Delta S1 is less proinflammatory than wild type S1 and fails to induce emergency myelopoiesis in zebrafish.Naïve and primed human white blood cells are unable to respond to S proteins.
PACAP-PAC1 Receptor Inhibition is Effective in Models of Opioid-Induced Medication Overuse Headache
Authors: Bertels Zachariah , Mangutov Elizaveta , Siegersma Kendra , Tipton Alycia , Pradhan Amynah A 
Published: December 2021

AbstractOpioids are regularly prescribed for migraine and can result in medication overuse headache and dependence. We recently showed that pituitary adenylate cyclase activating polypeptide (PACAP) is upregulated following opioid administration or in a model of chronic migraine. The goal of this study was to determine if PACAP was a link between opioid use and headache chronification. We tested the effect of PACAP-PAC1 receptor inhibition in novel models of opioid-exacerbated migraine pain and aura; and examined the co-expression between mu opioid receptor (MOR), PAC1, and PACAP in headache-associated brain and peripheral regions.To model opioid exacerbated migraine pain, mice were injected daily with morphine (10 mg/kg) or vehicle for 11 days. On days 3,5,7,9, and 11 they also received the known human migraine trigger nitroglycerin (0.1 mg/kg) or vehicle. To model opioid exacerbated aura, mice were treated with vehicle or morphine twice daily for 4 days (20 mg/kg on days 1-3, 40 mg/kg on day 4), a well-established paradigm for causing opioid-induced hyperalgesia. On day 5 they underwent cortical spreading depression, a physiological correlate of migraine aura. The effect of the PAC1 inhibitor, M65 (0.1 mg/kg), was tested in these models. Fluorescent in situ hybridization was used to investigate the expression of MOR, PAC1, and PACAP.Only mice treated with combined morphine and nitroglycerin developed chronic cephalic allodynia (n=18/group). M65 reversed this hypersensitivity (n=9/group). Morphine significantly increased the number of CSD events (n=8-9/group); and M65 decreased this exacerbation by morphine (n=8-12/group). PAC1 and/or PACAP were highly co-expressed with MOR, and varied by region (n=6/group). MOR and PACAP were co-expressed in the trigeminal ganglia, while MOR and PAC1 receptor showed near complete overlap in the trigeminal nucleus caudalis and periaqueductal gray. The cortex showed similar cellular co-expression between MOR-PACAP and MOR-PAC1.These results show that opioids facilitate the transition to chronic headache through induction of PACAPergic mechanisms. Antibodies or pharmacological agents targeting PACAP or PAC1 receptor may be particularly beneficial for the treatment of opioid-induced medication overuse headache.
“It was brutal. It still is”: A qualitative analysis of the challenges of bereavement during the COVID-19 pandemic reported in two national surveys
Authors: Torrens-Burton Anna , Goss Silvia , Sutton Eileen , Barawi Kali , Longo Mirella , Seddon Kathy , Carduff Emma , Farnell Damian JJ , Nelson Annmarie , Byrne Anthony , Phillips Rhiannon , Selman Lucy E. , Harrop Emily 
Published: December 2021

ABSTRACTThe COVID-19 pandemic has been a devastating, mass bereavement event characterised by sudden unexpected deaths and high levels of disruption to end-of-life, grieving and coping processes, as well as social life more broadly. We analysed qualitative free-text data from two independent UK-wide online surveys to describe in depth the experiences of 881 people bereaved during the Covid-19 pandemic using. We analysed the data in two phases, conducting an inductive thematic analysis and then applying Stroebe and Schut’s Dual Process Model (DPM) (1999; 2010) as an analytic lens to further contextualise and interpret the data. The DPM identifies loss-oriented and restoration-oriented coping processes between which grieving people naturally oscillate. Loss-oriented coping involves coming to terms with the death and lost relationship, while restoration-oriented coping involves adapting to new ways of life. We identified six main themes: troubled deaths (guilt, anger and unanswered questions); mourning, memorialisation and death administration; mass bereavement, the media and the ongoing threat of the pandemic; grieving and coping (alone and with others); work and employment; and support from the health and social care system. Examples of loss-oriented stressors included being unable to visit or say goodbye, the sudden and traumatic nature of many deaths, and restricted funeral and memorialisation practices. Associated reactions were feelings of guilt and anger, and problems accepting the death and starting to grieve. Examples of restoration-oriented stressors and reactions were stressful death-related administration and severely curtailed social networks, support systems and social/recreational activities, which impacted people’s ability to cope. Study results demonstrate the exceptionally difficult sets of experiences associated with pandemic bereavement, and the utility of the DPM for conceptualizing these additional challenges and their impacts on grieving. Our analysis builds and expands on previous use of the DPM (Stroebe and Schut, 2021) in explicating the impact of the pandemic on bereavement. We make recommendations for statutory, private and third sector organisations for improving the experiences of people bereaved during and following this and future pandemics.
Age-specific effects of body size on fracture risk in later life: A lifecourse Mendelian randomization study
Authors: Power Grace M. , Tobias Jon H. , Frayling Timothy M. , Tyrrell Jess , Hartley April , Heron Jon , Smith George Davey , Richardson Tom G. 
Published: December 2021

AbstractMusculoskeletal conditions, including fractures, can have severe and long-lasting consequences. Higher body mass index in adulthood is widely acknowledged to be protective for most fracture sites, indicated through previous clinical and epidemiological observational research. However, the association between weight and bone health is complex and sources of bias, induced by confounding factors, may have distorted earlier findings. Employing a lifecourse Mendelian randomization (MR) approach by using genetic instruments to separate effects at different life stages, this investigation aims to explore how prepubertal and adult body size independently influence fracture risk in later life.Using data from a large UK-based prospective cohort, univariable and multivariable MR with inverse variance weighted meta-analysis were conducted to simultaneously estimate the effects of age-specific genetic proxies for body size (n=453,169) on the odds of fracture in later life (n=416,795). A two-step MR framework was additionally applied to elucidate potential mediators. Univariable and multivariable MR indicated strong evidence that higher body size in childhood reduced fracture risk in later life (OR, 95% CI: 0.89, 0.82 to 0.96, P=0.005 and OR, 95% CI: 0.76, 0.69 to 0.85, P=1×10−6, respectively). Conversely, higher body size in adulthood increased fracture risk (OR, 95% CI: 1.08, 1.01 to 1.16, P=0.023 and OR, 95% CI: 1.26, 1.14 to 1.38, P=2×10−6, respectively). Two-step MR analyses suggested that the effect of higher body size in childhood on reduced fracture risk was mediated by its influence on higher estimated bone mineral density (eBMD) in adulthood.This investigation provides novel evidence that higher body size in childhood has a direct effect on reduced fracture risk in later life through its influence on increased eBMD. Results indicate that higher body size in adulthood is a risk factor for fractures, opposing findings from earlier research. Protective effect estimates previously observed are likely attributed to childhood effects.
Neural dynamics of causal inference in the macaque frontoparietal circuit
Authors: Qi Guangyao , Fang Wen , Li Shenghao , Li Junru , Wang Liping 
Published: December 2021

ABSTRACTNatural perception relies inherently on inferring causal structure in the environment. However, the neural mechanisms and functional circuits that are essential for representing and updating the hidden causal structure and corresponding sensory representations during multisensory processing are unknown. To address this, monkeys were trained to infer the probability of a potential common source from visual and proprioceptive signals on the basis of their spatial disparity in a virtual reality system. The proprioceptive drift reported by monkeys demonstrated that they combined historical information and current multisensory signals to estimate the hidden common source and subsequently updated both the causal structure and sensory representation. Single-unit recordings in premotor and parietal cortices revealed that neural activity in premotor cortex represents the core computation of causal inference, characterizing the estimation and update of the likelihood of integrating multiple sensory inputs at a trial-by-trial level. In response to signals from premotor cortex, neural activity in parietal cortex also represents the causal structure and further dynamically updates the sensory representation to maintain consistency with the causal inference structure. Thus, our results indicate how premotor cortex integrates historical information and sensory inputs to infer hidden variables and selectively updates sensory representations in parietal cortex to support behavior. This dynamic loop of frontal-parietal interactions in the causal inference framework may provide the neural mechanism to answer long-standing questions regarding how neural circuits represent hidden structures for body-awareness and agency.
TargetGeneReg 2.0: a comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation
Authors: Fischer Martin , Riege Konstantin , Schwarz Robert , DeCaprio James A. , Hoffmann Steve 
Published: December 2021

AbstractIn recent years, our web-atlas at www.TargetGeneReg.org has enabled many researchers to uncover new biological insights and to identify novel regulatory mechanisms that affect p53 and the cell cycle – signaling pathways that are frequently dysregulated in diseases like cancer. Here, we provide a substantial upgrade of the database that comprises an extension to include non-coding genes and the transcription factors ΔNp63 and RFX7. TargetGeneReg 2.0 combines gene expression profiling and transcription factor DNA binding data to determine, for each gene, the response to p53, ΔNp63, and cell cycle signaling. It can be used to dissect common, cell type, and treatment-specific effects, identify the most promising candidates, and validate findings. We demonstrate the increased power and more intuitive layout of the resource using realistic examples.
Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation
Authors: Soskic Blagoje , Cano-Gamez Eddie , Smyth Deborah J. , Ambridge Kirsty , Ke Ziying , Bossini-Castillo Lara , Kaplanis Joanna , Ramirez-Navarro Lucia , Nakic Nikolina , Esparza-Gordillo Jorge , Rowan Wendy , Wille David , Tough David F. , Bronson Paola G. , Trynka Gosia 
Published: December 2021

AbstractDuring activation, T cells undergo extensive changes in gene expression which shape the properties of cells to exert their effector function. Therefore, understanding the genetic regulation of gene expression during T cell activation provides essential insights into how genetic variants influence the response to infections and immune diseases. We generated a single-cell map of expression quantitative trait loci (eQTL) across a T cell activation time-course. We profiled 655,349 CD4+ naive and memory T cells, capturing transcriptional states of unstimulated cells and three time points of cell activation in 119 healthy individuals. We identified 38 cell clusters, including stable clusters such as central and effector memory T cells and transient clusters that were only present at individual time points of activation, such as interferon-responding cells. We mapped eQTLs using a T cell activation trajectory and identified 6,407 eQTL genes, of which a third (2,265 genes) were dynamically regulated during T cell activation. We integrated this information with GWAS variants for immune-mediated diseases and observed 127 colocalizations, with significant enrichment in dynamic eQTLs. Immune disease loci colocalized with genes that are involved in the regulation of T cell activation, and genes with similar functions tended to be perturbed in the same direction by disease risk alleles. Our results emphasize the importance of mapping context-specific gene expression regulation, provide insights into the mechanisms of genetic susceptibility of immune diseases, and help prioritize new therapeutic targets.
Polyunsaturated fatty acid arachidonic acid increases the virulence of gut pathogen, Yersinia enterocolitica
Authors: Chac Denise , Crebs Kelly , Yee Cara , DePaolo R. William 
Published: December 2021

ABSTRACTFood-borne illnesses are a major health concern worldwide. While 1 in 6 individuals are infected in the United States yearly, there is little research into which dietary factors can alter the risk of infection. Despite evidence suggesting a correlation between obesity and enteric infection, the few reported studies focus on the role of dietary factors and the impact on host tissues and susceptibility. The direct impact of dietary constituents on the virulence of a pathogen has largely been ignored. One component of the Western diet that has been correlated with increasing inflammatory diseases is increased consumption of omega-6 polyunsaturated fatty acids such as arachidonic acid. Here, we show that arachidonic acid directly alters the pathogenicity of the food-borne pathogen Yersinia enterocolitica. Using in vitro cellular adherence assays, proteomic peptide mass fingerprint profiles and in vivo mouse models, we show that arachidonic acid can alter the pathogenesis of Y. enterocolitica by increasing proliferation and intracellular invasion. These findings have major implications in more than food safety, potentially revealing how current dietary habits may increase the virulence of food-borne pathogens.
Cistrome and transcriptome analysis identifies unique androgen receptor (AR) and AR- V7 splice variant chromatin binding and transcriptional activities
Authors: Basil Paul , Robertson Matthew J. , Bingman William E. , Dash Amit K. , Krause William C. , Shafi Ayesha A. , Piyarathna Badrajee , Coarfa Cristian , Weigel Nancy L. 
Published: December 2021

AbstractThe constitutively active androgen receptor (AR) splice variant, AR-V7, plays an important role in resistance to androgen deprivation therapy in castration resistant prostate cancer (CRPC). Studies seeking to determine whether AR-V7 is a partial mimic of the AR, or also has unique activities, and whether the AR-V7 cistrome contains unique binding sites have yielded conflicting results. One limitation in many studies has been the low level of AR variant compared to AR. Here, LNCaP and VCaP cell lines in which AR-V7 expression can be induced to match the level of AR, were used to compare the activities of AR and AR-V7. The two AR isoforms shared many targets, but overall had distinct transcriptomes. Optimal induction of novel targets sometimes required more receptor isoform than classical targets such as PSA. The isoforms displayed remarkably different cistromes with numerous differential binding sites. Some of the unique AR-V7 sites were located proximal to the transcription start sites (TSS). A de novo binding motif similar to a half ARE was identified in many AR-V7 preferential sites and, in contrast to conventional half ARE sites that bind AR-V7, FOXA1 was not enriched at these sites. This supports the concept that the AR isoforms have unique actions with the potential to serve as biomarkers or novel therapeutic targets.