Shadowing the rotating annulus. Part II: Gradient descent in the perfect model scenario

Shadowing trajectories are model trajectories consistent with a sequence of observations of a system, given a distribution of observational noise. The existence of such trajectories is a desirable property of any forecast model. Gradient descent of indeterminism is a well-established technique for finding shadowing trajectories in low-dimensional analytical systems. Here we apply it to the thermally-driven rotating annulus, a laboratory experiment intermediate in model complexity and physical idealisation between analytical systems and global, comprehensive atmospheric models. We work in the perfect model scenario using the MORALS model to generate a sequence of noisy observations in a chaotic flow regime. We demonstrate that the gradient descent technique recovers a pseudo-orbit of model states significantly closer to a model trajectory than the initial sequence. Gradient-free descent is used, where the adjoint model is set to $\lambda$I in the absence of a full adjoint model. The indeterminism of the pseudo-orbit falls by two orders of magnitude during the descent, but we find that the distance between the pseudo-orbit and the initial, true, model trajectory reaches a minimum and then diverges from truth. We attribute this to the use of the $\lambda$-adjoint, which is well suited to noise reduction but not to finely-tuned convergence towards a model trajectory. We find that $\lambda=0.25$ gives optimal results, and that candidate model trajectories begun from this pseudo-orbit shadow the observations for up to 80 s, about the length of the longest timescale of the system, and similar to expected shadowing times based on the distance between the pseudo-orbit and the truth. There is great potential for using this method with real laboratory data.Comment: This paper was originally prepared for submission in 2011; but, after Part I was not accepted, it was not submitted. It has not been peer-reviewed. We no longer have the time or resources to work on this topic, but would like this record of our work to be available for others to read, cite, and follow up. 22 pages, 11 figure

Securing Your Relationship: Quality of Intimate Relationships During the COVID-19 Pandemic Can Be Predicted by Attachment Style

The COVID-19 pandemic along with the restrictions that were introduced within Europe starting in spring 2020 allows for the identification of predictors for relationship quality during unstable and stressful times. The present study began as strict measures were enforced in response to the rising spread of the COVID-19 virus within Austria, Poland, Spain and Czech Republic. Here, we investigated quality of romantic relationships among 313 participants as movement restrictions were implemented and subsequently phased out cross-nationally. Participants completed self-report questionnaires over a period of 7 weeks, where we predicted relationship quality and change in relationship quality using machine learning models that included a variety of potential predictors related to psychological, demographic and environmental variables. On average, our machine learning models predicted 29% (linear models) and 22% (non-linear models) of the variance with regard to relationship quality. Here, the most important predictors consisted of attachment style (anxious attachment being more influential than avoidant), age, and number of conflicts within the relationship. Interestingly, environmental factors such as the local severity of the pandemic did not exert a measurable influence with respect to predicting relationship quality. As opposed to overall relationship quality, the change in relationship quality during lockdown restrictions could not be predicted accurately by our machine learning models when utilizing our selected features. In conclusion, we demonstrate cross-culturally that attachment security is a major predictor of relationship quality during COVID-19 lockdown restrictions, whereas fear, pathogenic threat, sexual behavior, and the severity of governmental regulations did not significantly influence the accuracy of prediction

Antagonistic Role of Aqueous Complexation in the Solvent Extraction and Separation of Rare Earth Ions

Solvent extraction is used widely for chemical separations and environmental remediation. Although the kinetics and efficiency of this process rely upon the formation of ion–extractant complexes, it has proven challenging to identify the location of ion–extractant complexation within the solution and its impact on the separation. Here, we use tensiometry and X-ray scattering to characterize the surface of aqueous solutions of lanthanide chlorides and the water-soluble extractant bis(2-ethylhexyl) phosphoric acid (HDEHP), in the absence of a coexisting organic solvent. These studies restrict ion–extractant interactions to the aqueous phase and its liquid–vapor interface, allowing us to explore the consequences that one or the other is the location of ion–extractant complexation. Unexpectedly, we find that light lanthanides preferentially occupy the liquid–vapor interface. This contradicts our expectation that heavy lanthanides should have a higher interfacial density since they are preferentially extracted by HDEHP in solvent extraction processes. These results reveal the antagonistic role played by ion–extractant complexation within the aqueous phase and clarify the advantages of complexation at the interface. Extractants in common use are often soluble in water, in addition to their organic phase solubility, and similar effects to those described here are expected to be relevant to a variety of separations processes

Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains

The respiratory syncytial virus (RSV) group A variant with the 72-nucleotide duplication in the G gene, genotype ON1, was first detected in Kilifi in 2012 and has almost completely replaced previously circulating genotype GA2 strains. This replacement suggests some fitness advantage of ON1 over the GA2 viruses, and might be accompanied by important genomic substitutions in ON1 viruses. Close observation of such a new virus introduction over time provides an opportunity to better understand the transmission and evolutionary dynamics of the pathogen. We have generated and analyzed 184 RSV-A whole genome sequences (WGS) from Kilifi (Kenya) collected between 2011 and 2016, the first ON1 genomes from Africa and the largest collection globally from a single location. Phylogenetic analysis indicates that RSV-A transmission into this coastal Kenya location is characterized by multiple introductions of viral lineages from diverse origins but with varied success in local transmission. We identify signature amino acid substitutions between ON1 and GA2 viruses within genes encoding the surface proteins (G, F), polymerase (L) and matrix M2-1 proteins, some of which were identified as positively selected, and thereby provide an enhanced picture of RSV-A diversity. Furthermore, five of the eleven RSV open reading frames (ORF) (i.e. G, F, L, N and P), analyzed separately, formed distinct phylogenetic clusters for the two genotypes. This might suggest that coding regions outside of the most frequently studied G ORF play a role in the adaptation of RSV to host populations with the alternative possibility that some of the substitutions are nothing more than genetic hitchhikers. Our analysis provides insight into the epidemiological processes that define RSV spread, highlights the genetic substitutions that characterize emerging strains, and demonstrates the utility of large-scale WGS in molecular epidemiological studies

Structure and mechanism of monoclonal antibody binding to the junctional epitope of Plasmodium falciparum circumsporozoite protein.

Lasting protection has long been a goal for malaria vaccines. The major surface antigen on Plasmodium falciparum sporozoites, the circumsporozoite protein (PfCSP), has been an attractive target for vaccine development and most protective antibodies studied to date interact with the central NANP repeat region of PfCSP. However, it remains unclear what structural and functional characteristics correlate with better protection by one antibody over another. Binding to the junctional region between the N-terminal domain and central NANP repeats has been proposed to result in superior protection: this region initiates with the only NPDP sequence followed immediately by NANP. Here, we isolated antibodies in Kymab mice immunized with full-length recombinant PfCSP and two protective antibodies were selected for further study with reactivity against the junctional region. X-ray and EM structures of two monoclonal antibodies, mAb667 and mAb668, shed light on their differential affinity and specificity for the junctional region. Importantly, these antibodies also bind to the NANP repeat region with equal or better affinity. A comparison with an NANP-only binding antibody (mAb317) revealed roughly similar but statistically distinct levels of protection against sporozoite challenge in mouse liver burden models, suggesting that junctional antibody protection might relate to the ability to also cross-react with the NANP repeat region. Our findings indicate that additional efforts are necessary to isolate a true junctional antibody with no or much reduced affinity to the NANP region to elucidate the role of the junctional epitope in protection

Longitudinal associations of DNA methylation and sleep in children : a meta-analysis

Publisher Copyright: © 2022, The Author(s).Background: Sleep is important for healthy functioning in children. Numerous genetic and environmental factors, from conception onwards, may influence this phenotype. Epigenetic mechanisms such as DNA methylation have been proposed to underlie variation in sleep or may be an early-life marker of sleep disturbances. We examined if DNA methylation at birth or in school age is associated with parent-reported and actigraphy-estimated sleep outcomes in children. Methods: We meta-analysed epigenome-wide association study results. DNA methylation was measured from cord blood at birth in 11 cohorts and from peripheral blood in children (4–13 years) in 8 cohorts. Outcomes included parent-reported sleep duration, sleep initiation and fragmentation problems, and actigraphy-estimated sleep duration, sleep onset latency and wake-after-sleep-onset duration. Results: We found no associations between DNA methylation at birth and parent-reported sleep duration (n = 3658), initiation problems (n = 2504), or fragmentation (n = 1681) (p values above cut-off 4.0 × 10–8). Lower methylation at cg24815001 and cg02753354 at birth was associated with longer actigraphy-estimated sleep duration (p = 3.31 × 10–8, n = 577) and sleep onset latency (p = 8.8 × 10–9, n = 580), respectively. DNA methylation in childhood was not cross-sectionally associated with any sleep outcomes (n = 716–2539). Conclusion: DNA methylation, at birth or in childhood, was not associated with parent-reported sleep. Associations observed with objectively measured sleep outcomes could be studied further if additional data sets become available.Peer reviewe

Identification of NAD(P)H Quinone Oxidoreductase Activity in Azoreductases from P. aeruginosa: Azoreductases and NAD(P)H Quinone Oxidoreductases Belong to the Same FMN-Dependent Superfamily of Enzymes

Water soluble quinones are a group of cytotoxic anti-bacterial compounds that are secreted by many species of plants, invertebrates, fungi and bacteria. Studies in a number of species have shown the importance of quinones in response to pathogenic bacteria of the genus Pseudomonas. Two electron reduction is an important mechanism of quinone detoxification as it generates the less toxic quinol. In most organisms this reaction is carried out by a group of flavoenzymes known as NAD(P)H quinone oxidoreductases. Azoreductases have previously been separate from this group, however using azoreductases from Pseudomonas aeruginosa we show that they can rapidly reduce quinones. Azoreductases from the same organism are also shown to have distinct substrate specificity profiles allowing them to reduce a wide range of quinones. The azoreductase family is also shown to be more extensive than originally thought, due to the large sequence divergence amongst its members. As both NAD(P)H quinone oxidoreductases and azoreductases have related reaction mechanisms it is proposed that they form an enzyme superfamily. The ubiquitous and diverse nature of azoreductases alongside their broad substrate specificity, indicates they play a wide role in cellular survival under adverse conditions

Longitudinal associations of DNA methylation and sleep in children: a meta-analysis

Background: Sleep is important for healthy functioning in children. Numerous genetic and environmental factors, from conception onwards, may influence this phenotype. Epigenetic mechanisms such as DNA methylation have been proposed to underlie variation in sleep or may be an early-life marker of sleep disturbances. We examined if DNA methylation at birth or in school age is associated with parent-reported and actigraphy-estimated sleep outcomes in children. Methods: We meta-analysed epigenome-wide association study results. DNA methylation was measured from cord blood at birth in 11 cohorts and from peripheral blood in children (4-13 years) in 8 cohorts. Outcomes included parent-reported sleep duration, sleep initiation and fragmentation problems, and actigraphy-estimated sleep duration, sleep onset latency and wake-after-sleep-onset duration. Results: We found no associations between DNA methylation at birth and parent-reported sleep duration (n = 3658), initiation problems (n = 2504), or fragmentation (n = 1681) (p values above cut-off 4.0 × 10-8). Lower methylation at cg24815001 and cg02753354 at birth was associated with longer actigraphy-estimated sleep duration (p = 3.31 × 10-8, n = 577) and sleep onset latency (p = 8.8 × 10-9, n = 580), respectively. DNA methylation in childhood was not cross-sectionally associated with any sleep outcomes (n = 716-2539). Conclusion: DNA methylation, at birth or in childhood, was not associated with parent-reported sleep. Associations observed with objectively measured sleep outcomes could be studied further if additional data sets become available

Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III

Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft (“entropy reservoir”) as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies