Structure and Function of the α-Hydroxylation Bimodule of the Mupirocin Polyketide Synthase.

Mupirocin is a clinically important antibiotic produced by a trans-AT Type I polyketide synthase (PKS) in Pseudomonas fluorescens. The major bioactive metabolite, pseudomonic acid A (PA-A), is assembled on a tetrasubstituted tetrahydropyran (THP) core incorporating a 6-hydroxy group proposed to be introduced by α-hydroxylation of the thioester of the acyl carrier protein (ACP) bound polyketide chain. Herein, we describe an in vitro approach combining purified enzyme components, chemical synthesis, isotopic labelling, mass spectrometry and NMR in conjunction with in vivo studies leading to the first characterisation of the α-hydroxylation bimodule of the mupirocin biosynthetic pathway. These studies reveal the precise timing of hydroxylation by MupA, substrate specificity and the ACP dependency of the enzyme components that comprise this α-hydroxylation bimodule. Furthermore, using purified enzyme, it is shown that the MmpA KS0 shows relaxed substrate specificity, suggesting precise spatiotemporal control of in trans MupA recruitment in the context of the PKS. Finally, the detection of multiple intermodular MupA/ACP interactions suggests these bimodules may integrate MupA into their assembly.

VpROM: a novel variational autoencoder-boosted reduced order model for the treatment of parametric dependencies in nonlinear systems.

Reduced Order Models (ROMs) are of considerable importance in many areas of engineering in which computational time presents difficulties. Established approaches employ projection-based reduction, such as Proper Orthogonal Decomposition. The limitation of the linear nature of such operators is typically tackled via a library of local reduction subspaces, which requires the assembly of numerous local ROMs to address parametric dependencies. Our work attempts to define a more generalisable mapping between parametric inputs and reduced bases for the purpose of generative modeling. We propose the use of Variational Autoencoders (VAEs) in place of the typically utilised clustering or interpolation operations, for inferring the fundamental vectors, termed as modes, which approximate the manifold of the model response for any and each parametric input state. The derived ROM still relies on projection bases, built on the basis of full-order model simulations, thus retaining the imprinted physical connotation. However, it additionally exploits a matrix of coefficients that relates each local sample response and dynamics to the global phenomena across the parametric input domain. The VAE scheme is utilised for approximating these coefficients for any input state. This coupling leads to a high-precision low-order representation, which is particularly suited for problems where model dependencies or excitation traits cause the dynamic behavior to span multiple response regimes. Moreover, the probabilistic treatment of the VAE representation allows for uncertainty quantification on the reduction bases, which may then be propagated to the ROM response. The performance of the proposed approach is validated on an open-source simulation benchmark featuring hysteresis and multi-parametric dependencies, and on a large-scale wind turbine tower characterised by nonlinear material behavior and model uncertainty.

Effects of self-controlled practice and focus of attention on free throw accuracy: Exploring optimal theory among skilled basketball players.

Based on the OPTIMAL theory of motor learning (Wulf & Lewthwaite, 2016), optimal motor performance and learning will occur through the influence of the two motivational factors of enhanced expectancies and autonomy support (self-controlled practice) as well as the attentional factor of the external focus of attention. Recently, some researchers tested this theory on different motor tasks using novices. However, it seems that this theory has not been tested in skilled athletes. Therefore, the aim of the present study was to investigate the effect of self-controlled practice and focus of attention on the accuracy of free throws of skilled basketball players. The participants were 56 skilled adult basketball players (28 men; average age = 27.75 ± 3.31 years; 28 women, average age = 27.18 ± 3.63 years) who were randomly divided into two self-control and yoked groups. Each group performed 80 basketball free throw trials in four different attention conditions (external, internal, holistic, control) as a counterbalance, so that each participant made 20 basketball free throws in each attention condition. The results showed that skilled basketball players in the self-controlled group performed better than the yoked group when they could choose the color of the ball. The results also showed that focusing on external or holistic cues compared to focusing on internal cues improved basketball free throw performance in skilled players. However, the results did not show a difference between external and holistic attention with the control condition. The control condition was also similar to the internal attention condition. In summary, the results of this research could only partially support the OPTIMAL theory and showed that each of the two variables of self-controlled practice and external or holistic focus of attention separately and independently affect the motor performance of skilled basketball players and their additive effect was not observed. It is suggested that coaches try to use autonomy support as well as external or holistic focus of attention in practical situations to improve the motor performance of skilled athletes.

Avacopan for ANCA-associated vasculitis with hypoxic pulmonary haemorrhage.

BACKGROUND AND HYPOTHESIS: Pulmonary haemorrhage with hypoxia caused by ANCA-associated vasculitis (AAV) has a high early mortality. Avacopan, an oral C5a receptor antagonist, is an approved treatment for AAV, but patients with pulmonary haemorrhage requiring invasive pulmonary ventilation support were excluded from the ADVOCATE trial. METHODS: A retrospective, observational, multicentre case series of AAV patients with hypoxic pulmonary haemorrhage, requiring oxygen support or mechanical ventilation, who received avacopan. RESULTS: Eight patients (62.5% female), median age 64 years (range 17-80), seven with kidney involvement, median glomerular filtration rate (GFR) 11 (range 5-99) ml/min per 1.73m2, were followed for a median of 6 months from presentation. Seven were newly diagnosed (87.5%), five were MPO-ANCA and three PR3-ANCA positive. All had hypoxia, four requiring mechanical ventilation (three invasive and one non-invasive). Intensive care unit (ICU) stay for the four patients lasted a median of 9 days (range 6-60). Four received rituximab and cyclophosphamide combination, three rituximab and one cyclophosphamide. Four underwent plasma exchange and one received two months of daily extracorporeal membrane oxygenation (ECMO) therapy. Following the initiation of avacopan after a median of 10 days (range 2-40), pulmonary haemorrhage resolved in all patients, even two who had one month of refractory pulmonary haemorrhage prior to avacopan. Additionally, after one month, the median prednisolone dose was 5 mg/day (range 0-50), with three patients successfully discontinuing steroid use. Two patients suffered serious infections, two discontinued avacopan, one permanently due to a rash and one temporarily after three months due to neutropenia. All patients survived and no re-hospitalization occurred. CONCLUSION: We report the use of avacopan as a component of the treatment for pulmonary haemorrhage with hypoxia in AAV. Despite the life-threatening presentations all patients recovered, but attribution of the positive outcomes to avacopan is limited by the concomitant therapies and retrospective observational design.

BioNAR: an integrated biological network analysis package in bioconductor.

Motivation: Biological function in protein complexes emerges from more than just the sum of their parts: molecules interact in a range of different sub-complexes and transfer signals/information around internal pathways. Modern proteomic techniques are excellent at producing a parts-list for such complexes, but more detailed analysis demands a network approach linking the molecules together and analysing the emergent architectural properties. Methods developed for the analysis of networks in social sciences have proven very useful for splitting biological networks into communities leading to the discovery of sub-complexes enriched with molecules associated with specific diseases or molecular functions that are not apparent from the constituent components alone. Results: Here, we present the Bioconductor package BioNAR, which supports step-by-step analysis of biological/biomedical networks with the aim of quantifying and ranking each of the network's vertices based on network topology and clustering. Examples demonstrate that while BioNAR is not restricted to proteomic networks, it can predict a protein's impact within multiple complexes, and enables estimation of the co-occurrence of metadata, i.e. diseases and functions across the network, identifying the clusters whose components are likely to share common function and mechanisms. Availability and implementation: The package is available from Bioconductor release 3.17: https://bioconductor.org/packages/release/bioc/html/BioNAR.html.

Structure and Function of the α-Hydroxylation Bimodule of the Mupirocin Polyketide Synthase.

Mupirocin is a clinically important antibiotic produced by a trans-AT Type I polyketide synthase (PKS) in Pseudomonas fluorescens. The major bioactive metabolite, pseudomonic acid A (PA-A), is assembled on a tetrasubstituted tetrahydropyran (THP) core incorporating a 6-hydroxy group proposed to be introduced by α-hydroxylation of the thioester of the acyl carrier protein (ACP) bound polyketide chain. Herein, we describe an in vitro approach combining purified enzyme components, chemical synthesis, isotopic labelling, mass spectrometry and NMR in conjunction with in vivo studies leading to the first characterisation of the α-hydroxylation bimodule of the mupirocin biosynthetic pathway. These studies reveal the precise timing of hydroxylation by MupA, substrate specificity and the ACP dependency of the enzyme components that comprise this α-hydroxylation bimodule. Furthermore, using purified enzyme, it is shown that the MmpA KS0 shows relaxed substrate specificity, suggesting precise spatiotemporal control of in trans MupA recruitment in the context of the PKS. Finally, the detection of multiple intermodular MupA/ACP interactions suggests these bimodules may integrate MupA into their assembly.

Extreme pulses in gain-switched semiconductor lasers.

Semiconductor lasers subjected to strong current modulation produce gain-switched optical pulse trains. These lasers can also produce pulse trains at sub-harmonic repetition rates relative to the driving current modulation. We experimentally observe, and numerically model, that these pulse trains can be interrupted by single-cycle extreme pulses whose characteristics and statistics are similar to rogue waves. Modeling indicates that drops in the circulating optical power in the optical cavity precede the appearance of extreme pulses. At the single photon level, the stochastic source terms in the optical field equation dominate the circulating optical power.

Could the Emergency Department Facilitate the Start of a Holistic Follow-Up Pathway for Patients Recovering from COVID-19?

Background: For many patients suffering from COVID-19, Emergency Departments (ED) facilitate the first contact with clinicians. There is a high rate of psychiatric symptoms in COVID-19 survivors, including anxiety, depression, fatigue and sleep disturbance, which persist months after the acute phase. Aims: To investigate if COVID-19 patients discharged from ED have a higher prevalence of mental health symptoms than those admitted.In addition, this study will investigate if discharged ED patients who now require COVID-19 follow-up with the respiratory team had a higher prevalence of mental health symptoms than admitted patients requiring follow-up. Methods: This was a retrospective cohort study (n = 472) with the PHQ2 and GAD-2 scoring systems to quantify current anxiety and depression symptoms via a telephone consultation. Results: The PHQ-2 and GAD-2 scores were significantly higher for discharged ED patients than the admitted patients. There was a higher proportion of females with a positive PHQ2 or GAD-2 score. Of the patients requiring respiratory follow-up, discharged ED patients were more likely to have a positive PHQ-2 or GAD-2 score than those admitted. Conclusions: Clinicians should maintain a low threshold for referring patients with psychiatric complaints post-COVID alongside respiratory symptoms irrespective of admission. It is imperative that available psychological services, crisis lines and other avenues of support post-COVID-19 are signposted to patients before discharge to facilitate earlier intervention.

Effects of attentional focus and cognitive load on novice dart throwing: Evidence from quiet eye duration and pupillary responses.

The purpose of the present study was to investigate the effects of attentional focus and cognitive-load on motor performance, quiet-eye-duration, and pupil dilation. 18 participants completed a dart throwing task under four conditions, internal or external focus with high or low cognitive-load. Cognitive-load was created by a secondary tone detection task. During each trial participants pupil size and eye movements were recorded along with accuracy data of the dart throw. Results revealed that decreased cognitive-load increased accuracy while high load increased pupil size (p's < 0.05). An external focus resulted in the greatest accuracy while an external focus with high cognitive-load resulted in the longest quiet-eye-durations (p's < 0.05). Based on these findings an increase in pupil size is related to greater cognitive-load but doesn't explain the improvement in task performance. Likewise, an external focus of attention improved performance but was not strongly related to quiet-eye-duration. Results are further discussed in the article.

EFSUMB Clinical Practice Guidelines for Point-of-Care Ultrasound: Part One (Common Heart and Pulmonary Applications) SHORT VERSION.

OBJECTIVE: To evaluate the evidence and produce a summary and recommendations for the most common heart and lung point-of-care ultrasound (PoCUS). METHODS: We reviewed 10 clinical domains/questions related to common heart and lung applications of PoCUS. Following review of the evidence, a summary and recommendations were produced, including assigning levels of evidence (LoE) and grading of recommendation, assessment, development, and evaluation (GRADE). 38 international experts, the expert review group (ERG), were invited to review the evidence presented for each question. A level of agreement of over 75 % was required to progress to the next section. The ERG then reviewed and indicated their level of agreement of the summary and recommendation for each question (using a 5-point Likert scale), which was approved in the case of a level of agreement of greater than 75 %. A level of agreement was defined as a summary of "strongly agree" and "agree" on the Likert scale responses. FINDINGS AND RECOMMENDATIONS: One question achieved a strong consensus for an assigned LoE of 3 and a weak GRADE recommendation (question 1), the remaining 9 questions achieved broad agreement with an assigned LoE of 4 and a weak GRADE recommendation (question 2), three achieved an LoE of 3 with a weak GRADE recommendation (questions 3-5), three achieved an LoE of 3 with a strong GRADE recommendation (questions 6-8) and the remaining two were assigned an LoE of 2 with a strong GRADE recommendation (questions 9 and 10). CONCLUSION: These consensus-derived recommendations should aid clinical practice and highlight areas of further research for PoCUS in acute settings.

EFSUMB Clinical Practice Guidelines for Point-of-Care Ultrasound: Part One (Common Heart and Pulmonary Applications) LONG VERSION.

AIMS: To evaluate the evidence and produce a summary and recommendations for the most common heart and lung applications of point-of-care ultrasound (PoCUS). METHODS: We reviewed 10 clinical domains/questions related to common heart and lung applications of PoCUS. Following review of the evidence, a summary and recommendation were produced, including assignment of levels of evidence (LoE) and grading of the recommendation, assessment, development, and evaluation (GRADE). 38 international experts, the expert review group (ERG), were invited to review the evidence presented for each question. A level of agreement of over 75 % was required to progress to the next section. The ERG then reviewed and indicated their level of agreement regarding the summary and recommendation for each question (using a 5-point Likert scale), which was approved if a level of agreement of greater than 75 % was reached. A level of agreement was defined as a summary of "strongly agree" and "agree" on the Likert scale responses. FINDINGS AND RECOMMENDATIONS: One question achieved a strong consensus for an assigned LoE of 3 and a weak GRADE recommendation (question 1). The remaining 9 questions achieved broad agreement with one assigned an LoE of 4 and weak GRADE recommendation (question 2), three achieving an LoE of 3 with a weak GRADE recommendation (questions 3-5), three achieved an LoE of 3 with a strong GRADE recommendation (questions 6-8), and the remaining two were assigned an LoE of 2 with a strong GRADE recommendation (questions 9 and 10). CONCLUSION: These consensus-derived recommendations should aid clinical practice and highlight areas of further research for PoCUS in acute settings.

The 'emodin family' of fungal natural products-amalgamating a century of research with recent genomics-based advances.

Covering: up to 2022A very large group of biosynthetically linked fungal secondary metabolites are formed via the key intermediate emodin and its corresponding anthrone. The group includes anthraquinones such as chrysophanol and cladofulvin, the grisandienes geodin and trypacidin, the diphenyl ether pestheic acid, benzophenones such as monodictyphenone and various xanthones including the prenylated shamixanthones, the agnestins and dimeric xanthones such as the ergochromes, cryptosporioptides and neosartorin. Such compounds exhibit a wide range of bioactivities and as such have been utilised in traditional medicine for centuries, as well as garnering more recent interest from the pharmaceutical sector. Additional interest comes from industries such as textiles and cosmetics due to their use as natural colourants. A variety of biosynthetic routes and mechanisms have been proposed for this family of compounds, being altered and updated as new biosynthetic methods develop and new results emerge. After nearly 100 years of such research, this review aims to provide a comprehensive overview of what is currently known about the biosynthesis of this important family, amalgamating the early chemical and biosynthetic studies with the more recent genetics-based advances and comparative bioinformatics.

Naturally Occurring Partially Reduced Perylenequinones from Fungi.

This Review provides a critical analysis of the literature covering the naturally occurring partially reduced perylenequinones (PQs) from fungi without carbon substituents (which can be named class A perylenequinones) and discusses their structures, stereochemistry, biosynthesis, and biological activities as appropriate. Perylenequinones are natural pigments with a perylene skeleton produced by certain fungi, aphids, some plants, and animal species. These compounds display several biological activities, e.g., antimicrobial, anti-HIV, photosensitizers, cytotoxic, and phytotoxic. It describes 36 fungal PQs and cites 81 references, covering from 1956 to August 2022.

Effect of acute depression associated with COVID-19 infection on health-seeking behaviour: a psychiatrist's personal account and case report.

BACKGROUND: Despite the abundant research on COVID-19-related mental health problems, little attention has been paid to acute depression occurring concurrently with the infection as a neuropsychiatric manifestation. This is important because depression is known to adversely affect help-seeking. Decreased help-seeking is likely to be aggravated by the isolation measures demanded as part of fighting the pandemic, given the disruption of social support networks. AIMS: To study the effects of acute depression associated with COVID-19 infection on help-seeking behaviour. METHOD: We present a case report and personal account of a patient psychiatrist who developed a first onset of acute depression as part of COVID-19 infection. RESULTS: Despite being a mental health expert the patient lacked insight into his mood change and its negative effect on help-seeking behaviour, resulting in reliance on a family caregiver to raise the alarm. CONCLUSIONS: For those experiencing this complex interaction between COVID-19 infection and the brain, social support will be needed to ensure timely presentation to the healthcare system. Greater attention to behavioural change as part of COVID-19 infection is needed to optimise treatment outcome.

Cladobotric Acids: Metabolites from Cultures of Cladobotryum sp., Semisynthetic Analogues and Antibacterial Activity.

Three new polyketide-derived natural products, cladobotric acids G-I (1-3), and six known metabolites (4, 5, 8-11) were isolated from fermentation of the fungus Cladobotryum sp. grown on rice. Their structures were elucidated by extensive spectroscopic methods. Two metabolites, cladobotric acid A (4) and pyrenulic acid A (10), were converted to a series of new products (12-20) by semisynthesis. The antibacterial activities of all these compounds were investigated against the Gram-positive pathogen Staphylococcus aureus including methicillin-susceptible (MSSA), methicillin-resistant and vancomycin-intermediate (MRSA/VISA), and heterogeneous vancomycin-intermediate (hVISA) strains. Results of these antibacterial assays revealed structural features of the unsaturated decalins important for biological activity.

A virtual versus blended learning approach to higher education during the COVID-19 pandemic: The experiences of a sport and exercise science student cohort.

During the 2020/21 academic year most UK universities rapidly developed learning material as part of a move to blended learning, in response to the COVID-19 pandemic. This was interspersed with periods of virtual-only delivery, aligning with national lockdowns. The previous literature suggests there are both advantages and disadvantages to virtual-only and blended learning approaches, which may impact on student satisfaction. Student satisfaction scores may be especially insightful in a student cohort enrolled on an applied sport programme, whereby practical seminars and assessments would be severely impacted by social restrictions. Therefore, this study aimed to explore the experiences and perceptions of virtual and blended learning approaches in an undergraduate sport and exercise sciences cohort, during the COVID-19 pandemic. Additionally, this study aimed to explore whether student perceptions of both learning modes differed between and within-year groups. Students completed an adapted version of the national student survey (NSS), pertaining to periods of virtual learning-only (n = 81) and blended learning (n = 62). When all students were considered, blended learning yielded consistently higher satisfaction scores across all survey sub-sections (teaching on my course, learning opportunities, assessment and feedback, academic support, organisation and management, learning resources, learning community and student voice) resulting in a significantly higher overall course satisfaction score (3.93 ± 0.99 vs 3.55 ± 1.11; p = 0.33; ES = 0.36). When comparing Year 1 and Year 2 students, the former had significantly higher (p < 0.005) perception scores for teaching on my course, assessment and feedback, academic support, organisation and management, learning resources and learning community, but not learning opportunities, student voice or Covid-19-specific, for the virtual learning survey. Additionally, within-year group (Year 2) differences were found in assessment and feedback, academic support and learning community, with higher perception scores reported in the blended learning survey. No significant within-year group differences were observed in Year 1 students. This study provides the first data on student perceptions of a sport and exercise science programme during blended and virtual learning, amidst a global pandemic. The clear preference for blended learning in the current study, suggests sport and exercise science students appreciated the access to face-to-face teaching, despite the social distancing measures in place. Broadly, the findings may assist in governmental and institutional decision making, and in the designing of learning material during periods of social restrictions. These findings may be more beneficial to the design and implementation of face-to-face and/or online components for more applied, science-based courses.

Treatment of chronic or relapsing COVID-19 in immunodeficiency.

BACKGROUND: Patients with some types of immunodeficiency can experience chronic or relapsing infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This leads to morbidity and mortality, infection control challenges, and the risk of evolution of novel viral variants. The optimal treatment for chronic coronavirus disease 2019 (COVID-19) is unknown. OBJECTIVE: Our aim was to characterize a cohort of patients with chronic or relapsing COVID-19 disease and record treatment response. METHODS: We conducted a UK physician survey to collect data on underlying diagnosis and demographics, clinical features, and treatment response of immunodeficient patients with chronic (lasting ≥21 days) or relapsing (≥2 episodes) of COVID-19. RESULTS: We identified 31 patients (median age 49 years). Their underlying immunodeficiency was most commonly characterized by antibody deficiency with absent or profoundly reduced peripheral B-cell levels; prior anti-CD20 therapy, and X-linked agammaglobulinemia. Their clinical features of COVID-19 were similar to those of the general population, but their median duration of symptomatic disease was 64 days (maximum 300 days) and individual patients experienced up to 5 episodes of illness. Remdesivir monotherapy (including when given for prolonged courses of ≤20 days) was associated with sustained viral clearance in 7 of 23 clinical episodes (30.4%), whereas the combination of remdesivir with convalescent plasma or anti-SARS-CoV-2 mAbs resulted in viral clearance in 13 of 14 episodes (92.8%). Patients receiving no therapy did not clear SARS-CoV-2. CONCLUSIONS: COVID-19 can present as a chronic or relapsing disease in patients with antibody deficiency. Remdesivir monotherapy is frequently associated with treatment failure, but the combination of remdesivir with antibody-based therapeutics holds promise.

Interprofessional teamwork for managing medical deterioration in pregnancy: what contributes to good clinical performance in simulated practice?

OBJECTIVES: To identify the patterns of teamwork displayed by interprofessional teams during simulated management of medical deterioration in pregnancy and examine whether and how they are related to clinical performance in simulated practice. DESIGN: Exploratory observational cohort study. SETTING: Interprofessional clinical simulation training with scenarios involving the management of medical deterioration in pregnant women. PARTICIPANTS: Seventeen simulated scenarios involving 62 qualified healthcare staff working within the National Health Service attending clinical simulation training (midwives (n=18), obstetricians (n=24) and medical physicians (n=20)). MAIN OUTCOME MEASURES: Teamwork behaviours over time, obtained through detailed observational analysis of recorded scenarios, using the Temporal Observational Analysis of Teamwork (TOAsT) framework. Clinician rated measures of simulated clinical performance. RESULTS: Scenarios with better simulated clinical performance were characterised by shared leadership between obstetricians and midwives at the start of the scenario, with obstetricians delegating less and midwives disseminating rationale, while both engaged in more information gathering behaviour. Towards the end of the scenario, better simulated clinical performance was associated with dissemination of rationale to the team. More delegation at the start of a scenario was associated with less spontaneous sharing of information and rationale later in the scenario. Teams that shared their thinking at the start of a scenario continued to do so over time. CONCLUSIONS: Teamwork during the opening moments of a clinical situation is critical for simulated clinical performance in the interprofessional management of medical deterioration in pregnancy. Shared leadership and the early development of the shared mental model are associated with better outcomes.

Mixing and matching genes of marine and terrestrial origin in the biosynthesis of the mupirocin antibiotics.

With growing understanding of the underlying pathways of polyketide biosynthesis, along with the continual expansion of the synthetic biology toolkit, it is becoming possible to rationally engineer and fine-tune the polyketide biosynthetic machinery for production of new compounds with improved properties such as stability and/or bioactivity. However, engineering the pathway to the thiomarinol antibiotics has proved challenging. Here we report that genes from a marine Pseudoalternomonas sp. producing thiomarinol can be expressed in functional form in the biosynthesis of the clinically important antibiotic mupirocin from the soil bacterium Pseudomonas fluorescens. It is revealed that both pathways employ the same unusual mechanism of tetrahydropyran (THP) ring formation and the enzymes are cross compatible. Furthermore, the efficiency of downstream processing of 10,11-epoxy versus 10,11-alkenic metabolites are comparable. Optimisation of the fermentation conditions in an engineered strain in which production of pseudomonic acid A (with the 10,11-epoxide) is replaced by substantial titres of the more stable pseudomonic acid C (with a 10,11-alkene) pave the way for its development as a more stable antibiotic with wider applications than mupirocin.