Developing an online knowledge sharing platform and community of practice for health professionals: Experiences from C-WorKS developed in North East England and Yorkshire during COVID-19.

BACKGROUND: Although knowledge sharing online has been recognised as an important strategy for health professionals to apply research findings to their practice, limited research exists on how to develop and implement these platforms to help facilitate collaboration and knowledge sharing. OBJECTIVES: This study evaluated an online knowledge sharing platform and community of practice developed in the North East of England and Yorkshire during COVID-19 to support UK health and care professionals to reduce the impact of the wider consequences of COVID-19. METHODS: Semi-structured interviews with stakeholders (n = 8) and users of C-WorKS (n = 13), followed by an online survey (n = 19) among a wider group of users to analyse knowledge use. RESULTS: Interview and survey findings highlighted several strengths, weaknesses, opportunities and threats to support future development of online knowledge sharing platforms. DISCUSSION: Online knowledge sharing supports six 'pillars' of successful research and innovation partnerships. This requires distributed forms of leadership and linking of different knowledge sharing strategies, and careful combination of platforms with communities of practice. CONCLUSION: Online knowledge sharing provides pragmatic and timely strategies for health professionals in the UK to apply research evidence to their practice. Our study provides generalisable, practical insights in how to develop and implement a knowledge sharing platform.

PHA is not just a bioplastic!

Polyhydroxyalkanoates (PHA) have evolved into versatile biopolymers, transcending their origins as mere bioplastics. This extensive review delves into the multifaceted landscape of PHA applications, shedding light on the diverse industries that have harnessed their potential. PHA has proven to be an invaluable eco-conscious option for packaging materials, finding use in films foams, paper coatings and even straws. In the textile industry, PHA offers a sustainable alternative, while its application as a carbon source for denitrification in wastewater treatment showcases its versatility in environmental remediation. In addition, PHA has made notable contributions to the medical and consumer sectors, with various roles ranging from 3D printing, tissue engineering implants, and cell growth matrices to drug delivery carriers, and cosmetic products. Through metabolic engineering efforts, PHA can be fine-tuned to align with the specific requirements of each industry, enabling the customization of material properties such as ductility, elasticity, thermal conductivity, and transparency. To unleash PHA's full potential, bridging the gap between research and commercial viability is paramount. Successful PHA production scale-up hinges on establishing direct supply chains to specific application domains, including packaging, food and beverage materials, medical devices, and agriculture. This review underscores that PHA's future rests on ongoing exploration across these industries and more, paving the way for PHA to supplant conventional plastics and foster a circular economy.

Nonsterile microbial production of chemicals based on Halomonas spp.

The use of extremophile organisms such as Halomomas spp. can eliminate the need for fermentation sterilization, significantly reducing process costs. Microbial fermentation is considered a pivotal strategy to reduce reliance on fossil fuel resources; however, sustainable processes continue to incur higher costs than their chemical industry counterparts. Most organisms require equipment sterilization to prevent contamination, a practice that introduces complexity and financial strain. Fermentations involving extremophile organisms can eliminate the sterilization process, relying instead on conditions that are conductive solely to the growth of the desired organism. This review discusses current challenges in pilot- and industrial-scale bioproduction when using the extremophile bacteria Halomomas spp. under nonsterile conditions.

A bacterial sensor taxonomy across earth ecosystems for machine learning applications.

Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes. We hypothesized that an ecosystem's unique stimuli leave a sensor "fingerprint," able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection's nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient's disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.IMPORTANCEMicrobes infect, colonize, and proliferate due to their ability to sense and respond quickly to their surroundings. In this research, we extract the sensory proteins from a diverse range of environmental, engineered, and host-associated metagenomes. We trained machine learning classifiers using sensors as features such that it is possible to predict the ecosystem for a metagenome from its sensor profile. We use the optimized model's feature importance to identify the most impactful and predictive sensors in different environments. We next use the sensor profile from human gut metagenomes to classify their disease states and explore which sensors can explain differences between diseases. The sensors most predictive of environmental labels here, most of which correspond to uncharacterized proteins, are a useful starting point for the discovery of important environment signals and the development of possible diagnostic interventions.

Metabolic engineering of Halomonas bluephagenesis for production of five carbon molecular chemicals derived from L-lysine.

5-Aminovaleric acid (5-AVA), 5-hydroxyvalerate (5HV), copolymer P(3HB-co-5HV) of 3-hydroxybutyrate (3HB) and 5HV were produced from L-lysine as a substrate by recombinant Halomonas bluephagenesis constructed based on codon optimization, deletions of competitive pathway and L-lysine export protein, and three copies of davBA genes encoding L-lysine monooxygenase (DavB) and 5-aminovaleramide amidohydrolase (DavA) inserted into its genome to form H. bluephagenesis YF117ΔgabT1+2, which produced 16.4 g L-1 and 67.4 g L-1 5-AVA in flask cultures and in 7 L bioreactor, respectively. It was able to de novo synthesize 5-AVA from glucose by L-lysine-overproducing H. bluephagenesis TD226. Corn steep liquor was used instead of yeast extract for cost reduction during the 5-AVA production. Using promoter engineering based on Pporin mutant library for downstream genes, H. bluephagenesis YF117 harboring pSEVA341-Pporin42-yqhDEC produced 6 g L-1 5HV in shake flask growth, while H. bluephagenesis YF117 harboring pSEVA341-Pporin42-yqhDEC-Pporin278-phaCRE-abfT synthesized 42 wt% P(3HB-co-4.8 mol% 5HV) under the same condition. Thus, H. bluephagenesis was successfully engineered to produce 5-AVA and 5HV in supernatant and intracellular P(3HB-co-5HV) utilizing L-lysine as the substrate.

Recent Developments in Atomic Layer Deposition of Functional Overlayers in Perovskite Solar Cells.

Over the last decade, research in organic-inorganic lead halide perovskite solar cells (PSCs) has gathered unprecedented momentum, putting the technology on the brink of full-scale commercialization. A wide range of strategies have been implemented for enhancing the power conversion efficiency of devices and modules, as well as improving stability toward high levels of irradiation, temperature, and humidity. Another key element in the path to commercialization is the scalability of device manufacturing, which requires large-scale deposition of conformal layers without compromising the delicate structure of the perovskite film. In this context, atomic layer deposition (ALD) tools excel in depositing high-quality conformal films with precise control of film composition and thickness over large areas at relatively low processing temperatures. In this commentary, we will briefly outline recent progress in PSC technology enabled by ALD tools, focusing on layers deposited above the absorber layer. These interlayers include charge transport layers, passivation layers, buffer layers, and encapsulation techniques. Additionally, we will discuss some of the challenges and potential avenues for research in PSC technology underpinned by ALD tools.

Chemoautotrophic production of gaseous hydrocarbons, bioplastics and osmolytes by a novel Halomonas species.

BACKGROUND: Production of relatively low value, bulk commodity chemicals and fuels by microbial species requires a step-change in approach to decrease the capital and operational costs associated with scaled fermentation. The utilisation of the robust and halophilic industrial host organisms of the genus Halomonas could dramatically decrease biomanufacturing costs owing to their ability to grow in seawater, using waste biogenic feedstocks, under non-sterile conditions. RESULTS: We describe the isolation of Halomonas rowanensis, a novel facultative chemoautotrophic species of Halomonas from a natural brine spring. We investigated the ability of this species to produce ectoine, a compound of considerable industrial interest, under heterotrophic conditions. Fixation of radiolabelled NaH14CO3 by H. rowanensis was confirmed in mineral medium supplied with thiosulfate as an energy source. Genome sequencing suggested carbon fixation proceeds via a reductive tricarboxylic acid cycle, and not the Calvin-Bensen-Bassham cycle. The mechanism of energy generation to support chemoautotrophy is unknown owing to the absence of an annotated SOX-based thiosulfate-mediated energy conversion system. We investigated further the biotechnological potential of the isolated H. rowanensis by demonstrating production of the gaseous hydrocarbon (bio-propane), bioplastics (poly-3-hydroxybutyrate) and osmolytes (ectoine) under heterotrophic and autotrophic CO2 fixation growth conditions. CONCLUSIONS: This proof-of-concept study illustrates the value of recruiting environmental isolates as industrial hosts for chemicals biomanufacturing, where CO2 utilisation could replace, or augment, the use of biogenic feedstocks in non-sterile, industrialised bioreactors.

Investigation of machine learning algorithms for taxonomic classification of marine metagenomes.

Microbial communities play key roles in ocean ecosystems through regulation of biogeochemical processes such as carbon and nutrient cycling, food web dynamics, and gut microbiomes of invertebrates, fish, reptiles, and mammals. Assessments of marine microbial diversity are therefore critical to understanding spatiotemporal variations in microbial community structure and function in ocean ecosystems. With recent advances in DNA shotgun sequencing for metagenome samples and computational analysis, it is now possible to access the taxonomic and genomic content of ocean microbial communities to study their structural patterns, diversity, and functional potential. However, existing taxonomic classification tools depend upon manually curated phylogenetic trees, which can create inaccuracies in metagenomes from less well-characterized communities, such as from ocean water. Herein, we explore the utility of deep learning tools-DeepMicrobes and a novel Residual Network architecture-that leverage natural language processing and convolutional neural network architectures to map input sequence data (k-mers) to output labels (taxonomic groups) without reliance on a curated taxonomic tree. We trained both models using metagenomic reads simulated from marine microbial genomes in the MarRef database. The performance of both models (accuracy, precision, and percent microbe predicted) was compared with the standard taxonomic classification tool Kraken2 using 10 complex metagenomic data sets simulated from MarRef. Our results demonstrate that time, compute power, and microbial genomic diversity still pose challenges for machine learning (ML). Moreover, our results suggest that high genome coverage and rectification of class imbalance are prerequisites for a well-trained model, and therefore should be a major consideration in future ML work. IMPORTANCE Taxonomic profiling of microbial communities is essential to model microbial interactions and inform habitat conservation. This work develops approaches in constructing training/testing data sets from publicly available marine metagenomes and evaluates the performance of machine learning (ML) approaches in read-based taxonomic classification of marine metagenomes. Predictions from two models are used to test accuracy in metagenomic classification and to guide improvements in ML approaches. Our study provides insights on the methods, results, and challenges of deep learning on marine microbial metagenomic data sets. Future machine learning approaches can be improved by rectifying genome coverage and class imbalance in the training data sets, developing alternative models, and increasing the accessibility of computational resources for model training and refinement.

Pediatric chronic hand eczema: Epidemiology, clinical presentation, and management.

Chronic hand eczema (CHE) is persistent inflammatory dermatitis that may significantly affect the quality of life, with psychosocial effects, impact on school, work, and leisure activities, influence on socioeconomic status, and high health care costs. Pediatric-CHE (P-CHE) has a high prevalence yet has not been extensively studied in children and adolescents. There is minimal published data on P-CHE in North America, and no specific management guidelines. Limited prevalence data show broad ranges (0.9%-4.4%) in preschool and school children, with 1 study stating up to 10.0% 1-year prevalence for ages 16 to 19 years. Atopic dermatitis and allergic contact dermatitis appear important in the pathogenesis of this disease process, although there is limited pediatric data assessing disease associations and no standardized methodology for evaluating this disorder. Given the potential life-changing consequences of P-CHE, further research into this disease process is warranted to help generate best therapeutic practices and minimize this disease process' morbidity in adulthood.

Online Omics Platform Expedites Industrial Application of Halomonas bluephagenesis TD1.0.

Multi-omic data mining has the potential to revolutionize synthetic biology especially in non-model organisms that have not been extensively studied. However, tangible engineering direction from computational analysis remains elusive due to the interpretability of large datasets and the difficulty in analysis for non-experts. New omics data are generated faster than our ability to use and analyse results effectively, resulting in strain development that proceeds through classic methods of trial-and-error without insight into complex cell dynamics. Here we introduce a user-friendly, interactive website hosting multi-omics data. Importantly, this new platform allows non-experts to explore questions in an industrially important chassis whose cellular dynamics are still largely unknown. The web platform contains a complete KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis derived from principal components analysis, an interactive bio-cluster heatmap analysis of genes, and the Halomonas TD1.0 genome-scale metabolic (GEM) model. As a case study of the effectiveness of this platform, we applied unsupervised machine learning to determine key differences between Halomonas bluephagenesis TD1.0 cultivated under varied conditions. Specifically, cell motility and flagella apparatus are identified to drive energy expenditure usage at different osmolarities, and predictions were verified experimentally using microscopy and fluorescence labelled flagella staining. As more omics projects are completed, this landing page will facilitate exploration and targeted engineering efforts of the robust, industrial chassis H bluephagenesis for researchers without extensive bioinformatics background.

Diagnosis and Management of Pediatric Chronic Hand Eczema: The PeDRA CACHES Survey.

BACKGROUND: Chronic hand eczema (CHE) significantly impacts quality of life. Published literature on pediatric CHE (P-CHE) in North America including knowledge on epidemiology and standard evaluation and management is limited. OBJECTIVE: Our objective was to assess diagnostic practices when evaluating patients with P-CHE in the US and Canada, produce data on therapeutic agent prescribing practices for the disorder, and lay the foundation for future studies. METHODS: We surveyed pediatric dermatologists to collect data on clinician and patient population demographics, diagnostic methods, therapeutic agent selection, among other statistics. From June 2021 to January 2022, a survey was distributed to members of the Pediatric Dermatology Research Alliance (PeDRA). RESULTS: Fifty PeDRA members responded stating that they would be interested in participating, and 21 surveys were completed. For patients with P-CHE, providers most often utilize the diagnoses of irritant contact dermatitis, allergic contact dermatitis, dyshidrotic hand eczema, and atopic dermatitis. Contact allergy patch testing and bacterial hand culture are the most used tests for workup. Nearly all utilize topical corticosteroids as first line therapy. Most responders report that they have treated fewer than six patients with systemic agents and prefer dupilumab as first-line systemic therapy. CONCLUSIONS: This is the first characterization of P-CHE among pediatric dermatologists in the United States and Canada. This assessment may prove useful in designing further investigations including prospective studies of P-CHE epidemiology, morphology, nomenclature, and management.

Efficacy of a Primary Care-Based Mobile Application to Increase Hepatitis C Screening Among Asian Americans: A Secondary Analysis of a Randomized Clinical Trial.

Background: Hepatitis C virus (HCV) screening remains suboptimal. We assessed the efficacy of a mobile application and provider alert in enhancing HCV screening among Asian Americans. Methods: A secondary analysis of a cluster-randomized clinical trial was performed during the birth cohort screening era to assess the efficacy of a Hepatitis App (intervention), a multilingual mobile application delivering interactive video education on viral hepatitis and creating a Provider Alert printout, at primary care clinics within 2 healthcare systems in San Francisco from 2015 to 2017. A comparison group received usual care and a similar intervention on nutrition and physical activity. The outcome was electronic health record (EHR) documentation of HCV screening along with patient-provider communication about testing and test ordering. Results: Four hundred fifty-two participants (mean age 57 years, 36% male, 80% foreign-born) were randomized by provider clusters to the intervention (n = 270) or comparison groups (n = 182). At 3-month follow up, the intervention group was more likely than the comparison group to be aware of HCV (75% vs 59%, P = .006), to discuss HCV testing with their providers (63% vs 13%, P < .001), to have HCV testing ordered (39% vs 10%, P < .001), and to have EHR-verified HCV testing (30% vs 6%, P < .001). Within the intervention group, being born between 1945 and 1965 (odds ratio, 3.15; 95% confidence interval, 1.35-7.32) was associated with increased HCV testing. Conclusions: The Hepatitis App delivered in primary care settings was effective in increasing HCV screening in a socioeconomically diverse Asian American cohort. This highlights the importance of mobile technology as a patient-centered strategy to address gaps in HCV care.

Assessing pain catastrophizing and functional disability in pediatric epidermolysis bullosa patients.

BACKGROUND/OBJECTIVES: The primary objective was to assess pain catastrophizing and functional disability in pediatric patients with epidermolysis bullosa (EB) and their parents/guardians. Secondary objectives included examining relationships between pain catastrophizing, functional disability, and correlations with other factors (e.g., age, disease severity, and percent of body surface area (BSA) involved). METHODS: Patients with EB ages 8-16 and their parents/guardians who were English or Spanish speaking completed a one-time online survey. Parent measures included: demographics questionnaire, Pain Catastrophizing Scale-Parent (PCS), and Parent Functional Disability Inventory (FDI). Child measures included: PCS child and child FDI. Higher scores on both scales indicate higher levels of catastrophizing and functional disability. RESULTS: Of 31 children, the mean age was 11.47 years and the majority (70.97%) had dystrophic EB. Mean scores were: 35.84 = PCS parent; 34.58 = PCS child; 30.87 = parent FDI; 29.77 = child FDI. Total scores for PCS parent, parent FDI, and child FDI increased significantly with disease severity and percentage of involved BSA (p < .01 for all). Total scores for PCS child increased significantly with percent of EB skin involvement (p = .04) but not disease severity. Older children reported more functional disability than their parents and younger children (p = .02). CONCLUSIONS: Our results demonstrate significant positive correlations between negative thoughts related to pain and the experience of functional difficulties in patients with EB and their caregivers. Psychological, psychiatric, and/or behavioral interventions to help managing chronic pain may be effective for patients with EB.

Co-production of biofuel, bioplastics and biochemicals during extended fermentation of Halomonas bluephagenesis.

Halomonas bluephagenesis TD1.0 was engineered to produce the biofuel propane, bioplastic poly-3-hydroxybutyrate (PHB), and biochemicals mandelate and hydroxymandelate in a single, semi-continuous batch fermentation under non-sterile conditions. Multi-product separation was achieved by segregation of the headspace gas (propane), fermentation broth ([hydroxy]mandelate) and cellular biomass (PHB). Engineering was performed by incorporating the genes encoding fatty acid photodecarboxylase (CvFAP) and hydroxymandelic acid synthase (SyHMAS) into a H. bluephagenesis hmgCAB cassette knockout to channel flux towards (hydroxy)mandelate. Design of Experiment strategies were coupled with fermentation trials to simultaneously optimize each product. Propane and mandelate titres were the highest reported for H. bluephagenesis (62 g/gDCW and 71 ± 10 mg/L respectively) with PHB titres (69% g/gDCW) comparable to other published studies. This proof-of-concept achievement of four easily separated products within one fermentation is a novel achievement probing the versatility of biotechnology, further elevating H. bluephagenesis as a Next Generation Industrial Biotechnology (NGIB) chassis by producing highly valued products at a reduced cost.

Modification of SnO2 Electron Transport Layer in Perovskite Solar Cells.

Rapid development of the device performance of organic-inorganic lead halide perovskite solar cells (PSCs) are emerging as a promising photovoltaic technology. Current world-record efficiency of PSCs is based on tin oxide (SnO2) electron transport layers (ETLs), which are capable of being processed at low temperatures and possess high carrier mobilities with appropriate energy- band alignment and high optical transmittance. Modification of SnO2 has been intensely investigated by various approaches to tailor its conductivity, band alignment, defects, morphology, and interface properties. This review article organizes recent developments of modifying SnO2 ETLs to PSC advancement using surface and bulk modifications, while concentrating on photovoltaic (PV) device performance and long-term stability. Future outlooks for SnO2 ETLs in PSC research and obstacles remaining for commercialization are also discussed.

Mechanisms of innate and adaptive immunity to the Pfizer-BioNTech BNT162b2 vaccine.

Despite the success of the BNT162b2 mRNA vaccine, the immunological mechanisms that underlie its efficacy are poorly understood. Here we analyzed the innate and adaptive responses to BNT162b2 in mice, and show that immunization stimulated potent antibody and antigen-specific T cell responses, as well as strikingly enhanced innate responses after secondary immunization, which was concurrent with enhanced serum interferon (IFN)-γ levels 1 d following secondary immunization. Notably, we found that natural killer cells and CD8+ T cells in the draining lymph nodes are the major producers of this circulating IFN-γ. Analysis of knockout mice revealed that induction of antibody and T cell responses to BNT162b2 was not dependent on signaling via Toll-like receptors 2, 3, 4, 5 and 7 nor inflammasome activation, nor the necroptosis or pyroptosis cell death pathways. Rather, the CD8+ T cell response induced by BNT162b2 was dependent on type I interferon-dependent MDA5 signaling. These results provide insights into the molecular mechanisms by which the BNT162b2 vaccine stimulates immune responses.