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When evaluating soft self-assembling materials for use in any application, the structural or morphological characterisation is highly important. We know that the hierarchal molecular self-assembly of these materials into larger structures directly influences behaviours such as performance and stability. It is therefore imperative that these materials are characterised effectively over multiple length scales. Two effective methods of achieving this are small angle scattering (SAS) and imaging. Scattering giving us indirect information about the systems, whereas imaging is often looking at the material directly. In this review, we discuss the benefits, caveats and power of using both these techniques separately and together for the characterisation of supramolecular gels.

Abstract Biological soil covers (BSCs) play a pivotal role in ecosystem functioning by enhancing soil stability, mediating nutrient cycling, and influencing soil hydrology. Recognized as ecosystem engineers, they can physically modify, maintain, or create habitats, facilitating plant community development. Through these intricate interactions, BSCs contribute significantly to ecological processes, highlighting their importance in the overall health and functionality of the ecosystems of the Iberian Peninsula. Here we present the results obtained from the contributions of the citizen scientists uploaded from November 2019 to January 2021 with eBryoSoil, an app that allows citizens to participate in mapping the BSC communities across the Iberian Peninsula. Here, we emphasize the importance of habitats and consequently, their interaction with climatic variables for the persistence of BSCs (lichens and bryophytes). Conservation efforts targeted at preserving diverse habitats are essential to ensure the continued presence of lichen and bryophyte communities. Despite challenges posed by the SARS-CoV-2 outbreak, this citizen science project demonstrated success in utilizing a specifically tailored app to gather valuable information on BSC communities, providing insights into their vulnerability to climate change. This program serves as an illustrative example of how citizen science can effectively identify and study vulnerable habitats, offering a blueprint for future studies focused on understudied organisms.

Abstract Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary biased. We previously showed the RNA binding protein (RNAbp), Rbpms2, is required for ovary fate in zebrafish. Here, we identified Rbpms2 targets in oocytes (Rbpms2-bound oocyte RNAs; rboRNAs). We identify Rbpms2 as a translational regulator of rboRNAs, which include testis factors and ribosome biogenesis factors. Further, genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway, specifically through the mTorc1-activating Gap activity towards Rags 2 (Gator2) component, Missing oocyte (Mios). Cumulatively, our findings indicate that early gonocytes are in a dual poised, bipotential state in which Rbpms2 acts as a binary fate-switch. Specifically, Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2-mediated checkpoint, thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis.

Abstract Reticulocyte-binding protein homologue 5 (RH5), a leading blood-stage Plasmodium falciparum malaria vaccine target, interacts with cysteine-rich protective antigen (CyRPA) and RH5-interacting protein (RIPR) to form an essential heterotrimeric “RCR-complex”. We investigate whether RCR-complex vaccination can improve upon RH5 alone. Using monoclonal antibodies (mAbs) we show that parasite growth-inhibitory epitopes on each antigen are surface-exposed on the RCR-complex and that mAb pairs targeting different antigens can function additively or synergistically. However, immunisation of female rats with the RCR-complex fails to outperform RH5 alone due to immuno-dominance of RIPR coupled with inferior potency of anti-RIPR polyclonal IgG. We identify that all growth-inhibitory antibody epitopes of RIPR cluster within the C-terminal EGF-like domains and that a fusion of these domains to CyRPA, called “R78C”, combined with RH5, improves the level of in vitro parasite growth inhibition compared to RH5 alone. These preclinical data justify the advancement of the RH5.1 + R78C/Matrix-M™ vaccine candidate to Phase 1 clinical trial.

A novel process is reported that produces amorphous silica and nesquehonite (MgCO3·3H2O) from the magnesium silicate mineral olivine ((Mg, Fe)2·SiO4). The amorphous silica forms a supplementary cementitious material for use in concrete. The formation of nesquehonite sequesters carbon making the overall process carbon negative. Nesquehonite can also be used to form low-carbon construction products such as bricks, blocks and boards. This article reports on key process optimization studies. The potential for amorphous precipitated silica derived from olivine to produce carbon-negative concrete is discussed.

Summary: We show that a sleep-regulating, Ig-domain protein (NKT) is secreted from Drosophila mushroom body (MB) α′/β′ neurons to act locally on other MB cell types. Pan-neuronal or broad MB expression of membrane-tethered NKT (tNkt) protein reduced sleep, like that of an NKT null mutant, suggesting blockade of a receptor mediating endogenous NKT action. In contrast, expression in neurons requiring NKT (the MB α′/β′ cells), or non-MB sleep-regulating centers, did not reduce night sleep, indicating the presence of a local MB sleep-regulating circuit consisting of communicating neural subtypes. We suggest that the leucocyte-antigen-related like (Lar) transmembrane receptor may mediate NKT action. Knockdown or overexpression of Lar in the MB increased or decreased sleep, respectively, indicating the receptor promotes wakefulness. Surprisingly, selective expression of tNkt or knockdown of Lar in MB wake-promoting cells increased rather than decreased sleep, suggesting that NKT acts on wake- as well as sleep-promoting cell types to regulate sleep.

Abstract Respiratory mucosal immunity induced by vaccination is vital for protection from coronavirus infection in animal models. In humans, the capacity of peripheral vaccination to generate sustained immunity in the lung mucosa, and how this is influenced by prior SARS-CoV-2 infection, is unknown. Here we show using bronchoalveolar lavage samples that donors with history of both infection and vaccination have more airway mucosal SARS-CoV-2 antibodies and memory B cells than those only vaccinated. Infection also induces populations of airway spike-specific memory CD4+ and CD8+ T cells that are not expanded by vaccination alone. Airway mucosal T cells induced by infection have a distinct hierarchy of antigen specificity compared to the periphery. Spike-specific T cells persist in the lung mucosa for 7 months after the last immunising event. Thus, peripheral vaccination alone does not appear to induce durable lung mucosal immunity against SARS-CoV-2, supporting an argument for the need for vaccines targeting the airways.

Abstract The interaction between nitrogen monoxide (NO) and organic peroxy radicals (RO2) greatly impacts the formation of highly oxygenated organic molecules (HOM), the key precursors of secondary organic aerosols. It has been thought that HOM production can be significantly suppressed by NO even at low concentrations. Here, we perform dedicated experiments focusing on HOM formation from monoterpenes at low NO concentrations (0 – 82 pptv). We demonstrate that such low NO can enhance HOM production by modulating the RO2 loss and favoring the formation of alkoxy radicals that can continue to autoxidize through isomerization. These insights suggest that HOM yields from typical boreal forest emissions can vary between 2.5%-6.5%, and HOM formation will not be completely inhibited even at high NO concentrations. Our findings challenge the notion that NO monotonically reduces HOM yields by extending the knowledge of RO2-NO interactions to the low-NO regime. This represents a major advance towards an accurate assessment of HOM budgets, especially in low-NO environments, which prevails in the pre-industrial atmosphere, pristine areas, and the upper boundary layer.

Summary: Bacteriophages are a major component of the gut microbiome and are believed to play a role in establishment and stabilization of microbial communities by influencing taxonomic and functional diversity. We show that the activity of lytic and temperate phages can also significantly affect bacterial community structure in a model of extended colonic retention. Intact fresh human feces were incubated anaerobically at 37°C without homogenization and subjected to metagenomic sequencing. We observed subject-specific blooms and collapses of selected bacteriophage and bacterial populations within some individuals. Most notable were striking collapses of Prevotella populations accompanied by increases in specific bacteriophages. In a number of cases, we even observed a shift from one bacterial “enterotype” to another within 48 h. These results confirm that intact feces represents a highly dynamic ecological system and suggests that colonic retention time could have a profound effect on microbiome composition, including a significant impact by bacteriophages.

Background and aimRenal dysfunction is associated with poor outcomes in patients with coronavirus disease 2019 (COVID-19). In an effort to improve outcomes, intravenous remdesivir has been broadly used for the treatment of COVID-19 even in patients with low estimated glomerular filtration rate (eGFR). Our study assessed the residual risk of outcomes of patients with low eGFR despite treatment with remdesivir for COVID-19, during a timeframe prior to the expanded label across all levels of renal function.MethodsWe conducted an observational, retrospective, multi-site cohort study of adults hospitalized with COVID-19 treated with at least one dose of remdesivir between November 6, 2020, and November 5, 2021. Electronic medical records were reviewed to obtain patient characteristics, related laboratory data, and outcomes. The primary endpoint was all-cause mortality by day 28. Multivariable logistic regression was used to evaluate association between groups.ResultsThe study population consisted of 3024 patients hospitalized with COVID-19 and treated with remdesivir. The median age was 67 [IQR 55, 77] years; 42.7% were women, and 88.6% were white. The median eGFR was 76.6 mL/min/1.73 m2 [IQR 52.5, 95.2]; the majority (67.2%) of patients had an eGFR ≥ 60, while 9% had an eGFR ConclusionsLower eGFR remains an independent risk factor for mortality in COVID-19 even in patients treated with remdesivir.

Lymphangiogenesis is induced by local pro-lymphatic growth factors and bone marrow (BM)-derived myeloid-lymphatic endothelial cell progenitors (M-LECP). We previously showed that M-LECP play a significant role in lymphangiogenesis and lymph node metastasis in clinical breast cancer (BC) and experimental BC models. We also showed that differentiation of mouse and human M-LECP can be induced through sequential activation of colony stimulating factor-1 (CSF-1) and Toll-like receptor-4 (TLR4) pathways. This treatment activates the autocrine interleukin-10 (IL-10) pathway that, in turn, induces myeloid immunosuppressive M2 phenotype along with lymphatic-specific proteins. Because IL-10 is implicated in differentiation of numerous lineages, we sought to determine whether this pathway specifically promotes the lymphatic phenotype or multipotent progenitors that can give rise to M-LECP among other lineages. Analyses of BM cells activated either by CSF-1/TLR4 ligands in vitro or orthotopic breast tumors in vivo showed expansion of stem/progenitor population and coincident upregulation of markers for at least four lineages including M2-macrophage, lymphatic endothelial, erythroid, and T-cells. Induction of cell plasticity and multipotency was IL-10 dependent as indicated by significant reduction of stem cell markers and those for multiple lineages in differentiated cells treated with anti-IL-10 receptor (IL-10R) antibody or derived from IL-10R knockout mice. However, multipotent CD11b+/Lyve-1+/Ter-119+/CD3e+ progenitors detected in BM appeared to split into a predominant myeloid-lymphatic fraction and minor subsets expressing erythroid and T-cell markers upon establishing tumor residence. Each sub-population was detected at a distinct intratumoral site. This study provides direct evidence for differences in maturation status between the BM progenitors and those reaching tumor destination. The study results suggest preferential tumor bias towards expansion of myeloid-lymphatic cells while underscoring the role of IL-10 in early BM production of multipotent progenitors that give rise to both hematopoietic and endothelial lineages.

In low-to-middle-income countries (LMICs), enteric pathogens contribute to child malnutrition, affecting nutrient absorption, inducing inflammation, and causing diarrhoea. This is a substantial problem in LMICs due to high disease burden, poor sanitation and nutritional status, and the cyclical nature of pathogen infection and malnutrition. This relationship remains understudied in Timor-Leste. In our pilot study of enteric pathogens and malnutrition in Dili, Timor-Leste (July 2019-October 2020), we recruited 60 infants in a birth cohort from Hospital Nacional Guido Valadares (HNGV) with up to four home visits. We collected faecal samples and details of demographics, anthropometrics, diet and food practices, and animal husbandry. Additionally, we collected faecal samples, diagnostics, and anthropometrics from 160 children admitted to HNGV with a clinical diagnosis of severe diarrhoea or severe acute malnutrition (SAM). We tested faeces using the BioFire® FilmArray® Gastrointestinal Panel. We detected high prevalence of enteric pathogens in 68.8% (95%CI 60.4-76.2%) of infants at home, 88.6% of SAM cases (95%CI 81.7-93.3%) and 93.8% of severe diarrhoea cases (95%CI 67.7-99.7%). Diarrhoeagenic Escherichia coli and Campylobacter spp. were most frequently detected. Pathogen presence did not significantly differ in birth cohort diarrhoeal stool, but hospital data indicated associations between Salmonella and Shigella and diarrhoea. We observed wasting in 18.4% (95%CI 9.2-32.5%) to 30.8% (95%CI 17.5-47.7%) of infants across home visits, 57.9% (95%CI 34.0-78.9%) of severe diarrhoea cases, and 92.5% (95%CI 86.4-96.2%) of SAM cases. We associated bottle feeding with increased odds of pathogen detection when compared with exclusive breastfeeding at home (OR 8.3, 95%CI 1.1-62.7). We detected high prevalence of enteric pathogens and signs of malnutrition in children in Dili. Our pilot is proof of concept for a study to fully explore the risk factors and associations between enteric pathogens and malnutrition in Timor-Leste.

Abstract Germ cell tumors (GCTs) are neoplasms of the testis, ovary and extragonadal sites that occur in infants, children, adolescents and adults. Post-pubertal (type II) malignant GCTs may present as seminoma, non-seminoma or mixed histologies. In contrast, pre-pubertal (type I) GCTs are limited to (benign) teratoma and (malignant) yolk sac tumor (YST). Epidemiologic and molecular data have shown that pre- and post-pubertal GCTs arise by distinct mechanisms. Dedicated studies of the genomic landscape of type I and II GCT in children and adolescents are lacking. Here we present an integrated genomic analysis of extracranial GCTs across the age spectrum from 0–24 years. Activation of the WNT pathway by somatic mutation, copy-number alteration, and differential promoter methylation is a prominent feature of GCTs in children, adolescents and young adults, and is associated with poor clinical outcomes. Significantly, we find that small molecule WNT inhibitors can suppress GCT cells both in vitro and in vivo. These results highlight the importance of WNT pathway signaling in GCTs across all ages and provide a foundation for future efforts to develop targeted therapies for these cancers.

The role of keratinocyte subpopulations in the different phases of the viral cycle during HPV16 infection remains to be characterised. Here, single cell RNA sequencing of HPV16 infected and uninfected organoids identifies 12 distinct keratinocyte populations including an HPV-reprogrammed keratinocyte subpopulation that is linked to cancer.

Abstract Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, evolutionary history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a most recent common ancestor in 2018 carrying a low-fitness cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.

Basigin is an essential host receptor for invasion of Plasmodium falciparum into human erythrocytes, interacting with parasite surface protein PfRH5. PfRH5 is a leading blood-stage malaria vaccine candidate and a target of growth-inhibitory antibodies. Here, we show that erythrocyte basigin is exclusively found in one of two macromolecular complexes, bound either to plasma membrane Ca2+-ATPase 1/4 (PMCA1/4) or to monocarboxylate transporter 1 (MCT1). PfRH5 binds to each of these complexes with a higher affinity than to isolated basigin ectodomain, making it likely that these are the physiological targets of PfRH5. PMCA-mediated Ca2+ export is not affected by PfRH5, making it unlikely that this is the mechanism underlying changes in calcium flux at the interface between an erythrocyte and the invading parasite. However, our studies rationalise the function of the most effective growth-inhibitory antibodies targeting PfRH5. While these antibodies do not reduce the binding of PfRH5 to monomeric basigin, they do reduce its binding to basigin-PMCA and basigin-MCT complexes. This indicates that the most effective PfRH5-targeting antibodies inhibit growth by sterically blocking the essential interaction of PfRH5 with basigin in its physiological context.

Abstract In a time of rapid global change, the question of what determines patterns in species abundance distribution remains a priority for understanding the complex dynamics of ecosystems. The constrained maximization of information entropy provides a framework for the understanding of such complex systems dynamics by a quantitative analysis of important constraints via predictions using least biased probability distributions. We apply it to over two thousand hectares of Amazonian tree inventories across seven forest types and thirteen functional traits, representing major global axes of plant strategies. Results show that constraints formed by regional relative abundances of genera explain eight times more of local relative abundances than constraints based on directional selection for specific functional traits, although the latter does show clear signals of environmental dependency. These results provide a quantitative insight by inference from large-scale data using cross-disciplinary methods, furthering our understanding of ecological dynamics.

Tropical peatlands are among the most carbon-dense terrestrial ecosystems yet recorded. Collectively, they comprise a large but highly uncertain reservoir of the global carbon cycle, with wide-ranging estimates of their global area (441 025–1700 000 km ^2 ) and below-ground carbon storage (105–288 Pg C). Substantial gaps remain in our understanding of peatland distribution in some key regions, including most of tropical South America. Here we compile 2413 ground reference points in and around Amazonian peatlands and use them alongside a stack of remote sensing products in a random forest model to generate the first field-data-driven model of peatland distribution across the Amazon basin. Our model predicts a total Amazonian peatland extent of 251 015 km ^2 (95th percentile confidence interval: 128 671–373 359), greater than that of the Congo basin, but around 30% smaller than a recent model-derived estimate of peatland area across Amazonia. The model performs relatively well against point observations but spatial gaps in the ground reference dataset mean that model uncertainty remains high, particularly in parts of Brazil and Bolivia. For example, we predict significant peatland areas in northern Peru with relatively high confidence, while peatland areas in the Rio Negro basin and adjacent south-western Orinoco basin which have previously been predicted to hold Campinarana or white sand forests, are predicted with greater uncertainty. Similarly, we predict large areas of peatlands in Bolivia, surprisingly given the strong climatic seasonality found over most of the country. Very little field data exists with which to quantitatively assess the accuracy of our map in these regions. Data gaps such as these should be a high priority for new field sampling. This new map can facilitate future research into the vulnerability of peatlands to climate change and anthropogenic impacts, which is likely to vary spatially across the Amazon basin.

Abstract The significant advancement of inexpensive and portable virtual reality (VR) and augmented reality devices has re-energised the research in the immersive analytics field. The immersive environment is different from a traditional 2D display used to analyse 3D data as it provides a unified environment that supports immersion in a 3D scene, gestural interaction, haptic feedback and spatial audio. Genomic data analysis has been used in oncology to understand better the relationship between genetic profile, cancer type, and treatment option. This paper proposes a novel immersive analytics tool for cancer patient cohorts in a virtual reality environment, virtual reality to observe oncology data models. We utilise immersive technologies to analyse the gene expression and clinical data of a cohort of cancer patients. Various machine learning algorithms and visualisation methods have also been deployed in VR to enhance the data interrogation process. This is supported with established 2D visual analytics and graphical methods in bioinformatics, such as scatter plots, descriptive statistical information, linear regression, box plot and heatmap into our visualisation. Our approach allows the clinician to interrogate the information that is familiar and meaningful to them while providing them immersive analytics capabilities to make new discoveries toward personalised medicine.

Abstract We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.

IntroductionThere is an emerging need for the offshore renewable industry to have their own bespoke design guidelines because the associated projects and offshore facilities differ in fundamental ways to oil and gas facilities. Offshore renewable energy (ORE) facilities have already surpassed the numbers of installed facilities in the oil and gas industry by an order of magnitude and demand is forecast to continue growing exponentially. In addition ORE facilities often have different response characteristics and limit states or failure modes as well as profoundly different risk and consequence profiles given they are generally uncrewed and do not contain explosive hydrocarbon fluids which might be released into the environment. Therefore, the purpose of this paper is to advocate for licensing bodies and regulators (such as the various national PEL 114 committees) to challenge the process of automatic adoption of oil and gas design processes, while pushing for offshore renewables to be treated differently, when appropriate, with more relevant and applicable guidance.MethodsTo support this argument we present new bespoke design guidance developed for subsea cables based on specific modes of cable behaviour, which often differ from pipelines. We also show worked examples from recent project experience. The results from on-bottom stability analyses of a set of cables are compared between conventional oil and gas guidance following DNV-RP-F109 versus the stability using cable-optimised approaches.ResultsThe outcomes from the ‘conventional’ oil and gas results are not simply biased compared to cable-optimised design methods, with a trend of being either conservative or unconservative. Instead, the results of the two methods are very poorly correlated. This shows that the oil and gas approach isn't simply biased when applied to cables, but is instead unreliable because it doesn't capture the underlying failure conditions. These analytical comparisons are supported by field observation - the ocean doesn't lie, and makes short work of any anthropogenic structures which are designed with inadequate appreciation of the real world conditions.DiscussionTo support the rapid growth of ORE, we should therefore actively pursue opportunities to rewrite the design rules and standards, so that they better support the specific requirements of ORE infrastructure, rather than legacy oil and gas structures. With more appropriate design practices, we can accelerate the roll out of ORE to meet net zero, and mitigate the climate crisis.

Here, using genomic approaches, Rockett et al. identify Omicron and Delta SARS-CoV-2 co-infections in two adults, highlighting the usefulness of genomic surveillance for the timely recognition of co-infections in situations when different variants of the virus are circulating in the community.

Antibodies can have synergistic effects, but mechanisms are not well understood. Here, Ragotte et al. identify three antibodies that bind neighbouring epitopes on CyRPA, a malaria vaccine candidate, and show that lateral interactions between the antibodies slow dissociation and inhibit parasite growth synergistically.

BackgroundKetamine at subanaesthetic dosages (≤0.5mg/kg) exhibits rapid onset (over hours to days) antidepressant effects against major depressive disorder in people who are otherwise well. However, its safety, tolerability and efficacy are not known for major depressive disorder in people with advanced life-limiting illnesses.ObjectiveTo determine the feasibility, safety, tolerability, acceptability and any antidepressant signal/activity to justify and inform a fully powered study of subcutaneous ketamine infusions for major depressive disorder in the palliative setting.MethodsThis was a single arm, open-label, phase II feasibility study (Australian New Zealand Clinical Trial Registry Number-ACTRN12618001586202). We recruited adults (≥ 18-years-old) with advanced life-limiting illnesses referred to four palliative care services in Sydney, Australia, diagnosed with major depressive disorder from any care setting. Participants received weekly subcutaneous ketamine infusion (0.1-0.4mg/kg) over two hours using individual dose-titration design. Outcomes assessed were feasibility, safety, tolerability and antidepressant activity.ResultsOut of ninety-nine referrals, ten participants received ketamine and were analysed for responses. Accrual rate was 0.54 participants/month across sites with 50% of treated participants achieving ≥ 50% reduction in baseline Montgomery-Åsberg Depression Rating Scale, meeting feasibility criteria set a priori. There were no clinically relevant harms encountered.ConclusionsA future definitive trial exploring the effectiveness of subcutaneous infusion of ketamine for major depressive disorder in the palliative care setting may be feasible by addressing identified study barriers. Individual dose-titration of subcutaneous ketamine infusions over two hours from 0.1mg/kg can be well-tolerated and appears to produce transient antidepressant signals over hours to days.

Ecuador has a high diversity of orchids, but little is known about levels of genetic diversity for the great majority of species. Understanding how orchids might adapt to changes is crucial as deforestation and fragmentation of forest ecosystems threaten the survival of many epiphytic orchids that depend on other species, such as fungi and their host trees, for germination, growth, and establishment. Overcollection and the illegal trade are also major concerns for the survival of wild populations of orchids. Despite increasing awareness, effective interventions are often limited by a lack of data concerning the impacts that overexploitation might have. To fill this gap, we tested the effects of overcollection in the genetic diversity and structure of Masdevallia rosea, a narrow distributed epiphytic orchid historically collected in Ecuador, in comparison with the widely distributed Pleurothallis lilijae. Genotyping based on AFLPs showed reduced levels of diversity in wild populations but most especially in the overcollected, M. rosea. Overall, genetic admixture was high in P. lilijae segregating populations by altitude levels while fewer genetic groups were found in M. rosea. Genetic differentiation was low in both species. A spatial genetic structure was found in P. lilijae depending on altitude levels, while no spatial genetic structure was found in M. rosea. These results suggest different scenarios for the two species: while gene flow over long distance is possible in P. lilijae, the same seems to be unlikely in M. rosea possibly due to the low levels of individuals in the known populations. In situ and ex situ conservation strategies should be applied to protect the genetic pool in these epiphytic orchid species, and to promote the connectivity between wild populations. Adopting measures to reduce overexploitation and to understand the impacts of harvesting in wild populations are necessary to strengthen the legal trade of orchids.

Predators control prey abundance and behavior, both of which strongly influence community dynamics. However, the relative importance of these predator effects may shift with climate change stressors, suggesting understanding the potential effects on these different processes is critical to predicting effects of climate change on community function. We investigated the effects of global warming and ocean acidification on the transmission and detection of chemical cues from blue crab predators (Callinectes sapidus) by mud crab prey (Panopeus herbstii). We measured mud crab feeding rates in the presence of blue crab predator cues, using either predator cues stressed in acidified conditions or mud crabs stressed in warmed and acidified conditions. Mud crabs consumed less food in the presence of predator cues, but acidifying the cues or subjecting mud crabs receiving the cues to acidified environment did not affect this antipredator response. Mud crabs in warmed conditions consumed significantly less food regardless of predator cue, but this effect was reversed in ambient conditions. Therefore, climate change may produce shifts in community regulation as warming potentially compromises consumptive effects of predators by reducing motor function, whereas non-consumptive effects mediated by sensory transmission and detection remain unaffected by acidification. Overall, warming may have stronger effects than acidification on community dynamics in oyster reefs as global temperatures continue to rise.

Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by monoallelic mutation or deletion in the transcription factor 4 (TCF4) gene. Individuals with PTHS typically present in the first year of life with developmental delay and exhibit intellectual disability, lack of speech, and motor incoordination. There are no effective treatments available for PTHS, but the root cause of the disorder, TCF4 haploinsufficiency, suggests that it could be treated by normalizing TCF4 gene expression. Here, we performed proof-of-concept viral gene therapy experiments using a conditional Tcf4 mouse model of PTHS and found that postnatally reinstating Tcf4 expression in neurons improved anxiety-like behavior, activity levels, innate behaviors, and memory. Postnatal reinstatement also partially corrected EEG abnormalities, which we characterized here for the first time, and the expression of key TCF4-regulated genes. Our results support a genetic normalization approach as a treatment strategy for PTHS, and possibly other TCF4-linked disorders.

Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage (≥5 days post-fertilization). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA-sequencing studies that identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in the development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells, and ovarian stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, we used gene knockout experiments to determine the roles of foxl2l and wnt9b for oocyte development and sex determination and/or differentiation, respectively. Our results reveal novel insights into zebrafish ovarian development and function, and the transcriptome profiles will provide a valuable resource for future studies.

Abstract Crucial to the successful conservation of endangered species is the overlap of their ranges with protected areas. We analyzed protected areas in the continental USA to assess the extent to which they covered the ranges of endangered tetrapods. We show that in 80% of ecoregions, protected areas offer equal (25%) or worse (55%) protection for species than if their locations were chosen at random. Additionally, we demonstrate that it is possible to achieve sufficient protection for 100% of the USA’s endangered tetrapods through targeted protection of undeveloped public and private lands. Our results highlight that the USA is likely to fall short of its commitments to halting biodiversity loss unless more considerable investments in both public and private land conservation are made.

Abstract After preterm premature rupture of membranes (PPROM), antibiotics and antenatal steroids are effective evidence-based interventions, but the use of tocolysis is controversial. We investigated whether a unit policy of tocolysis use after PPROM is associated with prolonged gestation and improved outcomes for very preterm infants in units that systematically use these other evidence-based treatments. From the prospective, observational, population-based EPICE cohort study (all very preterm births in 19 regions from 11 European countries, 2011–2012), we included 607 women with a singleton pregnancy and PPROM at 24–29 weeks’ gestation, of whom 101, 195 and 311 were respectively managed in 17, 32 and 45 units with no-use, restricted and liberal tocolysis policies for PPROM. The association between unit policies and outcomes (early-onset sepsis, survival at discharge, survival at discharge without severe morbidity and survival at two years without gross motor impairment) was investigated using three-level random-intercept logistic regression models, showing no differences in neonatal or two-year outcomes by unit policy. Moreover, there was no association between unit policies and prolongation of gestation in a multilevel survival analysis. Compared to a unit policy of no-use of tocolysis after PPROM, a liberal or restricted policy is not associated with improved obstetric, neonatal or two-year outcomes.

BackgroundThe growing prevalence of non-communicable diseases (NCDs) in South African workers has been shown to be associated with absenteeism and increased risk of morbidity. Low-income workers living in urban settings are particularly vulnerable. Consultation with workers is crucial for understanding risks and identifying opportunities for intervention to promote health in the workplace. The purpose of this study was to examine South African pharmaceutical manufacturing workers' perspectives of health risk factors and absenteeism, and to identify how they perceived a role for the organisation to initiate interventions to improve their health.Materials and methodsFive focus groups were conducted to capture 27 employees' perspectives. The semi-structured focus group discussions were recorded and analysed using a thematic content analysis approach.ResultsParticipants indicated that they were aware of behavioural health risks such as prolonged sitting. They showed insight into strategies to prevent injuries and stay healthy, but also expressed dissatisfaction about the lack of organisational support, leading to stress and consequently absenteeism. Participants emphasized the responsibility of the organisation to support a range of health promoting strategies.ConclusionsThe findings of this study are important for cultivating a tailored workplace intervention to reduce NCD risk factors in the pharmaceutical manufacturing workforce. It is vital that these be supported by leadership of the company through the provision of funding and the development of internal healthcare services.

BackgroundIncreasing both the frequency and quality of social interactions within treatments for anxiety and depressive disorders in older adults may improve their mental health outcomes and quality of life. This study aims to evaluate the clinical efficacy and cost utility of an enhanced cognitive behavioural therapy (CBT) plus social participation program in a sample of older adults with depression and/or anxiety.MethodsA total of 172 community-dwelling adults aged 65 years or older with an anxiety and/or depressive disorder will be randomly allocated to either an enhanced CBT plus social participation program (n = 86) or standard CBT (n = 86). Both treatments will be delivered during 12 weekly individual sessions utilising structured manuals and workbooks. Participants will be assessed at pre-treatment, post-treatment, and 12-month follow-up. The primary outcome evaluates mean change in clinician-rated diagnostic severity of anxiety and depressive disorders from baseline to post-treatment (primary endpoint) based on a semi-structured diagnostic interview. Secondary outcomes evaluate changes in symptomatology on self-report anxiety and depression measures, as well as changes in social/community participation, social network, and perceived social support, loneliness, quality of life, and use of health services. Economic benefits will be evaluated using a cost-utility analysis to derive the incremental cost utility ratios for the enhanced CBT program.DiscussionOutcomes from this study will provide support for the establishment of improved psychosocial treatment for older adults with anxiety and/or depression. Study outcomes will also provide health systems with a clear means to reduce the impact of poor emotional health in older age and its associated economic burden. In addition to the empirical validation of a novel treatment, the current study will contribute to the current understanding of the role of social participation in older adult wellbeing.Trial registrationProspectively registered on the Australian New Zealand Clinical Trials Registry (ID: ACTRN12619000242123; registered 19th February 2019) and the ISRCTN registry (ID: ISRCTN78951376; registered 10th July 2019).

Background Increasing both the frequency and quality of social interactions within treatments for anxiety and depressive disorders in older adults may improve their mental health outcomes and quality of life. This study aims to evaluate the clinical efficacy and cost utility of an enhanced cognitive behavioural therapy (CBT) plus social participation program in a sample of older adults with depression and/or anxiety. Methods A total of 172 community-dwelling adults aged 65 years or older with an anxiety and/or depressive disorder will be randomly allocated to either an enhanced CBT plus social participation program (n = 86) or standard CBT (n = 86). Both treatments will be delivered during 12 weekly individual sessions utilising structured manuals and workbooks. Participants will be assessed at pre-treatment, post-treatment, and 12-month follow-up. The primary outcome evaluates mean change in clinician-rated diagnostic severity of anxiety and depressive disorders from baseline to post-treatment (primary endpoint) based on a semi-structured diagnostic interview. Secondary outcomes evaluate changes in symptomatology on self-report anxiety and depression measures, as well as changes in social/community participation, social network, and perceived social support, loneliness, quality of life, and use of health services. Economic benefits will be evaluated using a cost-utility analysis to derive the incremental cost utility ratios for the enhanced CBT program. Discussion Outcomes from this study will provide support for the establishment of improved psychosocial treatment for older adults with anxiety and/or depression. Study outcomes will also provide health systems with a clear means to reduce the impact of poor emotional health in older age and its associated economic burden. In addition to the empirical validation of a novel treatment, the current study will contribute to the current understanding of the role of social participation in older adult wellbeing. Trial registration Prospectively registered on the Australian New Zealand Clinical Trials Registry (ID: ACTRN12619000242123; registered 19th February 2019) and the ISRCTN registry (ID: ISRCTN78951376; registered 10th July 2019).

Summary: Nicotinamide riboside supplements (NRS) have been touted as a nutraceutical that promotes cardiometabolic and musculoskeletal health by enhancing nicotinamide adenine dinucleotide (NAD+) biosynthesis, mitochondrial function, and/or the activities of NAD-dependent sirtuin deacetylase enzymes. This investigation examined the impact of NRS on whole body energy homeostasis, skeletal muscle mitochondrial function, and corresponding shifts in the acetyl-lysine proteome, in the context of diet-induced obesity using C57BL/6NJ mice. The study also included a genetically modified mouse model that imposes greater demand on sirtuin flux and associated NAD+ consumption, specifically within muscle tissues. In general, whole body glucose control was marginally improved by NRS when administered at the midpoint of a chronic high-fat diet, but not when given as a preventative therapy upon initiation of the diet. Contrary to anticipated outcomes, the study produced little evidence that NRS increases tissue NAD+ levels, augments mitochondrial function, and/or mitigates diet-induced hyperacetylation of the skeletal muscle proteome.

There is a data gap in our current knowledge of the geospatial distribution, type and extent of C rich peatlands across the globe. The Pastaza Marañón Foreland Basin (PMFB), within the Peruvian Amazon, is known to store large amounts of peat, but the remoteness of the region makes field data collection and mapping the distribution of peatland ecotypes challenging. Here we review methods for developing high accuracy peatland maps for the PMFB using a combination of multi-temporal synthetic aperture radar (SAR) and optical remote sensing in a machine learning classifier. The new map produced has 95% overall accuracy with low errors of commission (1–6%) and errors of omission (0–15%) for individual peatland classes. We attribute this improvement in map accuracy over previous maps of the region to the inclusion of high and low water season SAR images which provides information about seasonal hydrological dynamics. The new multi-date map showed an increase in area of more than 200% for pole forest peatland (6% error) compared to previous maps, which had high errors for that ecotype (20–36%). Likewise, estimates of C stocks were 35% greater than previously reported (3.238 Pg in Draper et al. (2014) to 4.360 Pg in our study). Most of the increase is attributed to pole forest peatland which contributed 58% (2.551 Pg) of total C, followed by palm swamp (34%, 1.476 Pg). In an assessment of deforestation from 2010 to 2018 in the PMFB, we found 89% of the deforestation was in seasonally flooded forest and 43% of deforestation was occurring within 1 km of a river or road. Peatlands were found the least affected by deforestation and there was not a noticeable trend over time. With development of improved transportation routes and population pressures, future land use change is likely to put South American tropical peatlands at risk, making continued monitoring a necessity. Accurate mapping of peatland ecotypes with high resolution (

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

Multiplexed genome engineering with Cas9 can increase efficiency but also the risk of unintended alterations. Here the authors demonstrate the use of multiplexed base editors on primary T cells with reduced translocation frequency.

Proof of protection against blood-stage P. falciparum malaria by a single immunological mechanism has been elusive. Here, using engineered anti-PfRH5 chimeric monoclonal antibodies in non-human primates, the authors show that high levels of merozoite-neutralizing antibodies can achieve protection.

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

Falciparum malaria is clinically heterogeneous and the relative contribution of parasite and host in shaping disease severity remains unclear. We explored the interaction between inflammation and parasite variant surface antigen (VSA) expression, asking whether this relationship underpins the variation observed in controlled human malaria infection (CHMI). We uncovered marked heterogeneity in the host response to blood challenge; some volunteers remained quiescent, others triggered interferon-stimulated inflammation and some showed transcriptional evidence of myeloid cell suppression. Significantly, only inflammatory volunteers experienced hallmark symptoms of malaria. When we tracked temporal changes in parasite VSA expression to ask whether variants associated with severe disease rapidly expand in naive hosts, we found no transcriptional evidence to support this hypothesis. These data indicate that parasite variants that dominate severe malaria do not have an intrinsic growth or survival advantage; instead, they presumably rely upon infection-induced changes in their within-host environment for selection.

EUROCAT is a European network of population-based congenital anomaly (CA) registries. Twenty-one registries agreed to participate in the EUROlinkCAT study to determine if reliable information on the survival of children born with a major CA between 1995 and 2014 can be obtained through linkage to national vital statistics or mortality records. Live birth children with a CA could be linked using personal identifiers to either their national vital statistics (including birth records, death records, hospital records) or to mortality records only, depending on the data available within each region. In total, 18 of 21 registries with data on 192,862 children born with congenital anomalies participated in the study. One registry was unable to get ethical approval to participate and linkage was not possible for two registries due to local reasons. Eleven registries linked to vital statistics and seven registries linked to mortality records only; one of the latter only had identification numbers for 78% of cases, hence it was excluded from further analysis. For registries linking to vital statistics: six linked over 95% of their cases for all years and five were unable to link at least 85% of all live born CA children in the earlier years of the study. No estimate of linkage success could be calculated for registries linking to mortality records. Irrespective of linkage method, deaths that occurred during the first week of life were over three times less likely to be linked compared to deaths occurring after the first week of life. Linkage to vital statistics can provide accurate estimates of survival of children with CAs in some European countries. Bias arises when linkage is not successful, as early neonatal deaths were less likely to be linked. Linkage to mortality records only cannot be recommended, as linkage quality, and hence bias, cannot be assessed.

The systematic screening of asymptomatic and pre-symptomatic individuals is a powerful tool for controlling community transmission of infectious disease on college campuses. Faced with a paucity of testing in the beginning of the COVID-19 pandemic, many universities developed molecular diagnostic laboratories focused on SARS-CoV-2 diagnostic testing on campus and in their broader communities. We established the UC Santa Cruz Molecular Diagnostic Lab in early April 2020 and began testing clinical samples just five weeks later. Using a clinically-validated laboratory developed test (LDT) that avoided supply chain constraints, an automated sample pooling and processing workflow, and a custom laboratory information management system (LIMS), we expanded testing from a handful of clinical samples per day to thousands per day with the testing capacity to screen our entire campus population twice per week. In this report we describe the technical, logistical, and regulatory processes that enabled our pop-up lab to scale testing and reporting capacity to thousands of tests per day.

Summary: The human malaria parasite Plasmodium vivax remains vastly understudied, mainly due to the lack of suitable laboratory models. Here, we report a humanized mouse model to test interventions that block P. vivax parasite transition from liver stage infection to blood stage infection. Human liver-chimeric FRGN huHep mice infected with P. vivax sporozoites were infused with human reticulocytes, allowing transition of exo-erythrocytic merozoites to reticulocyte infection and development into all erythrocytic forms, including gametocytes, in vivo. In order to test the utility of this model for preclinical assessment of interventions, the invasion blocking potential of a monoclonal antibody targeting the essential interaction of the P. vivax Duffy Binding Protein with the Duffy antigen receptor was tested by passive immunization. This antibody inhibited invasion by over 95%, providing unprecedented in vivo evidence that PvDBP constitutes a promising blood stage vaccine candidate and proving our model highly suitable to test blood stage interventions.

Subjective Cognitive Complaints (SCCs) may represent one of the earliest stages of preclinical dementia. The objective of the present study was to extend previous work by our group to examine the relationship between participant-reported and informant-reported memory and non-memory SCCs, cognitive decline and incident dementia, over a six-year period. Participants were 873 community dwelling older adults (Mage = 78.65, SD = 4.79) without dementia and 843 informants (close friends or family) from the Sydney Memory and Ageing Study. Comprehensive neuropsychological testing and diagnostic assessments were carried out at baseline and biennially for six years. Linear mixed models and Cox proportional hazard models were performed to determine the association of SCCs, rate of cognitive decline and risk of incident dementia, controlling demographics and covariates of mood and personality. Participant and informant memory-specific SCCs were associated with rate of global cognitive decline; for individual cognitive domains, participant memory SCCs predicted decline for language, while informant memory SCCs predicted decline for executive function and memory. Odds of incident dementia were associated with baseline participant memory SCCs and informant memory and non-memory SCCs in partially adjusted models. In fully adjusted models, only informant SCCs were associated with increased risk of incident dementia. Self-reported memory-specific cognitive complaints are associated with decline in global cognition over 6-years and may be predictive of incident dementia, particularly if the individual is depressed or anxious and has increased neuroticism or decreased openness. Further, if and where possible, informants should be sought and asked to report on their perceptions of the individual's memory ability and any memory-specific changes that they have noticed as these increase the index of diagnostic suspicion.

There is increasing evidence that clinical trial participants are uninformed about the trials in which they participate, raising ethical concerns regarding informed consent. The aim of this pilot study was to explore clinical trial participants' use of consent discussions and information sheets when considering participating in clinical trials research. A qualitative, interview-based pilot study was designed in order to elicit, through dialogue, details of the reasons for participants' use of, and preferences regarding, different modes of information provision. Semi-structured interviews were undertaken with two different groups of patients who were participants in the Reinforcement of Closure of Stoma Site trial. The first group comprised newly-consented trial participants, who had been recruited up to 72 hours before our interview; the second group comprised patients attending a follow-up clinic 12 months after joining the trial. Thirteen participants were recruited in total: three newly-consented patients, and ten follow-up patients. The study found that participants' use of consent discussions to gain information about clinical trials was varied, and that they only minimally used information sheets after providing initial consent for the trial. Participants demonstrated varying degrees of knowledge about the trial, with some having forgotten that they were still involved in the trial. Participants reported a high level of trust in medical staff as a reason for not seeking more information about the trial. Some participants reported dissatisfaction with the timing of information provision. Some were amenable to novel ways of receiving trial information, such as web-based methods. The pilot study demonstrated the feasibility of a larger study into the provision of information to prospective clinical trial participants. The results suggest that considering alternative ways of providing information and the appropriateness of existing information provision may be acceptable to and useful for potential trial participants.

The prevalence of overweight and obesity is high among preschool age (3-5 years) children in South Africa, and children in urban low-income settings are particularly at risk. A better understanding of how parents or caregivers of young children perceive children's weight and size, as well as contextual factors influencing perceptions, is needed to inform interventions. The aim of this study was to examine how parents of preschool children in Soweto, South Africa, view childhood obesity, and to situate these perspectives in the context of the home environment in which preschool age children in Soweto live. Semi-structured in-depth interviews were conducted with 16 parents in four neighbourhoods of Soweto. Interviews were audio-recorded, transcribed verbatim, and analysed using reflexive thematic analysis following a contextualist approach. Three themes were developed: growing differently, the 'right' way to be, and weight is not health. These themes capture parents' views on complex and reportedly inevitable causes of obesity, ideas about acceptable and preferred body sizes, and the low priority of weight per se compared to health. The findings suggest that childhood obesity prevention in South Africa needs to be done in a non-stigmatising way that recognises environmental and contextual factors, such as parents' limited sense of agency in relation to their children's health and weight, and concrete resource constraints. Environmental barriers to healthy behaviours need to be addressed in order to overcome the coexisting challenges of childhood undernutrition and obesity in urban low-income South African settings.

Uncertainty affects estimates of the power potential of tidal currents, resulting in large ranges in values reported for sites such as the Pentland Firth, UK. Kreitmair et al. (2019, R. Soc. open sci. 6, 180941. (doi:10.1098/rsos.191127)) have examined the effect of uncertainty in bottom friction on tidal power estimates by considering idealized theoretical models. The present paper considers the role of bottom friction uncertainty in a realistic numerical model of the Pentland Firth spanned by different fence configurations. We find that uncertainty in removable power estimates resulting from bed roughness uncertainty depends on the case considered, with relative uncertainty between 2% (for a fully spanned channel with small values of mean roughness and input uncertainty) and 44% (for an asymmetrically confined channel with high values of bed roughness and input uncertainty). Relative uncertainty in power estimates is generally smaller than (input) relative uncertainty in bottom friction by a factor of between 0.2 and 0.7, except for low turbine deployments and very high mean values of friction. This paper makes a start at quantifying uncertainty in tidal stream power estimates, and motivates further work for proper characterization of the resource, accounting for uncertainty inherent in resource modelling.

Bacteriophages of the crAssphage family have not yet been isolated, despite being highly abundant in the human gut. Here, Shkoporov et al. isolate in pure culture one of these viruses and show that it infects the human gut symbiont Bacteroides intestinalis.