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Tropical peatlands cycle and store large amounts of carbon in their soil and biomass1–5. Climate and land-use change alters greenhouse gas (GHG) fluxes of tropical peatlands, but the magnitude of these changes remains highly uncertain6–19. Here we measure net ecosystem exchanges of carbon dioxide, methane and soil nitrous oxide fluxes between October 2016 and May 2022 from Acacia crassicarpa plantation, degraded forest and intact forest within the same peat landscape, representing land-cover-change trajectories in Sumatra, Indonesia. This allows us to present a full plantation rotation GHG flux balance in a fibre wood plantation on peatland. We find that the Acacia plantation has lower GHG emissions than the degraded site with a similar average groundwater level (GWL), despite more intensive land use. The GHG emissions from the Acacia plantation over a full plantation rotation (35.2 ± 4.7 tCO2-eq ha−1 year−1, average ± standard deviation) were around two times higher than those from the intact forest (20.3 ± 3.7 tCO2-eq ha−1 year−1), but only half of the current Intergovernmental Panel on Climate Change (IPCC) Tier 1 emission factor (EF)20 for this land use. Our results can help to reduce the uncertainty in GHG emissions estimates, provide an estimate of the impact of land-use change on tropical peat and develop science-based peatland management practices as nature-based climate solutions.

Global pollinator declines threaten food production and natural ecosystems. The drivers of declines are complicated and driven by numerous factors such as pesticide use, loss of habitat, rising pathogens due to commercial bee keeping and climate change. Halting and reversing pollinator declines will require a multidisciplinary approach and international cooperation. Here, we summarize 20 presentations given in the symposium ‘Protecting pollinators and our food supply: Understanding and managing threats to pollinator health’ at the 19th Congress of the International Union for the Study of Social Insects in San Diego, 2022. We then synthesize the key findings and discuss future research areas such as better understanding the impact of anthropogenic stressors on wild bees.

European ecosystems have been subject to extensive shifts in anthropogenic disturbance, primarily through atmospheric deposition, climate change, and land management. These changes have altered the macronutrient composition of aquatic systems, with widespread increases in organic carbon (C), and declines in nitrogen (N) and phosphorus (P). Less well known is how these disturbances have affected nutrient stoichiometry, which may be a more useful metric to evaluate the health of aquatic ecosystems than individual nutrient concentrations. The Swedish west coast has historically experienced moderate to high levels of atmospheric deposition of sulfate and N, and eutrophication. In addition, coastal waters have been darkening with damaging effects on marine flora and fauna. Here, we present three decades of macronutrient data from twenty lakes and watercourses along the Swedish west coast, extending from headwaters to river mouths, across a range of land covers, and with catchments ranging 0.037–40,000 km2. We find a high degree of consistency between these diverse sites, with widespread increasing trends in organic C, and declines in inorganic N and total P. These trends in individual macronutrients translate into large stoichiometric changes, with a doubling in C:P, and increases in C:N and N:P by 50% and 30%, showing that freshwaters are moving further away from the Redfield Ratio, and becoming even more C rich, and depleted in N and P. Although recovery from atmospheric deposition is linked to some of these changes, land cover also appears to have an effect; lakes buffer against C increases, and decreases in inorganic N have been greatest under arable land cover. Our analysis also detects coherently declining P concentrations in small forest lakes; so called (and unexplained) “oligotrophication.” Taken together, our findings show that freshwater macronutrient concentrations and stoichiometry have undergone substantial shifts during the last three decades, and these shifts can potentially explain some of the detrimental changes that adjacent coastal ecosystems are undergoing. Our findings are relevant for all European and North American waters that have experienced historically high levels of atmospheric deposition, and provide a starting point for understanding and mitigating against the trajectories of long-term change in aquatic systems.

Hematopoietic stem cell transplantation-associated thrombotic microangiopathy (HSCT-TMA) is a severe and potentially life-threatening complication. HSCT-TMA is often underdiagnosed due to multifactorial pathophysiology and a historic lack of standard diagnostic criteria. Identification of the multi-hit hypothesis and the key role of the complement system, particularly the lectin pathway of complement, has led to development of treatments targeting the underlying pathogenesis of HSCT-TMA. Additional research is ongoing to investigate the efficacy and safety of these targeted therapies in patients with HSCT-TMA. Advanced practice providers (APPs; nurse practitioners and physician assistants) and pharmacists are critical members of the multidisciplinary HSCT team and ensure management of patients throughout the continuum of care. Additionally, pharmacists and APPs can improve patient care through medication management of complex regimens; transplant education for patients, staff, and trainees; evidence-based protocol and clinical guideline development; assessment and reporting of transplant-related outcomes; and quality improvement initiatives to improve outcomes. Understanding the presentation, prognosis, pathophysiology, and treatment options for HSCT-TMA can improve each of these efforts.

The temperature dependence of infection reflects changes in performance of parasites and hosts. High temperatures often mitigate infection by favoring heat-tolerant hosts over heat-sensitive parasites. Honey bees exhibit endothermic thermoregulation—rare among insects—that can favor resistance to parasites. However, viruses are heavily host-dependent, suggesting that viral infection could be supported—not threatened—by optimum host function. To understand how temperature-driven changes in performance of viruses and hosts shape infection, we compared the temperature dependence of isolated viral enzyme activity, three honey bee traits, and infection of honey bee pupae. Viral enzyme activity varied 30 °C interval spanning temperatures typical of ectothermic insects and honey bees. In contrast, honey bee performance peaked at high (≥ 35 °C) temperatures and was highly temperature-sensitive. Although these results suggested that increasing temperature would favor hosts over viruses, the temperature dependence of pupal infection matched that of pupal development, falling only near pupae’s upper thermal limits. Our results reflect the host-dependent nature of viruses, suggesting that infection is accelerated—not curtailed—by optimum host function, contradicting predictions based on relative performance of parasites and hosts, and suggesting tradeoffs between infection resistance and host survival that limit the viability of bee ‘fever’.

Research has explored age-related and cultural differences in moral evaluations of dishonesty; however, this has not yet been examined in an aging context. The present study provided a novel account of how younger and older adults (in Canada, Singapore, and China;The online version contains supplementary material available at 10.1007/s12144-022-03785-6.

Host-parasite co-evolution is a process of reciprocal, adaptive genetic change. In natural conditions, parasites can shift to other host species, given both host and parasite genotypes allow this. Even though host-parasite co-evolution has been extensively studied both theoretically and empirically, few studies have focused on parasite gene flow between native and novel hosts. Nosema ceranae is a native parasite of the Asian honey bee Apis cerana, which infects epithelial cells of mid-guts. This parasite successfully switched to the European honey bee Apis mellifera, where high virulence has been reported. In this study, we used the parasite N. ceranae and both honey bee species as model organisms to study the impacts of two-host habitat sharing on parasite diversity and virulence. SNVs (Single Nucleotide Variants) were identified from parasites isolated from native and novel hosts from sympatric populations, as well as novel hosts from a parapatric population. Parasites isolated from native hosts showed the highest levels of polymorphism. By comparing the parasites isolated from novel hosts between sympatric and parapatric populations, habitat sharing with the native host significantly enhanced parasite diversity, suggesting there is continuing gene flow of parasites between the two host species in sympatric populations.

Honey bee colony losses worldwide call for a more in-depth understanding of the pathogenic and mutualistic components of the honey bee microbiota and their relation with the environment. In this descriptive study, we characterized the yeast and bacterial communities that arise from six substrates associated with honey bees: corbicular pollen, beebread, hive debris, intestinal contents, body surface of nurses and forager bees, comparing two different landscapes, Minas Gerais, Brazil and Maryland, United States. The sampling of five hives in Brazil and four in the USA yielded 217 yeast and 284 bacterial isolates. Whereas the yeast community, accounted for 47 species from 29 genera, was dominated in Brazil by Aureobasidium sp. and Candida orthopsilosis, the major yeast recovered from the USA was Debaryomyces hansenii. The bacterial community was more diverse, encompassing 65 species distributed across 31 genera. Overall, most isolates belonged to Firmicutes, genus Bacillus. Among LAB, species from Lactobacillus were the most prevalent. Cluster analysis evidenced high structuration of the microbial communities, with two distinguished microbial groups between Brazil and the United States. In general, the higher difference among sites and substrates were dependents on the turnover effect (~ 93% of the beta diversity), with a more pronounced effect of nestedness (~ 28%) observed from Brazil microbiota change. The relative abundance of yeasts and bacteria also showed the dissimilarity of the microbial communities between both environments. These results provide a comprehensive view of microorganisms associated with A. mellifera, highlighting the importance of the environment in the establishment of the microbiota associated with honey bees. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-021-00539-7.

Tropical peatlands are threatened by climate change and land-use changes, but there remain substantial uncertainties about their present and future role in the global carbon cycle due to limited measurements. Here, we present measurements of carbon dioxide and methane emissions between mid-2017 and mid-2020 as well as nitrous oxide emissions between 2019 and 2020 at two contrasting sites at a coastal peatland in Sumatra, Indonesia. We find that greenhouse-gas emissions from intact peatland increased substantially due to an extreme drought caused by a positive Indian Ocean Dipole phase combined with El Nino. The emission in the degraded site was two times greater than that at the intact site. The smaller emission from the intact peatland suggests that protecting the remaining intact tropical peatlands from degradation offers important climate benefits, avoiding greenhouse-gas emissions of 24 ± 5 tCO2e ha−1 yr−1 (average ± standard deviation) at our study site in Indonesia. During a period of drought, an intact tropical peatland in Indonesia released half the amount of greenhouse gases as was released from a degraded site, according to a direct comparison of eddy covariance measurements at a pair of peatland sites in Sumatra.

In fresh waters, the origins of dissolved organic matter (DOM) have been found to exert a fundamental control on its reactivity, and ultimately, its ecosystem functional role. A detailed understanding of landscape scale factors that control the export of DOM to aquatic ecosystems is, therefore, pivotal if the effects of DOM flux to fresh waters are to be fully understood. In this study we present data from a national sampling campaign across the United Kingdom in which we explore the variability in DOM composition in three broad landscape types defined by similar precipitation, geology, land use and management, hydrology, and nutrient enrichment status. We characterised samples from fifty-one sites, grouping them into one of three major underlying classifications: circumneutral streams underlain by clay and mudstone (referred to as ‘clay’), alkaline streams underlain by Cretaceous Chalk or by Carboniferous or Jurassic Limestone (‘limestone’), and acidic streams in peatland catchments underlain by a range of low permeability lithologies (‘peat’). DOM composition was assessed through organic matter stoichiometry (organic carbon: organic nitrogen; organic carbon: organic phosphorus; C/N(P)DOM) and metrics derived from ultra-violet (UV)/visible spectroscopic analysis of DOM such as specific UV absorption (a254 nm; SUVA254). We found similar SUVA254, C/NDOM and DOM/a254 relationships within classifications, demonstrating that despite a large degree of heterogeneity within environments, catchments with shared environmental character and anthropogenic disturbance export DOM with a similar composition and character. Improving our understanding of DOM characterisation is important to help predict shifts in stream ecosystem function, and ecological responses to enrichment or mitigation efforts and how these may result in species composition shifts and biodiversity loss in freshwater ecosystems.

Global peatlands store more carbon than is naturally present in the atmosphere1,2. However, many peatlands are under pressure from drainage-based agriculture, plantation development and fire, with the equivalent of around 3 per cent of all anthropogenic greenhouse gases emitted from drained peatland3–5. Efforts to curb such emissions are intensifying through the conservation of undrained peatlands and re-wetting of drained systems6. Here we report eddy covariance data for carbon dioxide from 16 locations and static chamber measurements for methane from 41 locations in the UK and Ireland. We combine these with published data from sites across all major peatland biomes. We find that the mean annual effective water table depth (WTDe; that is, the average depth of the aerated peat layer) overrides all other ecosystem- and management-related controls on greenhouse gas fluxes. We estimate that every 10 centimetres of reduction in WTDe could reduce the net warming impact of CO2 and CH4 emissions (100-year global warming potentials) by the equivalent of at least 3 tonnes of CO2 per hectare per year, until WTDe is less than 30 centimetres. Raising water levels further would continue to have a net cooling effect until WTDe is within 10 centimetres of the surface. Our results suggest that greenhouse gas emissions from peatlands drained for agriculture could be greatly reduced without necessarily halting their productive use. Halving WTDe in all drained agricultural peatlands, for example, could reduce emissions by the equivalent of over 1 per cent of global anthropogenic emissions. Halving average drainage depths in agricultural peatlands could reduce greenhouse gas emissions by the equivalent of 1 per cent of all anthropogenic emissions.

Dietary protein is often considered a factor that limits the growth of primate populations. The ratio of crude protein (CP) to fiber in common mature leaves in a forest reliably predicts colobine biomass across Africa and Asia. This relationship is puzzling because CP of mature leaves is notably high in some forests, including Kibale National Park, Uganda, where mature leaves have a higher protein concentration (ca. 18% CP on a dry matter basis) than what is required for primate growth, maintenance, and reproduction. We used an in vitro assay that incorporates the role of fiber and tannins to assess the biological relevance of CP in the leaves that comprise the diets of colobines (Colobus guereza, Piliocolobus tephrosceles) in Kibale (N = 37 spp. mature leaves, 39 spp. young leaves). Relative to CP, available (digestible) protein (AP) concentrations were 50% lower in mature leaves and 38% lower in young leaves, and protein-to-fiber ratios were lower when incorporating AP. Surprisingly, leaf AP did not differ among sites within Kibale, and AP at all sites exceeded primate protein requirements. Future research, particularly in protein-rich forests like Kibale, should consider focusing on fiber, energy, and other nutritional factors to assess the relationship between colobine biomass and leaf nutritional quality. Our study expands on the way that primate ecologists measure protein, integrates several traits into a single currency of AP, and contributes to conservation management plans.

Terrestrial ecosystems remove about 30 per cent of the carbon dioxide (CO2) emitted by human activities each year1, yet the persistence of this carbon sink depends partly on how plant biomass and soil organic carbon (SOC) stocks respond to future increases in atmospheric CO2 (refs. 2,3). Although plant biomass often increases in elevated CO2 (eCO2) experiments4–6, SOC has been observed to increase, remain unchanged or even decline7. The mechanisms that drive this variation across experiments remain poorly understood, creating uncertainty in climate projections8,9. Here we synthesized data from 108 eCO2 experiments and found that the effect of eCO2 on SOC stocks is best explained by a negative relationship with plant biomass: when plant biomass is strongly stimulated by eCO2, SOC storage declines; conversely, when biomass is weakly stimulated, SOC storage increases. This trade-off appears to be related to plant nutrient acquisition, in which plants increase their biomass by mining the soil for nutrients, which decreases SOC storage. We found that, overall, SOC stocks increase with eCO2 in grasslands (8 ± 2 per cent) but not in forests (0 ± 2 per cent), even though plant biomass in grasslands increase less (9 ± 3 per cent) than in forests (23 ± 2 per cent). Ecosystem models do not reproduce this trade-off, which implies that projections of SOC may need to be revised. A synthesis of elevated carbon dioxide experiments reveals that when plant biomass is strongly stimulated by elevated carbon dioxide levels, soil carbon storage declines, and where biomass is weakly stimulated, soil carbon accumulates.

Population declines and demographic changes of Chinook salmon (Oncorhynchus tshawytscha), have been documented throughout this species’ range, though information on natural and anthropogenic mechanisms related to these changes are not fully understood. To provide insights into marine behaviors and survival of Chinook salmon, 40 pop-up satellite archival tags (PSATs), that collected environmental data, were attached to large (69–100 cm FL) Chinook salmon caught in the marine waters of Cook Inlet, Alaska. PSATs provided evidence of predation on tagged Chinook salmon by ectothermic and unconfirmed predators, and provided valuable information about the migratory characteristics and occupied depths and temperatures of this species while occupying Cook Inlet and the Gulf of Alaska. The results from this study suggest that late-marine mortality of Chinook salmon of a variety of stock-origins by apex predators is more common in Cook Inlet than previously thought, and may be used to improve our understanding this species’ population dynamics. Furthermore, results from this study adds to the existing knowledge of marine habitat use by Chinook Salmon and may be useful in assessing the vulnerability and interactions between this species and anthropogenic activities.

Hygienic behavior is a social defense mechanism against parasites and pathogens in honeybees. We studied the genetic basis of hygienic behavior in African-derived Apis mellifera by performing RNA sequencing on brains of individual honeybee workers observed performing hygienic behavior, in order to identify expression changes linked with this behavior. We also used the transcriptome data to search for single nucleotide polymorphism (SNP) variation in genes previously associated with the trait in other A. mellifera populations. The analysis revealed 49 differentially expressed genes (DEG), most of them upregulated during hygienic acts. One DEG, Apidaecin, also showed SNP variation across samples, providing a promising candidate gene for both expression-based and heritable variation in hygienic behavior. We also identified 27 additional SNPs in the coding regions of five candidate genes previously linked with honeybee hygienic behavior. These results provide a useful starting place to analyze the genetic basis of hygienic behavior in African-derived honeybees.

Environmental disturbances and fishing are well known drivers of coral reef fish population size, length-frequency, and assemblage structure. However, few studies have partitioned the spatial and temporal impacts of multiple disturbance events and long-term no-take marine reserve (NTMR) protection on the biomass of juvenile and adult reef-fishes based on the known size of sexual maturity. Here, we document responses in the biomass of juvenile and adult wrasses (Labridae) Hemigymnus melapterus, H. fasciatus, Cheilinus fasciatus, and Oxycheilinus digramma, to environmental disturbance events, NTMR protection, and predator density on inshore fringing coral reefs at the Palm and Whitsunday Island groups, Great Barrier Reef (GBR), Australia from 2007 to 2018 (12 years). The biomass of juvenile and adult wrasses on inshore GBR reefs were driven predominantly by benthic habitat associations, rather than by NTMR protection or density of wrasse predators (Plectropomus spp.). Despite similar species-specific associations of juvenile and adult wrasses with benthic cover, juvenile wrasse biomass consistently declined following coral bleaching and cyclone events. Conversely, adult wrasses had variable responses to disturbance events, including some increases in biomass. Disturbance-mediated declines in the biomass of juvenile wrasses are likely to generate ongoing reductions in the abundance of these species on inshore GBR reefs. Our findings provide further evidence that habitat loss impacts a range of coral reef fishes beyond those that are directly reliant upon live coral. Shifts in assemblage structure, loss of biodiversity, and reductions in fishery productivity will become increasingly apparent in coral reef ecosystems if anthropogenic global warming continues unabated.

Organoids can shed light on the dynamic interplay between complex tissues and rare cell types within a controlled microenvironment. Here, we develop gut organoid cocultures with type-1 innate lymphoid cells (ILC1) to dissect the impact of their accumulation in inflamed intestines. We demonstrate that murine and human ILC1 secrete transforming growth factor β1, driving expansion of CD44v6 + epithelial crypts. ILC1 additionally express MMP9 and drive gene signatures indicative of extracellular matrix remodelling. We therefore encapsulated human epithelial–mesenchymal intestinal organoids in MMP-sensitive, synthetic hydrogels designed to form efficient networks at low polymer concentrations. Harnessing this defined system, we demonstrate that ILC1 drive matrix softening and stiffening, which we suggest occurs through balanced matrix degradation and deposition. Our platform enabled us to elucidate previously undescribed interactions between ILC1 and their microenvironment, which suggest that they may exacerbate fibrosis and tumour growth when enriched in inflamed patient tissues.

Lymph node (LN)–positive cervical cancer is associated with a poor prognosis. We report outcomes for women with LN-positive cervical cancer treated with intensity-modulated radiation therapy (IMRT) with dose-escalated simultaneous integrated boost (SIB) to involved LNs. Between 2005 and 2017, 59 women with LN-positive, non-metastatic, cervical cancer underwent definitive chemoradiotherapy (CRT) with an image-guided LN boost to a median dose of 56.25 Gy in 25 fractions. Acute and late adverse events (AEs) were recorded per common terminology criteria for adverse events. The Kaplan-Meier method was used to estimate the overall survival (OS), progression-free survival (PFS), and locoregional control (LRC). Median age was 49 years (IQR 37–56). Women had involved LNs in the pelvis (56%) or pelvis and para-aortic (PA) LNs (44%), with a median of 3 (IQR 2–6) grossly involved LNs per patient. Median follow-up was 30 months (IQR 11–45). Estimated 3-year OS, PFS, and LRC were 67% (95% CI, 51%–84%), 60% (95% CI, 45%–76%), and 89% (95% CI, 76%–99%), respectively. PA LN involvement (HR 2.51; 95% CI, 1.05–5.99; p = 0.04) and the presence of ≥ 4 grossly involved LNs (HR 2.79; 95% CI, 1.16–6.71; p = 0.02) were associated with a higher risk of disease progression on univariate analysis. The incidence of treatment-related acute grade 3+ acute GI or GU AEs was 3%, while late GI or GU treatment-related AEs occurred in 12%. Chemoradiation with a LN-directed SIB for women with LN-positive cervical cancer is well tolerated and is associated with excellent oncologic outcomes. In this report, we evaluated the oncologic efficacy and adverse events associated with definitive chemoradiotherapy with a simultaneous integrated boost to grossly involved lymph nodes for women with lymph node–positive cervical cancer. We have identified acceptable rates of adverse events and excellent oncologic outcomes, even in a very high risk cohort of women with cervical cancer.

Cricket is a popular and increasingly wealthy bat-and-ball sport. Cricket bats made from willow are the focus of increasing scientific research and innovation, and in this paper, an innovative approach to improving the performance of cricket bats is described. Parametric modeling and genetic algorithms were used to converge the location of two points on a bat that are associated with increased velocity of a ball rebounding off bats: vibrational nodal points and center of percussion (COP). This modeling was able to reduce the distance between nodal points and COP from 174.5 to 98.1 mm. This change occurred as a result of modifications to the geometry of the bat notably shifting its mass toward its end, and keel-shaped sculpting of the back of the bat. These features are seen in some modern high-performance bats. However, the keel-shaped sculpting of the new bat was more sharply incurvate at the center and ends of the bat. The authors conclude that the combination of parametric modeling and optimization using genetic algorithms is a powerful tool for exploring virtual designs for cricket bats that are based on performance criteria, and suggest that additional novel bat designs could arise through multi-objective modeling and optimization using genetic algorithms.

BACKGROUND: Hyperpolarized helium 3 magnetic resonance imaging ((3)He MRI) is useful for investigating pulmonary physiology of pediatric asthma, but a detailed assessment of the safety profile of this agent has not been performed in children. OBJECTIVE: To evaluate the safety of (3)He MRI in children and adolescents with asthma. MATERIALS AND METHODS: This was a retrospective observational study. (3)He MRI was performed in 66 pediatric patients (mean age 12.9 years, range 8–18 years, 38 male, 28 female) between 2007 and 2017. Fifty-five patients received a single repeated examination and five received two repeated examinations. We assessed a total of 127 (3)He MRI exams. Heart rate, respiratory rate and pulse oximetry measured oxygen saturation (SpO(2)) were recorded before, during (2 min and 5 min after gas inhalation) and 1 h after MRI. Blood pressure was obtained before and after MRI. Any subjective symptoms were also noted. Changes in vital signs were tested for significance during the exam and divided into three subject age groups (8–12 years, 13–15 years, 16–18 years) using linear mixed-effects models. RESULTS: There were no serious adverse events, but three minor adverse events (2.3%; headache, dizziness and mild hypoxia) were reported. We found statistically significant increases in heart rate and SpO(2) after (3)He MRI. The youngest age group (8–12 years) had an increased heart rate and a decreased respiratory rate at 2 min and 5 min after (3)H inhalation, and an increased SpO(2) post MRI. CONCLUSION: The use of (3)He MRI is safe in children and adolescents with asthma.

Lie-telling and secret-keeping are common behaviors during adolescence. Given the importance of honesty for building trust in positive relationships, the present study examined relations between lie-telling, secret-keeping, and relationship quality over time. Additionally, given the protective role of positive relationships in developing depression, the present study examined how lying to and keeping secrets from parents related to depressive symptoms over time. Children and adolescents (N = 1313; 8 to 15 years old at Time 1, Mage= 11.65, SD = 11.75; 50.04% male) reported on lying to parents, secret-keeping from parents, relationship quality with parents, and depressive symptoms at two time points one year apart. The results indicated that greater secret-keeping was bidirectionally associated with poorer parent-child relationship quality and greater depressive symptoms over time. Thus, keeping secrets from parents appears to be an important behavior to examine in the context of development between late childhood and adolescence.

Clinical classification is essential for estimating disease prevalence but is difficult, often requiring complex investigations. The widespread availability of population level genetic data makes novel genetic stratification techniques a highly attractive alternative. We propose a generalizable mathematical framework for determining disease prevalence within a cohort using genetic risk scores. We compare and evaluate methods based on the means of genetic risk scores’ distributions; the Earth Mover’s Distance between distributions; a linear combination of kernel density estimates of distributions; and an Excess method. We demonstrate the performance of genetic stratification to produce robust prevalence estimates. Specifically, we show that robust estimates of prevalence are still possible even with rarer diseases, smaller cohort sizes and less discriminative genetic risk scores, highlighting the general utility of these approaches. Genetic stratification techniques offer exciting new research tools, enabling unbiased insights into disease prevalence and clinical characteristics unhampered by clinical classification criteria., Estimating disease prevalence in biobanks is prone to error, especially for self-reported traits. Here, the authors propose a method to estimate the prevalence of a disease within a cohort based on genetic risk scores.

The optical characteristics of materials, such as their magnetooptical effects, birefringence, optical activities, linear and circular dichroism, are probed via the polarisation states of light transmitted through or reflected from the specimens. As such, the measurements of the polarisation states play an important role in many research disciplines. Experimentally, Stokes parameters provide a full description of the polarisation states of light. We report the implementation of a dual- photoelastic modulator based polarimeter in a light microscope, enabling the determination of Stokes parameters at each pixel. As a case study, polarimetric images of liquid crystal droplets of different internal structures are obtained, showing their distinct polarisation characteristics. We demonstrate that the prototype Stokes polarimetric microscope allows the quantitative determination of the polarisation characteristics of light at the object plane and enables the access of the information of full polarisation states as compared to a conventional cross polariser microscope. This work shows that Stokes polarimetric microscopy may find potential applications in a wide range of research fields.

We have developed a high-throughput drug discovery platform, measuring fluorescence resonance energy transfer (FRET) with fluorescent alpha-synuclein (αSN) biosensors, to detect spontaneous pre-fibrillar oligomers in living cells. Our two αSN FRET biosensors provide complementary insight into αSN oligomerization and conformation in order to improve the success of drug discovery campaigns for the treatment of Parkinson’s disease. We measure FRET by fluorescence lifetime, rather than traditional fluorescence intensity, providing a structural readout with greater resolution and precision. This facilitates identification of compounds that cause subtle but significant conformational changes in the ensemble of oligomeric states that are easily missed using intensity-based FRET. We screened a 1280-compound small-molecule library and identified 21 compounds that changed the lifetime by >5 SD. Two of these compounds have nanomolar potency in protecting SH-SY5Y cells from αSN-induced death, providing a nearly tenfold improvement over known inhibitors. We tested the efficacy of several compounds in a primary mouse neuron assay of αSN pathology (phosphorylation of mouse αSN pre-formed fibrils) and show rescue of pathology for two of them. These hits were further characterized with biophysical and biochemical assays to explore potential mechanisms of action. In vitro αSN oligomerization, single-molecule FRET, and protein-observed fluorine NMR experiments demonstrate that these compounds modulate αSN oligomers but not monomers. Subsequent aggregation assays further show that these compounds also deter or block αSN fibril assembly.

Organisations acting to conserve and protect species across large spatial scales prioritise to optimise use of resources. Spatial conservation prioritization tools typically focus on identifying areas containing species groups of interest, with few tools used to identify the best areas for single-species conservation, in particular, to conserve currently widespread but declining species. A single-species prioritization framework, based on temporal and spatial patterns of occupancy and abundance, was developed to spatially prioritize conservation action for widespread species by identifying smaller areas to work within to achieve predefined conservation objectives. We demonstrate our approach for 29 widespread bird species in the UK, using breeding bird atlas data from two periods to define distribution, relative abundance and change in relative abundance. We selected occupied 10-km squares with abundance trends that matched species conservation objectives relating to maintaining or increasing population size or range, and then identified spatial clusters of squares for each objective using a Getis-Ord-Gi* or near neighbour analysis. For each species, the framework identified clusters of 20-km squares that enabled us to identify small areas in which species recovery action could be prioritized. Our approach identified a proportion of species’ ranges to prioritize for species recovery. This approach is a relatively quick process that can be used to inform single-species conservation for any taxa if sufficiently fine-scale occupancy and abundance information is available for two or more time periods. This is a relatively simple first step for planning single-species focussed conservation to help optimise resource use.

Due to investments in interdisciplinary research endeavors, the number and variety of interdisciplinary research centers have grown exponentially during the past decades. While interdisciplinary research centers rely on varied organizational arrangements, we know little about the conditions and processes that mediate collaborative arrangements and interdisciplinary research outcomes. This study examines how different collaborative arrangements shape scholars’ experiences of interdisciplinary research and understandings of interdisciplinary knowledge culminations in the context of university-based research centers. We conducted three in-depth qualitative case studies on different centers, which recruited researchers from natural sciences, medicine, and social sciences. We refer to them as the Biotech Center, the Environmental Center, and the Premature Birth Center. Our analysis of 53 interviews with interdisciplinary scholars across the three centers demonstrates that the scholars perceive particular features of the centers’ collaborative arrangements as meaningful for interdisciplinary collaboration. Specifically, the center’s mission, physical architecture, and leadership and task structure were seen as affecting scholars’ motivation, interaction, and inclusion in the centers, which then shaped the interdisciplinary knowledge culminations. At the Biotech Center, knowledge was translated towards concrete products, at the Environmental Center knowledge was pooled together from varied fields to create new problem framings, and at the Premature Birth Center, interdisciplinary collaboration was crafted through top-down knowledge brokerage.

Companies are increasing their use of cause-related marketing as a means of communicating their commitment to corporate social responsibility while accomplishing their strategic goals. Although prior studies suggest that consumers react positively to cause-related marketing programs, understanding of their impact on financial performance remains limited. To address this gap, the authors employ an event study to examine the effects of cause-related marketing announcements on shareholder value using a sample of firms that appeared on Fortune’s Most Admired All-Star list between 2005 and 2017. Study results show that announcement of these initiatives results in a significant loss of shareholder value. These losses are most pronounced for firms making monetary-only contributions, in comparison to those that make in-kind donations. In addition, the negative effects are mitigated for firms that have stronger reputations, have greater resource slack, and operate in more dynamic industries. Moreover, low-reputation and low-slack firms benefit most from in-kind contributions.

Western Australia’s coral reefs have largely escaped the chronic pressures affecting other reefs around the world, but are regularly affected by seasonal storms and cyclones, and increasingly by heat stress and coral bleaching. Reef systems north of 18°S have been impacted by heat stress and coral bleaching during strong El Nino phases and those further south during strong La Nina phases. Cumulative heat stress and the extent of bleaching throughout the northern reefs in 2016 were higher than at any other time on record. To assess the changing regime of disturbance to reef systems across Western Australia (WA), we linked their site-specific exposure to damaging waves and heat stress since 1990 with mean changes in coral cover. Since 2010, there has been a noticeable increase in heat stress and coral bleaching across WA. Over half the reef systems have been severely impacted by coral bleaching since 2010, which was further compounded by cyclones at some reefs. For most (75%) reef systems with long-term data (5–26 yrs), mean coral cover is currently at (or near) the lowest on record and a full recovery is unlikely if disturbances continue to intensify with climate change. However, some reefs have not yet experienced severe bleaching and their coral cover has remained relatively stable or increased in recent years. Additionally, within all reef systems the condition of communities and their exposure to disturbances varied spatially. Identifying the communities least susceptible to future disturbances and linking them through networks of protected areas, based on patterns of larval connectivity, are important research and management priorities in coming years while the causes of climate change are addressed.

Ocular injury and vision loss are rare complications of surgery. Spine surgery has been identified as particularly high risk for postoperative vision loss; nevertheless, ocular injuries have not been comprehensively assessed in this patient population. This historical cohort study assessed incidence, cause, and risk factors of perioperative ocular injury after spine surgery at a tertiary care medical centre from January 1, 2006 through January 31, 2018. Patients were included who had ocular injury identified during an ophthalmology consultation in the first seven postoperative days. Differences in demographic, laboratory, intraoperative, and postoperative characteristics between those experiencing or not experiencing ocular injury were assessed with Fisher exact and Wilcoxon signed-rank tests for categorical and continuous variables, respectively. Of 20,128 qualifying spine surgeries, 39 cases of perioperative ocular injuries were identified (39/20,128; 0.19% [95% confidence interval (CI), 0.14 to 0.26]). The most common ocular injury was blurry vision of unknown cause (13/39; 33%; 95% CI, 18.6 to 46.4), followed by ischemic optic neuropathy (9/39; 23%; 95% CI, 12.6 to 38.3) and corneal abrasion (7/39; 18%; 95% CI, 9.0 to 32.7). All cases of blurry vision of unknown cause were diagnosed via ophthalmology consultation and resolved within several days. Patients with perioperative ocular injury were more likely to have baseline anemia, have undergone fusion and instrumentation procedures, and had longer operative times with greater crystalloid, colloid, and transfusion requirements and more blood loss. Although not representing a causal relationship, these data suggest that surgical factors may have a greater role than demographic characteristics or other clinical factors in the development of perioperative ocular injury. Surgeons, anesthesiologists, and patients should be aware of the increased risk of ocular injury that accompanies longer, more extensive spine operations.

Transmission routes impact pathogen virulence and genetics, therefore comprehensive knowledge of these routes and their contribution to pathogen circulation is essential for understanding host-pathogen interactions and designing control strategies. Deformed wing virus (DWV), a principal viral pathogen of honey bees associated with increased honey bee mortality and colony losses, became highly virulent with the spread of its vector, the ectoparasitic mite Varroa destructor. Reproduction of Varroa mites occurs in capped brood cells and mite-infested pupae from these cells usually have high levels of DWV. The removal of mite-infested pupae by worker bees, Varroa Sensitive Hygiene (VSH), leads to cannibalization of pupae with high DWV loads, thereby offering an alternative route for virus transmission. We used genetically tagged DWV to investigate virus transmission to and between worker bees following pupal cannibalisation under experimental conditions. We demonstrated that cannibalization of DWV-infected pupae resulted in high levels of this virus in worker bees and that the acquired virus was then transmitted between bees via trophallaxis, allowing circulation of Varroa-vectored DWV variants without the mites. Despite the known benefits of hygienic behaviour, it is possible that higher levels of VSH activity may result in increased transmission of DWV via cannibalism and trophallaxis.

Asthma with severe exacerbation is the most common cause of hospitalization among young children. We aim to increase the understanding of this clinically important disease entity through a genome-wide association study. The discovery analysis comprises 2866 children experiencing severe asthma exacerbation between ages 2 and 6 years, and 65,415 non-asthmatic controls, and we replicate findings in 918 children from the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC) birth cohorts. We identify rs281379 near FUT2/MAMSTR on chromosome 19 as a novel risk locus (OR = 1.18 (95% CI = 1.11–1.25), Pdiscovery = 2.6 × 10−9) as well as a biologically plausible interaction between functional variants in FUT2 and ABO. We further discover and replicate a potential causal mechanism behind this interaction related to S. pneumoniae respiratory illnesses. These results suggest a novel mechanism of early childhood asthma and demonstrates the importance of phenotype-specificity for discovery of asthma genes and epistasis., Genetic variants discovered through genome-wide association studies for asthma together account for a small portion of the heritability. Here, the authors identify a possible epistatic relationship between coding variants in FUT2 and ABO, especially pronounced in severe and early onset asthma.

Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remain poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate a globally consistent, continuous index of forest condition as determined by the degree of anthropogenic modification. Globally, only 17.4 million km2 of forest (40.5%) has high landscape-level integrity (mostly found in Canada, Russia, the Amazon, Central Africa, and New Guinea) and only 27% of this area is found in nationally designated protected areas. Of the forest inside protected areas, only 56% has high landscape-level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally., Mapping and quantifying degree of forest modification is critical to conserve and manage forests. Here the authors propose a new quantitative metric for landscape integrity and apply it to a global forest map, showing that less than half of the world’s forest cover has high integrity, most of which is outside nationally designed protected areas.

Biofluid-based metabolomics has the potential to provide highly accurate, minimally invasive diagnostics. Metabolomics studies using mass spectrometry typically reduce the high-dimensional data to only a small number of statistically significant features, that are often chemically identified—where each feature corresponds to a mass-to-charge ratio, retention time, and intensity. This practice may remove a substantial amount of predictive signal. To test the utility of the complete feature set, we train machine learning models for health state-prediction in 35 human metabolomics studies, representing 148 individual data sets. Models trained with all features outperform those using only significant features and frequently provide high predictive performance across nine health state categories, despite disparate experimental and disease contexts. Using only non-significant features it is still often possible to train models and achieve high predictive performance, suggesting useful predictive signal. This work highlights the potential for health state diagnostics using all metabolomics features with data-driven analysis.

Background Gut microbial communities can contribute positively and negatively to host health. So far, eight core bacterial taxonomic clusters have been reported in honey bees. These bacteria are involved in host metabolism and defenses. Nosema ceranae is a gut intracellular parasite of honey bees which destroys epithelial cells and gut tissue integrity. Studies have shown protective impacts of honey bee gut microbiota towards N. ceranae infection. However, the impacts of N. ceranae on the relative abundance of honey bee gut microbiota remains unclear, and has been confounded during prior infection assays which resulted in the co-inoculation of bacteria during Nosema challenges. We used a novel method, the suppression of N. ceranae with specific siRNAs, to measure the impacts of Nosema on the gut microbiome. Results Suppressing N. ceranae led to significant positive effects on microbial abundance. Nevertheless, 15 bacterial taxa, including three core taxa, were negatively correlated with N. ceranae levels. In particular, one co-regulated group of 7 bacteria was significantly negatively correlated with N. ceranae levels. Conclusions N. ceranae are negatively correlated with the abundance of 15 identified bacteria. Our results provide insights into interactions between gut microbes and N. ceranae during infection.

Recognising timescale as an adjustable dimension in porous solids provides a new perspective to develop novel four-dimensional framework materials. The deliberate design of three-dimensional porous framework architectures is a developed field; however, the understanding of dynamics in open frameworks leaves a number of key questions unanswered: What factors determine the spatiotemporal evolution of deformable networks? Can we deliberately engineer the response of dynamic materials along a time-axis? How can we engineer energy barriers for the selective recognition of molecules? Answering these questions will require significant methodological development to understand structural dynamics across a range of time and length scales., As the field of metal-organic frameworks is maturing, understanding the dynamics of open frameworks is progressing and rational approaches are under development. Here, the authors outline challenges and potential routes to engineering the spatio-temporal evolution of dynamic metal-organic frameworks.

Revealing the mechanisms underlying the reversible physiology of hibernation could have applications to both human and animal health as hibernation is often associated with disease-like states. The present study uses RNA-sequencing to reveal the tissue and seasonal transcriptional changes occurring in grizzly bears (

Understanding structural transitions within macromolecules remains an important challenge in biochemistry, with important implications for drug development and medicine. Insight into molecular behavior often requires residue-specific dynamics measurement at micromolar concentrations. We studied MP01-Gen4, a library peptide selected to rapidly undergo bioconjugation, by using electron paramagnetic resonance (EPR) to measure conformational dynamics. We mapped the dynamics of MP01-Gen4 with residue-specificity and identified the regions involved in a structural transformation related to the conjugation reaction. Upon reaction, the conformational dynamics of residues near the termini slow significantly more than central residues, indicating that the reaction induces a structural transition far from the reaction site. Arrhenius analysis demonstrates a nearly threefold decrease in the activation energy of conformational diffusion upon reaction (8.0 kBT to 3.4 kBT), which occurs across the entire peptide, independently of residue position. This novel approach to EPR spectral analysis provides insight into the positional extent of disorder and the nature of the energy landscape of a highly reactive, intrinsically disordered library peptide before and after conjugation.

Diabetes mellitus (DM) is a chronic disease that results in a variety of systemic complications. Recently, stem cell-based therapies have been proposed as potential modalities to manage DM related complications. Mesenchymal stem cell (MSC) based therapies are often considered as an ideal stem cell-based treatment for DM management due to their immunosuppressive characteristics, anti-inflammatory properties and differentiation potential. While MSCs show tremendous promise, the underlying functional deficits of MSCs in DM patients is not well understood. Using the MEDLINE database to define these functional deficits, our search yielded 1826 articles of which 33 met our inclusion criteria. This allowed us to review the topic and illuminate four major molecular categories by which MSCs are compromised in both Type 1 DM and Type II DM models which include: (1) changes in angiogenesis/vasculogenesis, (2) altered pro-inflammatory cytokine secretion, (3) increased oxidative stress markers and (4) impaired cellular differentiation and decreased proliferation. Knowledge of the deficits in MSC function will allow us to more clearly assess the efficacy of potential biologic therapies for reversing these dysfunctions when treating the complications of diabetic disease.

Genetic diversity and connectivity are key factors in determining a population’s resilience to future disturbance. This is especially relevant to corals, which are in global decline due to increasing frequency and strength of thermal anomalies and severe tropical cyclones. While many studies have investigated genetic diversity and population structure in corals, they focused on species being removed at the greatest rate from coral reefs, acroporids and pocilloporids, and it is unclear whether the patterns observed in these species reflects those found in more resilient species. Here, we use microsatellite markers and two Lagrangian models with differing resolutions, to investigate population structure in a stress-tolerant coral survivor Cyphastrea microphthalma, Family Merulinidae, along the north-western Australian coastline. We found evidence of four genetic clusters with some level of admixture among them. However, while there was evidence of population structure within the intensively sampled Pilbara region, the patterns of connectivity differed to those reported previously. WA populations of C. microphthalma were also characterised by lower levels of genetic diversity at higher latitudes. High- and moderate-resolution Lagrangian models did not significantly predict regional-scale genetic connectivity across the Pilbara and Ningaloo (500 km). Although the high-resolution model explained an order of magnitude more genetic variation, suggesting model resolution and resolving coastal processes are important. Over broad spatial scales (nearly 2000 km), all moderate-resolution model particle release durations significantly predicted the genetic differentiation, although over-water distance best-predicted the genetic distance across this spatial scale. This study improves the understanding of connectivity in this region by focusing on a stress-tolerant species incorporating a spatially more intensive sampling effort than previous coral studies. It also shows that further development of Lagrangian models is required, such as inclusion of multi-generational stepwise models and larval behaviour, to improve predictions of connectivity for this coral species in this region.

This study was funded by the Chevron-operated Wheatstone Project's State Environmental Offsets Program and administered by the Department of Biodiversity, Conservation and Attractions. The Wheatstone Project is a joint venture between Australian subsidiaries of Chevron, Kuwait Foreign Petroleum Exploration Company (KUFPEC), Woodside Petroleum Limited and Kyushu Electric Power Company, together with PE Wheatstone Pty Ltd (part owned by TEPCO). Funding support was also received from the Gorgon Barrow Island Net Conservation Benefits Fund, which is administered by the Department of Biodiversity, Conservation and Attractions. Thank you to Helen Chedzey and Mark Broomhall from the Remote Sensing and Satellite Research Group at Curtin University for generating and providing the remotely sensed total suspended solids data for this study.

Nosema ceranae causes widespread infection in adult workers of European honey bees, Apis mellifera, and has often been linked to honey bee colony losses worldwide. Previous investigations of honey bee immune response to N. ceranae infection were largely based on laboratory experiment, however, little is known about the immune response of honey bees that are naturally infected by N. ceranae. Here, we compared the infection levels of N. ceranae in three different categories of adult bees (emergent bees, nurses, and foragers) and detected the host immune response to the N. ceranae infection under natural conditions. Our studies showed that the Nosema spore load and infection prevalence varied among the different types of adult workers, and both of them increased as honey bees aged: No infection was detected in emergent bees, nurses had a medium spore load and prevalence, while foragers were with the highest Nosema infection level and prevalence. Quantification of the mRNA levels of antimicrobial peptides (abaecin, apidaecin, defensin-1, defensin-2, and hymenoptaecin) and microbial recognition proteins (PGRP-S1, PGRP-S2, PGRP-S3, PGRP-LC, GNBP1-1, and GNBP1-2) confirmed the involvement of the Toll and/or Imd immune pathways in the host response to N. ceranae infection, and revealed an activation of host immune response by N. ceranae infection under natural conditions. Additionally, the levels of immune response were positively correlated with the Nosema spore loads in the infected bees. The information gained from this study will be relevant to the predictive modeling of honey bee disease dynamics for Nosema disease prevention and management.

Adherence to antiretroviral therapy (ART) is associated with positive health outcomes among HIV+ patients. However, non-adherence remains high. Though factors that account for non-adherence remain unclear, social support has been consistently associated with ART adherence. As such, identifying malleable factors that hinder patients' ability to form supportive relationships may have consequence for improving ART adherence. Emotional avoidance (EA) may be one such factor given that it has been linked to difficulties in social situations. The present study examined relations among EA, the patient-provider relationship, other sources of social support, and ART adherence within a sample of HIV+ ART-prescribed patients. High EA was related to poor adherence and patient-provider relationships. EA was indirectly related to poor adherence through poorer patient-provider interactions. The indirect relation of EA to ART adherence through other sources of social support was not significant. Implications for developing targeted behavioral interventions focused on improving ART adherence are discussed.

Atom probe tomography and transmission electron microscopy are used to analyze magnetron-sputtered MoS2 films containing Ti and Au/Sb2O3 as a model system for tribological coatings. Transmission electron microscopy characterization showed that the Ti–MoS2 film is dense and featureless whereas Sb2O3/Au–MoS2 film is less dense and have columnar morphology. Three-dimensional atom probe reconstructions revealed that the Ti–MoS2 films have a homogeneous composition and contain about 15 at.% Ti, which is uniformly distributed throughout the MoS2 matrix without any evidence of Ti precipitation. Sb2O3/Au–MoS2 films also showed homogeneous distribution of Sb2O3 throughout the MoS2 matrix and the presence of Au-rich precipitates. The complementary techniques of atom probe tomography and transmission electron microscopy indicate that Ti and Sb2O3 incorporation in the deposition of MoS2 produces amorphous microstructures, whereas the addition of Au forms nano-sized and well-dispersed precipitates.

Coral reefs are periodically impacted by disturbance events that reduce live coral cover and habitat complexity, with concomitant effects on fish assemblage structure. While the density of some fish species may increase following coral loss, most species decline. Determining which species are ‘winners’ and ‘losers’ following disturbances is fundamental to inform projections of future reef community structure, biodiversity, and productivity. Here, we analyse a long-term (2006–2018), spatially extensive (≈ 700 km) ‘natural experiment’ in which the responses of 11 wrasse taxa to acute disturbance events and no-take marine reserve (NTMR) protection were quantified on fringing coral reefs in the Palm (18°34′ S, 146°29′ E), Whitsunday (20°08′ S, 148°56′ E), and Keppel Island (23°10′ S, 150°57′ E) groups, Great Barrier Reef, Australia. The responses of wrasse densities to benthic habitat change were taxa specific and temporally consistent. Disturbance-mediated reductions in live hard coral cover and/or habitat complexity resulted in density declines for Hemigymnus melapterus, Hemigymnus fasciatus, Cheilinus fasciatus, Labroides spp., Oxycheilinus digramma, and Thalassoma spp. Conversely, Halichoeres spp. densities correlated positively with increased relative cover of sand and rubble, while Stethojulis spp., Anampses spp., Epibulus insidiator, and Bodianus spp. displayed variable responses to habitat changes. No wrasses exhibited an NTMR effect and predator density, irrespective of NTMR status, only influenced five taxa across all island groups. The lack of NTMR effects and variable top-down predator effects suggest that taxa-specific benthic habitat associations were the predominant drivers of wrasse densities on inshore GBR reefs.