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Abstract Choline is recognized as an essential nutrient for Atlantic salmon at all developmental stages. However, its dietary requirement is not well defined. Choline plays a critical role in lipid transport, and the clearest deficiency sign is intestinal steatosis. The present work, aiming to find whether lipid source and fish size may affect steatosis symptoms, was one of a series of studies conducted to identify which production-related conditions may influence choline requirement. Six choline-deficient diets were formulated varying in ratios of rapeseed oil to fish oil and fed to Atlantic salmon of 1.5 and 4.5 kg. After eight weeks, somatic characteristics were observed, and the severity of intestinal steatosis was assessed by histological, biochemical, and molecular analyses. Fatty acid composition in pyloric intestine, mesenteric tissue, and liver samples was also quantified. The increasing rapeseed oil level increased lipid digestibility markedly, enhancing lipid supply to the fish. Moreover, small fish consumed more feed, and consequently had a higher lipid intake. In conclusion, the results showed that choline requirement depends on dietary lipid load, which depends on the fatty acid profile as well as the fish size.

Abstract An influenza vaccine approach that overcomes the problem of viral sequence diversity and provides long-lived heterosubtypic protection is urgently needed to protect against pandemic influenza viruses. Here, to determine if lung-resident effector memory T cells induced by cytomegalovirus (CMV)-vectored vaccines expressing conserved internal influenza antigens could protect against lethal influenza challenge, we immunize Mauritian cynomolgus macaques (MCM) with cynomolgus CMV (CyCMV) vaccines expressing H1N1 1918 influenza M1, NP, and PB1 antigens (CyCMV/Flu), and challenge with heterologous, aerosolized avian H5N1 influenza. All six unvaccinated MCM died by seven days post infection with acute respiratory distress, while 54.5% (6/11) CyCMV/Flu-vaccinated MCM survived. Survival correlates with the magnitude of lung-resident influenza-specific CD4 + T cells prior to challenge. These data demonstrate that CD4 + T cells targeting conserved internal influenza proteins can protect against highly pathogenic heterologous influenza challenge and support further exploration of effector memory T cell-based vaccines for universal influenza vaccine development.

In every Intergovernmental Panel on Climate Change (IPCC) Assessment cycle, a multitude of scenarios are assessed, with different scope and emphasis throughout the various Working Group reports and special reports, as well as their respective chapters. Within the reports, the ambition is to integrate knowledge on possible climate futures across the Working Groups and scientific research domains based on a small set of “framing pathways” such as the so-called representative concentration pathways (RCPs) in the Fifth IPCC Assessment Report (AR5) and the shared socioeconomic pathway (SSP) scenarios in the Sixth Assessment Report (AR6). This perspective, initiated by discussions at the IPCC Bangkok workshop in April 2023 on the “Use of Scenarios in AR6 and Subsequent Assessments”, is intended to serve as one of the community contributions to highlight the needs for the next generation of framing pathways that is being advanced under the Coupled Model Intercomparison Project (CMIP) umbrella, which will influence or even predicate the IPCC AR7 consideration of framing pathways. Here we suggest several policy research objectives that such a set of framing pathways should ideally fulfil, including mitigation needs for meeting the Paris Agreement objectives, the risks associated with carbon removal strategies, the consequences of delay in enacting that mitigation, guidance for adaptation needs, loss and damage, and for achieving mitigation in the wider context of societal development goals. Based on this context, we suggest that the next generation of climate scenarios for Earth system models should evolve towards representative emission pathways (REPs) and suggest key categories for such pathways. These framing pathways should address the most critical mitigation policy and adaptation plans that need to be implemented over the next 10 years. In our view, the most important categories are those relevant in the context of the Paris Agreement long-term goal, specifically an immediate action (low overshoot) 1.5 °C pathway and a delayed action (high overshoot) 1.5 °C pathway. Two other key categories are a pathway category approximately in line with current (as expressed by 2023) near- and long-term policy objectives, as well as a higher-emission category that is approximately in line with “current policies” (as expressed by 2023). We also argue for the scientific and policy relevance in exploring two “worlds that could have been”. One of these categories has high-emission trajectories well above what is implied by current policies and the other has very-low-emission trajectories which assume that global mitigation action in line with limiting warming to 1.5 °C without overshoot had begun in 2015. Finally, we note that the timely provision of new scientific information on pathways is critical to inform the development and implementation of climate policy. Under the Paris Agreement, for the second global stocktake, which will occur in 2028, and to inform subsequent development of nationally determined contributions (NDCs) up to 2040, scientific inputs are required by 2027. These needs should be carefully considered in the development timeline of community modelling activities, including those under CMIP7.

Simian immunodeficiency virus (SIV) vaccines based upon 68-1 Rhesus Cytomegalovirus (RhCMV) vectors show remarkable protection against pathogenic SIVmac239 challenge. Across multiple independent rhesus macaque (RM) challenge studies, nearly 60% of vaccinated RM show early, complete arrest of SIVmac239 replication after effective challenge, whereas the remainder show progressive infection similar to controls. Here, we performed viral sequencing to determine whether the failure to control viral replication in non-protected RMs is associated with the acquisition of viral escape mutations. While low level viral mutations accumulated in all animals by 28 days-post-challenge, which is after the establishment of viral control in protected animals, the dominant circulating virus in virtually all unprotected RMs was nearly identical to the challenge stock, and there was no difference in mutation patterns between this cohort and unvaccinated controls. These data definitively demonstrate that viral mutation does not explain lack of viral control in RMs not protected by RhCMV/SIV vaccination. We further demonstrate that during chronic infection RhCMV/SIV vaccinated RMs do not acquire escape mutation in epitopes targeted by RhCMV/SIV, but instead display mutation in canonical MHC-Ia epitopes similar to unvaccinated RMs. This suggests that after the initial failure of viral control, unconventional T cell responses induced by 68-1 RhCMV/SIV vaccination do not exert strong selective pressure on systemically replicating SIV.

Our limited knowledge of the marine mammal fauna in northernmost Greenland and Canada, specifically north of 80°N, relies largely on opportunistic observations collected during expeditions with different objectives. The narwhal (Monodon monoceros) migrates long distances in response to ice formation and decay and is notoriously skittish, avoiding areas with ice breakers. Scattered observations from the past 20 years, assessed together with historical observations after 1881, suggest that there is a population of narwhals that uses Hall Basin and its adjacent fjord systems—for example, Nares Strait—as a summer ground. Dating the tusks and bones that have been found shows that narwhals were present in this area as far back as nearly 7000 years ago. The wintering locations of these narwhals remain unknown, highlighting the need to investigate whether they are vulnerable to hunting activities in north-west Greenland. By gaining a better understanding of the narwhals’ winter behaviour and potential hunting risks, we can develop more informed conservation and management strategies for this population.

Abstract The Hippo pathway’s main effector, Yes-associated protein (YAP), plays a crucial role in tumorigenesis as a transcriptional coactivator. YAP’s phosphorylation by core upstream components of the Hippo pathway, such as mammalian Ste20 kinase 1/2 (MST1/2), mitogen-activated protein kinase kinase kinase kinases (MAP4Ks), and their substrate, large tumor suppressor 1/2 (LATS1/2), influences YAP’s subcellular localization, stability, and transcriptional activity. However, recent research suggests the existence of alternative pathways that phosphorylate YAP, independent of these core upstream Hippo pathway components, raising questions about additional means to inactivate YAP. In this study, we present evidence demonstrating that TSSK1B, a calcium/calmodulin-dependent protein kinase (CAMK) superfamily member, is a negative regulator of YAP, suppressing cellular proliferation and oncogenic transformation. Mechanistically, TSSK1B inhibits YAP through two distinct pathways. Firstly, the LKB1–TSSK1B axis directly phosphorylates YAP at Ser94, inhibiting the YAP–TEAD complex’s formation and suppressing its target genes’ expression. Secondly, the TSSK1B–LATS1/2 axis inhibits YAP via phosphorylation at Ser127. Our findings reveal the involvement of TSSK1B-mediated molecular mechanisms in the Hippo–YAP pathway, emphasizing the importance of multilevel regulation in critical cellular decision-making processes.

Ozone depletion over the polar regions is monitored each year by satellite- and ground-based instruments. In this study, the vortex-averaged ozone loss over the last 3 decades is evaluated for both polar regions using the passive ozone tracer of the chemical transport model TOMCAT/SLIMCAT and total ozone observations from Système d'Analyse par Observation Zénithale (SAOZ) ground-based instruments and Multi-Sensor Reanalysis (MSR2). The passive-tracer method allows us to determine the evolution of the daily rate of column ozone destruction and the magnitude of the cumulative column loss at the end of the winter. Three metrics are used in trend analyses that aim to assess the ozone recovery rate over both polar regions: (1) the maximum ozone loss at the end of the winter, (2) the onset day of ozone loss at a specific threshold, and (3) the ozone loss residuals computed from the differences between annual ozone loss and ozone loss values regressed with respect to sunlit volume of polar stratospheric clouds (VPSCs). This latter metric is based on linear and parabolic regressions for ozone loss in the Northern Hemisphere and Southern Hemisphere, respectively. In the Antarctic, metrics 1 and 3 yield trends of −2.3 % and −2.2 % per decade for the 2000–2021 period, significant at 1 and 2 standard deviations (σ), respectively. For metric 2, various thresholds were considered at the total ozone loss values of 20 %, 25 %, 30 %, 35 %, and 40 %, all of them showing a time delay as a function of year in terms of when the threshold is reached. The trends are significant at the 2σ level and vary from 3.5 to 4.2 d per decade between the various thresholds. In the Arctic, metric 1 exhibits large interannual variability, and no significant trend is detected; this result is highly influenced by the record ozone losses in 2011 and 2020. Metric 2 is not applied in the Northern Hemisphere due to the difficulty in finding a threshold value in enough of the winters. Metric 3 provides a negative trend in Arctic ozone loss residuals with respect to the sunlit VPSC fit of −2.00 ± 0.97 (1σ) % per decade, with limited significance at the 2σ level. With such a metric, a potential quantitative detection of ozone recovery in the Arctic springtime lower stratosphere can be made.

Abstract The relative abundance of Wnt receptors plays a crucial role in controlling Wnt signaling in tissue homeostasis and human disease. While the ubiquitin ligases that ubiquitylate Wnt receptors are well-characterized, the deubiquitylase that reverses these reactions remains unclear. Herein, we identify USP46, UAF1, and WDR20 (USP46 complex) as positive regulators of Wnt signaling in cultured human cells. We find that the USP46 complex is similarly required for Wnt signaling in Xenopus and zebrafish embryos. We demonstrate that Wnt signaling promotes the association between the USP46 complex and cell surface Wnt coreceptor, LRP6. Knockdown of USP46 decreases steady-state levels of LRP6 and increases the level of ubiquitylated LRP6. In contrast, overexpression of the USP46 complex blocks ubiquitylation of LRP6 by the ubiquitin ligases RNF43 and ZNFR3. Size exclusion chromatography studies suggest that the size of the USP46 cytoplasmic complex increases upon Wnt stimulation. Finally, we show that USP46 is essential for Wnt-dependent intestinal organoid viability, likely via its role in LRP6 receptor homeostasis. We propose a model in which the USP46 complex increases the steady-state level of cell surface LRP6 and facilitates the assembly of LRP6 into signalosomes via a pruning mechanism that removes sterically hindering ubiquitin chains.

While abduction remains a rare occurrence in the United States, many parents and caregivers have concerns about children's reactions to strangers and other safety-related behaviors. Abduction is a risk for all children, but may be of specific concern for people with disabilities due to social skill and communication deficits. Behavior analytic interventions can be used to address skill deficits that may leave children with disabilities vulnerable. Systematic searches of electronic databases, forward, and ancestral searches were conducted to find available research on interventions that address abduction-prevention skills for people with disabilities. Fifteen articles were found and summarized. Current interventions assessed in this research included: behavior skills training, in-situ training, video modeling, and social stories, which were used both alone and in combination. Lures were presented mostly by unknown strangers with some studies including responding to uniformed police officers and known individuals. Generalization and maintenance data were included in the majority of studies, and many studies assessed social validity. Research methods were assessed using the What Works Clearinghouse standards and data were assessed using standards for visual analysis. Limitations of the current research are discussed, and future research recommendations are presented.

Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.

ABSTRACTPredators play a central role in shaping community structure, function, and stability. The degree to which bacteriophage predators (viruses that infect bacteria) evolve to be specialists with a single bacterial prey species versus generalists able to consume multiple types of prey has implications for their effect on microbial communities. The presence and abundance of multiple bacterial prey types can alter selection for phage generalists, but less is known about how interactions between prey shape predator specificity in microbial systems. Using a phenomenological mathematical model of phage and bacterial populations, we find that the dominant phage strategy depends on prey ecology. Given a fitness cost for generalism, generalist predators maintain an advantage when prey species compete, while specialists dominate when prey are obligately engaged in cross-feeding interactions. We test these predictions in a synthetic microbial community with interacting strains of Escherichia coli and Salmonella enterica by competing a generalist T5-like phage able to infect both prey against P22vir, an S. enterica-specific phage. Our experimental data conform to our modeling expectations when prey species are competing or obligately mutualistic, although our results suggest that the in vitro cost of generalism is caused by a combination of biological mechanisms not anticipated in our model. Our work demonstrates that interactions between bacteria play a role in shaping ecological selection on predator specificity in obligately lytic bacteriophages and emphasizes the diversity of ways in which fitness trade-offs can manifest.IMPORTANCEThere is significant natural diversity in how many different types of bacteria a bacteriophage can infect, but the mechanisms driving this diversity are unclear. This study uses a combination of mathematical modeling and an in vitro system consisting of Escherichia coli, Salmonella enterica, a T5-like generalist phage, and the specialist phage P22vir to highlight the connection between bacteriophage specificity and interactions between their potential microbial prey. Mathematical modeling suggests that competing bacteria tend to favor generalist bacteriophage, while bacteria that benefit each other tend to favor specialist bacteriophage. Experimental results support this general finding. The experiments also show that the optimal phage strategy is impacted by phage degradation and bacterial physiology. These findings enhance our understanding of how complex microbial communities shape selection on bacteriophage specificity, which may improve our ability to use phage to manage antibiotic-resistant microbial infections.

Narwhal abundance in West Greenland (WG) and East Greenland (EG) was estimated from aerial surveys conducted between 2007 and 2019 at their summer grounds. Analyses were completed using Mark Recapture Distance Sampling and Hidden Markov Line Transect Models taking account of the stochastic availability of diving whales. No statistically significant difference in abundance of narwhals could be detected for the two summer grounds (Melville Bay and Inglefield Bredning) in WG between 2007 and 2019. The distribution of narwhals in Inglefield Bredning was similar between years but in Melville Bay, area usage has decreased >80% since the first survey in 2007. Few detections of narwhals were obtained during the surveys in EG and a common detection function was fitted from combining sightings from seven surveys. Narwhals were found in small aggregations distributed between Nordostrundingen and south to and including Tasiilaq. Abundance of narwhals was estimated for the first time in the relatively unexplored Northeast Greenland (Dove Bay and a restricted coastal area of the Greenland Sea). The abundance in these two areas was 2908 narwhals (CV=0.30; 95% CI:1639-5168) estimated in 2017 for the Greenland Sea and 2297 (0.38; 1123-4745) and 1395 (0.33; 744-2641) narwhals were estimated for Dove Bay in 2017 and 2018, respectively. Both abundance and distribution range of narwhals in Southeast Greenland, where narwhals are subject to subsistence harvest, has decreased significantly between 2008-2017 and narwhals have even disappeared at the southernmost area since the first surveys in 2008.

This article applies object detection to CCTV video material to investigate the potential of using machine learning to automate behavior tracking. This study includes video tapings of two captive Bornean orangutans and their behavior. From a 2 min training video containing the selected behaviors, 334 images were extracted and labeled using Rectlabel. The labeled training material was used to construct an object detection model using Create ML. The use of object detection was shown to have potential for automating tracking, especially of locomotion, whilst filtering out false positives. Potential improvements regarding this tool are addressed, and future implementation should take these into consideration. These improvements include using adequately diverse training material and limiting iterations to avoid overfitting the model.

After the decrease of ozone-depleting substances (ODSs) as a consequence of the Montreal Protocol, it is still challenging to detect a recovery in the total column amount of ozone (total ozone) at northern high latitudes. To assess regional total ozone changes in the “ozone-recovery” period (2000–2020) at northern high latitudes, this study investigates trends from ground-based total ozone measurements at three stations in Norway (Oslo, Andøya, and Ny-Ålesund). For this purpose, we combine measurements from Brewer spectrophotometers, ground-based UV filter radiometers (GUVs), and a SAOZ (Système d'Analyse par Observation Zénithale) instrument. The Brewer measurements have been extended to work under cloudy conditions using the global irradiance (GI) technique, which is also presented in this study. We derive trends from the combined ground-based time series with the multiple linear regression model from the Long-term Ozone Trends and Uncertainties in the Stratosphere (LOTUS) project. We evaluate various predictors in the regression model and found that tropopause pressure and lower-stratospheric temperature contribute most to ozone variability at the three stations. We report significantly positive annual trends at Andøya (0.9±0.7 % per decade) and Ny-Ålesund (1.5±0.1 % per decade) and no significant annual trend at Oslo (0.1±0.5 % per decade) but significantly positive trends in autumn at all stations. Finally we found positive but insignificant trends of around 3 % per decade in March at all three stations, which may be an indication of Arctic springtime ozone recovery. Our results contribute to a better understanding of regional total ozone trends at northern high latitudes, which is essential to assess how Arctic ozone responds to changes in ODSs and to climate change.

The Spitsbergen population of bowhead whales (Balaena mysticetus) was harvested to near extinction during the whaling era. Here, we show possible signs of recovery of the population by reporting observations of two calves in the Scoresby Sund polynya in East Greenland on 2 and 4 May 2022, and it is the first observation of this kind in this area since the early 1900s.

Abstract Background Type 2 Diabetes mellitus (T2DM) is a major risk factor for cardiovascular disease and associated with poor outcome after myocardial infarction (MI). In T2DM, cardiac metabolic flexibility, i.e. the switch between carbohydrates and lipids as energy source, is disturbed. The RabGTPase-activating protein TBC1D4 represents a crucial regulator of insulin-stimulated glucose uptake in skeletal muscle by controlling glucose transporter GLUT4 translocation. A human loss-of-function mutation in TBC1D4 is associated with impaired glycemic control and elevated T2DM risk. The study’s aim was to investigate TBC1D4 function in cardiac substrate metabolism and adaptation to MI. Methods Cardiac glucose metabolism of male Tbc1d4-deficient (D4KO) and wild type (WT) mice was characterized using in vivo [18F]-FDG PET imaging after glucose injection and ex vivo basal/insulin-stimulated [3H]-2-deoxyglucose uptake in left ventricular (LV) papillary muscle. Mice were subjected to cardiac ischemia/reperfusion (I/R). Heart structure and function were analyzed until 3 weeks post-MI using echocardiography, morphometric and ultrastructural analysis of heart sections, complemented by whole heart transcriptome and protein measurements. Results Tbc1d4-knockout abolished insulin-stimulated glucose uptake in ex vivo LV papillary muscle and in vivo cardiac glucose uptake after glucose injection, accompanied by a marked reduction of GLUT4. Basal cardiac glucose uptake and GLUT1 abundance were not changed compared to WT controls. D4KO mice showed mild impairments in glycemia but normal cardiac function. However, after I/R D4KO mice showed progressively increased LV endsystolic volume and substantially increased infarction area compared to WT controls. Cardiac transcriptome analysis revealed upregulation of the unfolded protein response via ATF4/eIF2α in D4KO mice at baseline. Transmission electron microscopy revealed largely increased extracellular matrix (ECM) area, in line with decreased cardiac expression of matrix metalloproteinases of D4KO mice. Conclusions TBC1D4 is essential for insulin-stimulated cardiac glucose uptake and metabolic flexibility. Tbc1d4-deficiency results in elevated cardiac endoplasmic reticulum (ER)-stress response, increased deposition of ECM and aggravated cardiac damage following MI. Hence, impaired TBC1D4 signaling contributes to poor outcome after MI.

Abstract Background Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportionate subunits. To determine how human cells coordinate mitochondrial and nuclear gene expression processes, we tailored ribosome profiling for the unique features of the human mitoribosome. Results We resolve features of mitochondrial translation initiation and identify a small ORF in the 3′ UTR of MT-ND5. Analysis of ribosome footprints in five cell types reveals that average mitochondrial synthesis levels correspond precisely to cytosolic levels across OXPHOS complexes, and these average rates reflect the relative abundances of the complexes. Balanced mitochondrial and cytosolic synthesis does not rely on rapid feedback between the two translation systems, and imbalance caused by mitochondrial translation deficiency is associated with the induction of proteotoxicity pathways. Conclusions Based on our findings, we propose that human OXPHOS complexes are synthesized proportionally to each other, with mitonuclear balance relying on the regulation of OXPHOS subunit translation across cellular compartments, which may represent a proteostasis vulnerability.

Abstract Background Increased head and neck cancer (HNC) survival requires attention to long-term treatment sequelae. Irradiated HNC survivors have a higher ischemic stroke risk. However, the pathophysiology of radiation-induced vasculopathy is unclear. Arterial stiffness could be a biomarker. This study examined alterations in intima-media thickness (IMT) and stiffness-related parameters, shear wave (SWV) and pulse wave velocity (PWV), in irradiated compared to control carotids in unilateral irradiated patients. Methods Twenty-six patients, median 40.5 years, 5–15 years after unilateral irradiation for head and neck neoplasms underwent a bilateral carotid ultrasound using an Aixplorer system with SL18-5 and SL10-2 probes. IMT, SWV, and PWV were assessed in the proximal, mid, and distal common (CCA) and internal carotid artery (ICA). Plaques were characterized with magnetic resonance imaging. Measurements were compared between irradiated and control sides, and radiation dose effects were explored. Results CCA-IMT was higher in irradiated than control carotids (0.54 [0.50–0.61] vs. 0.50 [0.44–0.54] mm, p = 0.001). For stiffness, only anterior mid-CCA and posterior ICA SWV were significantly higher in the irradiated side. A radiation dose–effect was only (weakly) apparent for PWV (R2: end-systolic = 0.067, begin-systolic = 0.155). Ultrasound measurements had good–excellent intra- and interobserver reproducibility. Plaques had similar characteristics but were more diffuse in the irradiated side. Conclusions Increased CCA-IMT and SWV in some segments were seen in irradiated carotids. These alterations, even in young patients, mark the need for surveillance of radiation-induced vasculopathy. Trial registration: clinicaltrials.gov ( https://clinicaltrials.gov/ct2/show/NCT04257968 ).

[This corrects the article DOI: 10.1371/journal.ppat.1009565.].

Evidence of the impact of community-based forest management (CBFM) on conservation outcomes is mixed. Local governance is a key moderating factor, but what constitutes good governance is still up for debate. Desirable institutional features typically arise endogenously, which complicates the analysis of causality. We use an experimental design to analyze the impact on environmental outcomes of adding an externally implemented monitoring regime to an existing CBFM initiative in Ethiopia. We distinguish between bottom-up and top-down monitoring to improve the accountability of local leaders. We find that enhanced bottom-up monitoring by community members does not affect forest outcomes, but top-down monitoring promotes forest conservation. We also identify a mechanism linking top-down monitoring to conservation: leaders work harder to protect the forest, which “crowds in” effort by community members. Our results are not about reducing the role of communities in forest management, they are a plea for oversight by the relevant authority to help communities overcome local power asymmetries.

The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.

Rhesus cytomegalovirus–based (RhCMV-based) vaccine vectors induce immune responses that protect ~60% of rhesus macaques (RMs) from SIVmac239 challenge. This efficacy depends on induction of effector memory–based (EM-biased) CD8+ T cells recognizing SIV peptides presented by major histocompatibility complex-E (MHC-E) instead of MHC-Ia. The phenotype, durability, and efficacy of RhCMV/SIV-elicited cellular immune responses were maintained when vector spread was severely reduced by deleting the antihost intrinsic immunity factor phosphoprotein 71 (pp71). Here, we examined the impact of an even more stringent attenuation strategy on vector-induced immune protection against SIV. Fusion of the FK506-binding protein (FKBP) degradation domain to Rh108, the orthologue of the essential human CMV (HCMV) late gene transcription factor UL79, generated RhCMV/SIV vectors that conditionally replicate only when the FK506 analog Shield-1 is present. Despite lacking in vivo dissemination and reduced innate and B cell responses to vaccination, Rh108-deficient 68-1 RhCMV/SIV vectors elicited high-frequency, durable, EM-biased, SIV-specific T cell responses in RhCMV-seropositive RMs at doses of ≥ 1 × 106 PFU. Strikingly, elicited CD8+ T cells exclusively targeted MHC-Ia–restricted epitopes and failed to protect against SIVmac239 challenge. Thus, Rh108-dependent late gene expression is required for both induction of MHC-E–restricted T cells and protection against SIV.

Mercury (Hg) is a concerning contaminant due to its widespread distribution and tendency to accumulate to harmful concentrations in biota. We used a machine learning approach called random forest (RF) to test for different predictors of Hg concentrations in three species of Colorado reservoir sport fish. The RF approach indicated that the best predictors of 864 mm northern pike (Esox lucius) Hg concentrations were covariates related to salmonid stocking in each study system, while system-specific metrics related to productivity and forage base were the best predictors of Hg concentrations of 381 mm smallmouth bass (Micropterus dolomieu), and walleye (Sander vitreus). Protecting human and ecological health from Hg contamination requires an understanding of fish Hg concentrations and variability across the landscape and through time. The RF approach could be applied to identify potential areas/systems of concern, and predict whether sport fish Hg concentrations may change as a result of a variety of factors to help prioritize, focus, and streamline monitoring efforts to effectively and efficiently inform human and ecological health.

Abstract Background With a growing, younger population of head and neck cancer survivors, attention to long-term side-effects of prior, often radiotherapeutic, treatment is warranted. Therefore, we studied the long-term cognitive effects in young adult patients irradiated for head and neck neoplasms (HNN). Methods Young to middle-aged adults with HNN (aged 18-40 years) and treated with unilateral neck irradiation ≥ 5 years before inclusion underwent cardiovascular risk and neuropsychological assessments and answered validated questionnaires regarding subjective cognitive complaints, fatigue, depression, quality of life, and cancer-specific distress. Additionally, magnetic resonance imaging (MRI) of the brain was performed to assess white matter hyperintensities (WMH), infarctions, and atrophy. Results Twenty-nine patients (aged 24–61, 13 men) median 9.2 [7.3–12.9] years post-treatment were included. HNN patients performed worse in episodic memory (Z-score = -1.16 [-1.58–0.34], p

The Zeppelin Observatory (78.90∘ N, 11.88∘ E) is located on Zeppelin Mountain at 472 m a.s.l. on Spitsbergen, the largest island of the Svalbard archipelago. Established in 1989, the observatory is part of Ny-Ålesund Research Station and an important atmospheric measurement site, one of only a few in the high Arctic, and a part of several European and global monitoring programmes and research infrastructures, notably the European Monitoring and Evaluation Programme (EMEP); the Arctic Monitoring and Assessment Programme (AMAP); the Global Atmosphere Watch (GAW); the Aerosol, Clouds and Trace Gases Research Infrastructure (ACTRIS); the Advanced Global Atmospheric Gases Experiment (AGAGE) network; and the Integrated Carbon Observation System (ICOS). The observatory is jointly operated by the Norwegian Polar Institute (NPI), Stockholm University, and the Norwegian Institute for Air Research (NILU). Here we detail the establishment of the Zeppelin Observatory including historical measurements of atmospheric composition in the European Arctic leading to its construction. We present a history of the measurements at the observatory and review the current state of the European Arctic atmosphere, including results from trends in greenhouse gases, chlorofluorocarbons (CFCs) and hydrochlorofluorocarbons (HCFCs), other traces gases, persistent organic pollutants (POPs) and heavy metals, aerosols and Arctic haze, and atmospheric transport phenomena, and provide an outline of future research directions.

Atmospheric aerosols are an important element of Earth's climate system and have significant impacts on the environment and on human health. Global aerosol modeling has been increasingly used for operational forecasting and as support for decision making. For example, aerosol analyses and forecasts are routinely used to provide air quality information and alerts in both civilian and military applications. The growing demand for operational aerosol forecasting calls for additional observational data that can be assimilated into models to improve model accuracy and predictive skill. These factors have motivated the development, testing, and release of a new near real-time (NRT) level 2 (L2) aerosol product from the Multi-angle Imaging SpectroRadiometer (MISR) instrument on NASA's Terra platform. The NRT product capitalizes on the unique attributes of the MISR aerosol retrieval approach and product contents, such as reliable aerosol optical depth as well as aerosol microphysical information. Several modifications are described that allow for rapid product generation within a 3 h window following acquisition of the satellite observations. Implications for the product quality and consistency are discussed and compared to the current operational L2 MISR aerosol product. Several ways of implementing additional use-specific retrieval screenings are also highlighted.

Interaction of photons with Rydberg atoms can be used to modify quantum states of light. Here the authors demonstrate a controlled nonlinear quantum behavior of multi-photon subtraction in a cascaded system based on Rydberg superatoms.

The increased emergence of cereal stem rust in southern and western Europe, caused by the pathogen Puccinia graminis, and the prevalence of alternate (sexual) host, Berberis species, have regained attention as the sexual host may serve as source of novel pathogen variability that may pose a threat to cereal supply. The main objective of the present study was to investigate the functional role of Berberis species in the current epidemiological situation of cereal stem rust in Europe. Surveys in 11 European countries were carried out from 2018 to 2020, where aecial infections from five barberry species were collected. Phylogenetic analysis of 121 single aecial clusters of diverse origin using the elongation factor 1-α gene indicated the presence of different special forms (aka formae speciales) of P. graminis adapted to different cereal and grass species. Inoculation studies using aecial clusters from Spain, United Kingdom, and Switzerland resulted in 533 stem rust isolates sampled from wheat, barley, rye, and oat, which confirmed the presence of multiple special forms of P. graminis. Microsatellite marker analysis of a subset of 192 sexually-derived isolates recovered on wheat, barley and rye from the three populations confirmed the generation of novel genetic diversity revealed by the detection of 135 multilocus genotypes. Discriminant analysis of principal components resulted in four genetic clusters, which grouped at both local and country level. Here, we demonstrated that a variety of Berberis species may serve as functional alternate hosts for cereal stem rust fungi and highlights the increased risks that the sexual cycle may pose to cereal production in Europe, which calls for new initiatives within rust surveillance, epidemiological research and resistance breeding.

Free-hand volumetric ultrasound (FVUS) facilitates 3D US imaging of large anatomical areas. However, this method is user-dependent and image quality, especially in the scan direction (elevational direction), depends on the number of US images acquired per distance unit. This might affect clinical decision making for example in quantitative ultrasound muscle imaging. This study addresses three goals. First, to determine quantitatively below which number of acquisitions per cm (acq/cm) image quality is affected: the acquisition limit. Second, to determine the translation speed used naturally by sonographers. Third, to demonstrate in vivo possible benefits of utilizing plane wave imaging for FVUS, so-called fast FVUS in order to boost translation speed while maintaining quantitative image information. Fast FVUS enables imaging at much higher framerates and hence the acquisition limit is easier met which allows for much faster transducer translation. From an analysis of the contrast and elevational resolution in a phantom, the average acquisition limit was determined to be 33 acq/cm. Above this limit, the quantitative ultrasound information remained unchanged. This would imply that when imaging at 30 frames per second, a common frame-rate of current 2D ultrasound devices, suboptimal imaging quality is obtained above transducer translation speeds of 9.1 mm/s. The median and maximum transducer translation speed observed in 10 sonographers were 15.8 mm/s and 30.1 mm/s, thus above this limit. Finally, we presented a design of fast FVUS that enabled acquiring 200 fps, and hence, would allow imaging up to speeds of 60.6 mm/s. We demonstrated in vivo in tibialis anterior muscles that more anatomical details were visible with fast FVUS which were lost at the typical framerate. These observations support our hypothesis that fast FVUS would be an ideal method for 3D quantitative muscle ultrasound.

With the intensification of eutrophication, many artificial water supply lakes that act as a biological filter for water diverted from rivers have been built to alleviate water scarcity in Eastern China. In this study, we selected Lake Yanlong, a representative artificial water supply lake in Yancheng City, as our experimental lake to explore how the community composition of fishes changed among different habitat types and assess potential consequences for effective water treatment. From October 2015 to October 2020, we conducted quarterly surveys of fish communities and environmental factors in the Mangshe River (MR; water for lake) compared to four different water treatment zones of Lake Yanlong (PZ, the pretreatment zone with inlet from the MR; EZ, the emergent macrophyte zone; SZ, the submerged macrophyte zone; DZ, the deep purification zone with outlet to urban waterworks). A total of 16,339 individual fish belonging to 11 families and 49 species were collected. Six of the eight dominant species observed across zones were small-bodied fishes. Despite reduced fish species richness, the relative abundance and biomass of fishes tended to be higher in Lake Yanlong relative to the MR. The Shannon-Wiener diversity index, Pielou evenness index, Simpson’s diversity index all decreased from the MR to the DZ in the following sequence: MR < PZ < EZ < SZ < DZ. Analysis of similarities and similarity percentage analysis confirmed that fish communities differed significantly among zones and Coilia ectenes, Carassius auratus, Pseudobrama simony, Hemiculter leucisculus, and Hemiculter bleekeri were the major differentiating species. Mantel’s test and redundancy analysis revealed that water depth, aquatic vegetation coverage, and phytoplankton concentrations were the major factors determining the spatial distribution of fishes when moving from the MR to the DZ of Lake Yanlong. Stocking piscivorous fish can be used as an effective measure to control the abundance of prolific small-bodied fishes in Lake Yanlong. The details backing these findings are important for understanding how the community composition of fishes among habitat types in Lake Yanlong influence water quality, and to develop suitable biomanipulation strategies for the management of fish resources and maintaining proper function of these artificial water supply lakes.

CCR5 is a co-receptor for many transmitted HIV strains. Here, the authors show that biweekly injection of the CCR5-specific antibody Leronlimab protects rhesus macaques against infection following repeated intrarectal challenges of a CCR5-tropic SHIV.

Abstract The impact of breast cancer-related lymphedema (BCRL) on long-term quality of life is unknown. The aim of this study was to investigate the impact of BCRL on health-related quality of life (HRQoL) up to 10 years after breast cancer treatment. This regional population-based study enrolled patients treated for breast cancer with axillary lymph node dissection between January 1st 2007 and December 31th 2017. Follow up and assessments of the included patients were conducted between January 2019 and May 2020. The study outcome was HRQoL, evaluated with the Lymphedema Functioning, Disability and Health Questionnaire, the Disabilities of the Arm, Shoulder and Hand Questionnaire and the Short Form (36) Health Survey Questionnaire. Multivariate linear logistic regression models adjusted for confounders provided mean score differences (MDs) with 95% confidence intervals in each HRQoL scale and item. This study enrolled 244 patients with BCRL and 823 patients without BCRL. Patients with BCRL had significantly poorer HRQoL than patients without BCRL in 16 out of 18 HRQoL subscales, for example, in physical function (MDs 27, 95%CI: 24; 30), mental health (MDs 24, 95%CI: 21; 27) and social role functioning (MDs 20, 95%CI: 17; 23). Age, BMI, BCRL severity, hand and dominant arm affection had only minor impact on HRQoL (MDs

The objective of this study was to investigate the re-emergence of a previously important crop pathogen in Europe, Puccinia graminis f.sp. tritici, causing wheat stem rust. The pathogen has been insignificant in Europe for more than 60 years, but since 2016 it has caused epidemics on both durum wheat and bread wheat in local areas in southern Europe, and additional outbreaks in Central- and West Europe. The prevalence of three distinct genotypes/races in many areas, Clade III-B (TTRTF), Clade IV-B (TKTTF) and Clade IV-F (TKKTF), suggested clonal reproduction and evolution by mutation within these. None of these genetic groups and races, which likely originated from exotic incursions, were detected in Europe prior to 2016. A fourth genetic group, Clade VIII, detected in Germany (2013), was observed in several years in Central- and East Europe. Tests of representative European wheat varieties with prevalent races revealed high level of susceptibility. In contrast, high diversity with respect to virulence and Simple Sequence Repeat (SSR) markers were detected in local populations on cereals and grasses in proximity to Berberis species in Spain and Sweden, indicating that the alternate host may return as functional component of the epidemiology of wheat stem rust in Europe. A geographically distant population from Omsk and Novosibirsk in western Siberia (Russia) also revealed high genetic diversity, but clearly different from current European populations. The presence of Sr31-virulence in multiple and highly diverse races in local populations in Spain and Siberia stress that virulence may emerge independently when large geographical areas and time spans are considered and that Sr31-virulence is not unique to Ug99. All isolates of the Spanish populations, collected from wheat, rye and grass species, were succesfully recovered on wheat, which underline the plasticity of host barriers within P. graminis. The study demonstrated successful alignment of two genotyping approaches and race phenotyping methodologies employed by different laboratories, which also allowed us to line up with previous European and international studies of wheat stem rust. Our results suggest new initiatives within disease surveillance, epidemiological research and resistance breeding to meet current and future challenges by wheat stem rust in Europe and beyond.

This brief report discusses our experiences of exploring recruitment challenges in family-focused alcohol treatment and seeking possible solutions to these challenges. We used methods, inspired by Action Research and Systems Thinking, to engage and mobilize participants in two Danish rural municipalities. In the project, local participation from a broad range of stakeholders and a shared understanding of the local context gave rise to increased focus on and awareness of alcohol challenges in the community. We reflect on the importance of assessing whether a community is ready for change; the importance of integrating capacity-building and implementation from the beginning; the importance of engaging a wide range of stakeholders when creating a system map and the importance of recruiting community leaders to workshops, as implementation requires the engagement of persons who have the authority, capacity, and networks to lead systems changes across the community.

Abstract Persistent neutrophilic inflammation drives host damage in autoimmune diseases that are characterized by abundant immune complexes. Insoluble immune complexes (iICs) potently activate pro-inflammatory neutrophil effector functions. We and others have shown that iICs also promote resolution of inflammation via stimulation of neutrophil apoptosis. We demonstrate here that iICs trigger FcγRIIa-dependent neutrophil macropinocytosis, leading to the rapid uptake, and subsequent degradation of iICs. We provide evidence that concurrent iIC-induced neutrophil apoptosis is distinct from phagocytosis-induced cell death. First, uptake of iICs occurs by FcγRII-stimulated macropinocytosis, rather than phagocytosis. Second, production of reactive oxygen species, but not iIC-internalization is a pre-requisite for iIC-induced neutrophil apoptosis. Our findings identify a previously unknown mechanism by which neutrophils can remove pro-inflammatory iICs from the circulation. Together iIC clearance and iIC-induced neutrophil apoptosis may act to prevent the potential escalation of neutrophilic inflammation in response to iICs.

The CCR5-specific antibody Leronlimab is being investigated as a novel immunotherapy that can suppress HIV replication with minimal side effects. Here we studied the virological and immunological consequences of Leronlimab in chronically CCR5-tropic HIV-1 infected humans (n = 5) on suppressive antiretroviral therapy (ART) and in ART-naïve acutely CCR5-tropic SHIV infected rhesus macaques (n = 4). All five human participants transitioned from daily combination ART to self-administered weekly subcutaneous (SC) injections of 350 mg or 700 mg Leronlimab and to date all participants have sustained virologic suppression for over seven years. In all participants, Leronlimab fully occupied CCR5 receptors on peripheral blood CD4+ T cells and monocytes. In ART-naïve rhesus macaques acutely infected with CCR5-tropic SHIV, weekly SC injections of 50 mg/kg Leronlimab fully suppressed plasma viremia in half of the macaques. CCR5 receptor occupancy by Leronlimab occurred concomitant with rebound of CD4+ CCR5+ T-cells in peripheral blood, and full CCR5 receptor occupancy was found in multiple anatomical compartments. Our results demonstrate that weekly, self-administered Leronlimab was safe, well-tolerated, and efficacious for long-term virologic suppression and should be included in the arsenal of safe, easily administered, longer-acting antiretroviral treatments for people living with HIV-1. Trial Registration: ClinicalTrials.gov Identifiers: NCT02175680 and NCT02355184.

Abstract The narwhal (Monodon monoceros) is a high‐Arctic species inhabiting areas that are experiencing increases in sea temperatures, which together with reduction in sea ice are expected to modify the niches of several Arctic marine apex predators. The Scoresby Sound fjord complex in East Greenland is the summer residence for an isolated population of narwhals. The movements of 12 whales instrumented with Fastloc‐GPS transmitters were studied during summer in Scoresby Sound and at their offshore winter ground in 2017–2019. An additional four narwhals provided detailed hydrographic profiles on both summer and winter grounds. Data on diving of the whales were obtained from 20 satellite‐linked time‐depth recorders and 16 Acousonde™ recorders that also provided information on the temperature and depth of buzzes. In summer, the foraging whales targeted depths between 300 and 850 m where the preferred areas visited by the whales had temperatures ranging between 0.6 and 1.5°C (mean = 1.1°C, SD = 0.22). The highest probability of buzzing activity during summer was at a temperature of 0.7°C and at depths > 300 m. The whales targeted similar depths at their offshore winter ground where the temperature was slightly higher (range: 0.7–1.7°C, mean = 1.3°C, SD = 0.29). Both the probability of buzzing events and the spatial distribution of the whales in both seasons demonstrated a preferential selection of cold water. This was particularly pronounced in winter where cold coastal water was selected and warm Atlantic water farther offshore was avoided. It is unknown if the small temperature niche of whales while feeding is because prey is concentrated at these temperature gradients and is easier to capture at low temperatures, or because there are limitations in the thermoregulation of the whales. In any case, the small niche requirements together with their strong site fidelity emphasize the sensitivity of narwhals to changes in the thermal characteristics of their habitats.