Characterizing the polygenic overlap and shared loci between rheumatoid arthritis and cardiovascular diseases

BACKGROUND

Despite substantial research revealing that patients with rheumatoid arthritis (RA) have excessive morbidity and mortality of cardiovascular disease (CVD), the mechanism underlying this association has not been fully known. This study aims to systematically investigate the phenotypic and genetic correlation between RA and CVD.

METHODS

Based on UK Biobank, we conducted two cohort studies to evaluate the phenotypic relationships between RA and CVD, including atrial fibrillation (AF), coronary artery disease (CAD), heart failure (HF), and stroke. Next, we used linkage disequilibrium score regression, Local Analysis of [co]Variant Association, and bivariate causal mixture model (MiXeR) methods to examine the genetic correlation and polygenic overlap between RA and CVD, using genome-wide association summary statistics. Furthermore, we explored specific shared genetic loci by conjunctional false discovery rate analysis and association analysis based on subsets.

RESULTS

Compared with the general population, RA patients showed a higher incidence of CVD (hazard ratio [HR] = 1.21, 95% confidence interval [CI]: 1.15-1.28). We observed positive genetic correlations of RA with AF and stroke, and a mixture of negative and positive local genetic correlations underlying the global genetic correlation for CAD and HF, with 13 ~ 33% of shared genetic variants for these trait pairs. We further identified 23 pleiotropic loci associated with RA and at least one CVD, including one novel locus (rs7098414, TSPAN14, 10q23.1). Genes mapped to these shared loci were enriched in immune and inflammatory-related pathways, and modifiable risk factors, such as high diastolic blood pressure.

CONCLUSIONS

This study revealed the shared genetic architecture of RA and CVD, which may facilitate drug target identification and improved clinical management.

Characterisation of HNF1A variants in paediatric diabetes in Norway using functional and clinical investigations to unmask phenotype and monogenic diabetes

AIMS/HYPOTHESIS

Correctly diagnosing MODY is important, as individuals with this diagnosis can discontinue insulin injections; however, many people are misdiagnosed. We aimed to develop a robust approach for determining the pathogenicity of variants of uncertain significance in hepatocyte nuclear factor-1 alpha (HNF1A)-MODY and to obtain an accurate estimate of the prevalence of HNF1A-MODY in paediatric cases of diabetes.

METHODS

We extended our previous screening of the Norwegian Childhood Diabetes Registry by 830 additional samples and comprehensively genotyped HNF1A variants in autoantibody-negative participants using next-generation sequencing. Carriers of pathogenic variants were treated by local healthcare providers, and participants with novel likely pathogenic variants and variants of uncertain significance were enrolled in an investigator-initiated, non-randomised, open-label pilot study (ClinicalTrials.gov registration no. NCT04239586). To identify variants associated with HNF1A-MODY, we functionally characterised their pathogenicity and assessed the carriers' phenotype and treatment response to sulfonylurea.

RESULTS

In total, 615 autoantibody-negative participants among 4712 cases of paediatric diabetes underwent genetic sequencing, revealing 19 with HNF1A variants. We identified nine carriers with novel variants classified as variants of uncertain significance or likely to be pathogenic, while the remaining ten participants carried five pathogenic variants previously reported. Of the nine carriers with novel variants, six responded favourably to sulfonylurea. Functional investigations revealed their variants to be dysfunctional and demonstrated a correlation with the resulting phenotype, providing evidence for reclassifying these variants as pathogenic.

CONCLUSIONS/INTERPRETATION

Based on this robust classification, we estimate that the prevalence of HNF1A-MODY is 0.3% in paediatric diabetes. Clinical phenotyping is challenging and functional investigations provide a strong complementary line of evidence. We demonstrate here that combining clinical phenotyping with functional protein studies provides a powerful tool to obtain a precise diagnosis of HNF1A-MODY.

Genotyping tool for salmonid gill pox virus (SGPV) obtained from farmed and wild Atlantic salmon (Salmo salar)

Poxviruses are common viruses found in vertebrate species. In 2006, the first poxvirus associated with salmon, salmonid gill poxvirus (SGPV), was identified during an outbreak of gill disease at a smolt production site in northern Norway and at two marine farms in western Norway. Poxviruses had previously been detected in ayu (Plecoglossus altivelis) and koi carp (Cyprinus carpio). In all three fish species, poxviruses are associated with gill disease. It has not been possible to culture SGPV from Norway, and little is known about its virulence. However, the association between SGPV and gill disease in salmon has shown the need for molecular tools to identify reservoirs and transmission routes. Sequencing the genome of a second isolate of SGPV has made it possible to compare variable regions between two strains of the virus, showing the presence of a large number of variable regions that exhibit both variable numbers of tandem repeats and intra-ORF variation. We present eight regions that are suitable for distinguishing strains of SGPV and determining their phylogenetic relationship, and these were used to compare SGPV isolates obtained from both farmed and wild salmon in fresh and sea water. The prevalence of the virus was found to be higher in wild salmon in rivers than in returning wild salmon collected from traps in Norwegian fjords. Genotyping based on the eight selected variable regions, suggests the presence of geographically distinct isolates in freshwater among both farmed and wild salmon, while SGPV from marine farms shows high local diversity and a wide geographical distribution of similar strains of the virus.

Accurate and fast graph-based pangenome annotation and clustering with ggCaller

Bacterial genomes differ in both gene content and sequence mutations, which underlie extensive phenotypic diversity, including variation in susceptibility to antimicrobials or vaccine-induced immunity. To identify and quantify important variants, all genes within a population must be predicted, functionally annotated, and clustered, representing the "pangenome." Despite the volume of genome data available, gene prediction and annotation are currently conducted in isolation on individual genomes, which is computationally inefficient and frequently inconsistent across genomes. Here, we introduce the open-source software graph-gene-caller (ggCaller). ggCaller combines gene prediction, functional annotation, and clustering into a single workflow using population-wide de Bruijn graphs, removing redundancy in gene annotation and resulting in more accurate gene predictions and orthologue clustering. We applied ggCaller to simulated and real-world bacterial data sets containing hundreds or thousands of genomes, comparing it to current state-of-the-art tools. ggCaller has considerable speed-ups with equivalent or greater accuracy, particularly with data sets containing complex sources of error, such as assembly contamination or fragmentation. ggCaller is also an important extension to bacterial genome-wide association studies, enabling querying of annotated graphs for functional analyses. We highlight this application by functionally annotating DNA sequences with significant associations to tetracycline and macrolide resistance in Streptococcus pneumoniae, identifying key resistance determinants that were missed when using only a single reference genome. ggCaller is a novel bacterial genome analysis tool with applications in bacterial evolution and epidemiology.

Movement syndromes of a Neotropical frugivorous bat inhabiting heterogeneous landscapes in Brazil

BACKGROUND

There is growing evidence that individuals within populations can vary in both habitat use and movement behavior, but it is still not clear how these two relate to each other. The aim of this study was to test if and how individual bats in a Stunira lilium population differ in their movement activity and preferences for landscape features in a correlated manner.

METHODS

We collected data on movements of 27 individuals using radio telemetry. We fitted a heterogeneous-space diffusion model to the movement data in order to evaluate signals of movement variation among individuals.

RESULTS

S. lilium individuals generally preferred open habitat with Solanum fruits, regularly switched between forest and open areas, and showed high site fidelity. Movement variation among individuals could be summarized in four movement syndromes: (1) average individuals, (2) forest specialists, (3) explorers which prefer Piper, and (4) open area specialists which prefer Solanum and Cecropia.

CONCLUSIONS

Individual preferences for landscape features plus food resource and movement activity were correlated, resulting in different movement syndromes. Individual variation in preferences for landscape elements and food resources highlight the importance of incorporating explicitly the interaction between landscape structure and individual heterogeneity in descriptions of animal movement.

Extreme home range sizes among Eurasian lynx at the northern edge of their biogeographic range

Eurasian lynx (Lynx lynx) have a wide distribution across Eurasia. The northern edge of this distribution is in Norway, where they reach up to 72 degrees north. We conducted a study of lynx space use in this region from 2007 to 2013 using GPS telemetry. The home range sizes averaged 2,606 (± 438 SE) km2 for males (n = 9 ranges) and 1,456 (± 179 SE) km2 for females (n = 24 ranges). These are the largest home ranges reported for any large felid, and indeed are only matched by polar bears, arctic living wolves, and grizzly bears among all the Carnivora. The habitat occupied was almost entirely treeless alpine tundra, with home ranges only containing from 20% to 25% of forest. These data have clear implications for the spatial planning of lynx management in the far north as the current management zones are located in unsuitable habitats and are not large enough to encompass individual lynx movements.

Fitness, Fatness, and Mortality in Men and Women From the UK Biobank: Prospective Cohort Study

Background Cardiorespiratory fitness may moderate the association between obesity and all-cause mortality (ie, the "fat-but-fit" hypothesis), but unaddressed sources of bias are a concern. Methods and Results Cardiorespiratory fitness was estimated as watts per kilogram from a submaximal bicycle test in 77 169 men and women from the UK Biobank cohort and combined with World Health Organization standard body mass index categories, yielding 9 unique fitness-fatness combinations. We also formed fitness-fatness combinations based on bioimpedance as a direct measure of body composition. All-cause mortality was ascertained from death registries. Multivariable-adjusted Cox regression models were used to estimate hazard ratios and 95% CIs. We examined the association between fitness-fatness combinations and all-cause mortality in models with progressively more conservative approaches for accounting for reverse causation, misclassification of body composition, and confounding. Over a median follow-up of 7.7 years, 1731 participants died. In our base model, unfit men and women had higher risk of premature mortality irrespective of levels of adiposity, compared with the normal weight-fit reference. This pattern was attenuated but maintained with more conservative approaches in men, but not in women. In analysis stratified by sex and excluding individuals with prevalent major chronic disease and short follow-up and using direct measures of body composition, mortality risk was 1.78 (95% CI, 1.17-2.71) times higher in unfit-obese men but not higher in obese-fit men (0.94 [95% CI, 0.60-1.48]). In contrast, there was no increased risk in obese-unfit women (1.09 [95% CI, 0.44-1.05]) as compared with the reference. Conclusions Cardiorespiratory fitness modified the association between obesity and mortality in men, but this pattern appeared susceptible to biases in women.

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving biomedical and environmental problems. However, the biological insight obtained from these models is limited by multiple heterogeneous sources of uncertainty, which are often difficult to quantify. Here we review the major sources of uncertainty and survey existing approaches developed for representing and addressing them. A unified formal characterization of these uncertainties through probabilistic approaches and ensemble modeling will facilitate convergence towards consistent reconstruction pipelines, improved data integration algorithms, and more accurate assessment of predictive capacity.

Between diagnostic precision and rapid decision-making: Using institutional ethnography to explore diagnostic work in the context of Cancer Patient Pathways in Norway

Alongside other Nordic countries, the Norwegian government has introduced Cancer Patient Pathways (CPPs) for faster diagnostic assessment and timely treatment to improve the quality of cancer care. A key aspect of CPPs is the introduction of time limits for each phase of the diagnostic investigation. Occurring simultaneously are ongoing advances in medical technology, complicating the process of diagnosing and treating cancer. In this article, using institutional ethnography, we examine: how does the CPP policy influence physicians' experiences of diagnostic work? Data were collected from May 2018 to May 2019, through semi-structured interviews with physicians across five hospitals in Norway (N = 27). Our findings indicate that the implementation of various strategies aimed at enhancing quality in cancer care collide, compelling physicians to negotiate between diagnostic precision and rapid decision-making. We conclude that attention to interfaces between multiple guidelines and their implications for practice is crucial for understanding and developing quality of care.

Blood Metal Levels and Amyotrophic Lateral Sclerosis Risk: A Prospective Cohort

OBJECTIVE

Metals have been suggested as a risk factor for amyotrophic lateral sclerosis (ALS), but only retrospective studies are available to date. We compared metal levels in prospectively collected blood samples from ALS patients and controls, to explore whether metals are associated with ALS mortality.

METHODS

A nested ALS case-control study was conducted within the prospective EPIC (European Prospective Investigation into Cancer and Nutrition) cohort. Cases were identified through death certificates. We analyzed metal levels in erythrocyte samples obtained at recruitment, as a biomarker for metal exposure from any source. Arsenic, cadmium, copper, lead, manganese, mercury, selenium, and zinc concentrations were measured by inductively coupled plasma-mass spectrometry. To estimate ALS risk, we applied conditional logistic regression models.

RESULTS

The study population comprised 107 cases (65% female) and 319 controls matched for age, sex, and study center. Median time between blood collection and ALS death was 8 years (range = 1-15). Comparing the highest with the lowest tertile, cadmium (odds ratio [OR] = 2.04, 95% confidence interval [CI] = 1.08-3.87) and lead (OR = 1.89, 95% CI = 0.97-3.67) concentrations suggest associations with increased ALS risk. Zinc was associated with a decreased risk (OR = 0.50, 95% CI = 0.27-0.94). Associations for cadmium and lead remained when limiting analyses to noncurrent smokers.

INTERPRETATION

This is the first study to compare metal levels before disease onset, minimizing reverse causation. The observed associations suggest that cadmium, lead, and zinc may play a role in ALS etiology. Cadmium and lead possibly act as intermediates on the pathway from smoking to ALS. ANN NEUROL 20209999:n/a-n/a.

Nitrogen-Doped Carbon-Assisted One-pot Tandem Reaction for Vinyl Chloride Production via Ethylene Oxychlorination

A bifunctional catalyst comprising CuCl2 /Al2 O3 and nitrogen-doped carbon was developed for an efficient one-pot ethylene oxychlorination process to produce vinyl chloride monomer (VCM) up to 76 % yield at 250 °C and under ambient pressure, which is higher than the conventional industrial two-step process (≈50 %) in a single pass. In the second bed, active sites containing N-functional groups on the metal-free N-doped carbon catalyzed both ethylene oxychlorination and ethylene dichloride (EDC) dehydrochlorination under the mild conditions. Benefitting from the bifunctionality of the N-doped carbon, VCM formation was intensified by the surface Cl*-looping of EDC dehydrochlorination and ethylene oxychlorination. Both reactions were enhanced by in situ consumption of surface Cl* by oxychlorination, in which Cl* was generated by EDC dehydrochlorination. This work offers a promising alternative pathway to VCM production via ethylene oxychlorination at mild conditions through a single pass reactor.

The core clock transcription factor BMAL1 drives circadian β-cell proliferation during compensatory regeneration of the endocrine pancreas

Circadian clocks in pancreatic islets participate in the regulation of glucose homeostasis. Here we examined the role of these timekeepers in β-cell regeneration after the massive ablation of β cells by doxycycline-induced expression of diphtheria toxin A (DTA) in Insulin-rtTA/TET-DTA mice. Since we crossed reporter genes expressing α- and β-cell-specific fluorescent proteins into these mice, we could follow the fate of α- and β cells separately. As expected, DTA induction resulted in an acute hyperglycemia, which was accompanied by dramatic changes in gene expression in residual β cells. In contrast, only temporal alterations of gene expression were observed in α cells. Interestingly, β cells entered S phase preferentially during the nocturnal activity phase, indicating that the diurnal rhythm also plays a role in the orchestration of β-cell regeneration. Indeed, in arrhythmic Bmal1-deficient mice, which lack circadian clocks, no compensatory β-cell proliferation was observed, and the β-cell ablation led to aggravated hyperglycemia, hyperglucagonemia, and fatal diabetes.

Parasitoids indicate major climate-induced shifts in arctic communities

Climatic impacts are especially pronounced in the Arctic, which as a region is warming twice as fast as the rest of the globe. Here, we investigate how mean climatic conditions and rates of climatic change impact parasitoid insect communities in 16 localities across the Arctic. We focus on parasitoids in a widespread habitat, Dryas heathlands, and describe parasitoid community composition in terms of larval host use (i.e., parasitoid use of herbivorous Lepidoptera vs. pollinating Diptera) and functional groups differing in their closeness of host associations (koinobionts vs. idiobionts). Of the latter, we expect idiobionts-as being less fine-tuned to host development-to be generally less tolerant to cold temperatures, since they are confined to attacking hosts pupating and overwintering in relatively exposed locations. To further test our findings, we assess whether similar climatic variables are associated with host abundances in a 22 year time series from Northeast Greenland. We find sites which have experienced a temperature rise in summer while retaining cold winters to be dominated by parasitoids of Lepidoptera, with the reverse being true for the parasitoids of Diptera. The rate of summer temperature rise is further associated with higher levels of herbivory, suggesting higher availability of lepidopteran hosts and changes in ecosystem functioning. We also detect a matching signal over time, as higher summer temperatures, coupled with cold early winter soils, are related to high herbivory by lepidopteran larvae, and to declines in the abundance of dipteran pollinators. Collectively, our results suggest that in parts of the warming Arctic, Dryas is being simultaneously exposed to increased herbivory and reduced pollination. Our findings point to potential drastic and rapid consequences of climate change on multitrophic-level community structure and on ecosystem functioning and highlight the value of collaborative, systematic sampling effort.

Global Radiative Impacts of Black Carbon Acting as Ice Nucleating Particles

Black carbon (BC) aerosols from incomplete combustion generally warm the climate, but the magnitudes of their various interactions with climate are still uncertain. A key knowledge gap is their role as ice nucleating particles (INPs), enabling ice formation in clouds. Here we assess the global radiative impacts of BC acting as INPs, using simulations with the Community Earth System Model 2 climate model updated to include new laboratory-based ice nucleation parameterizations. Overall, we find a moderate cooling through changes to stratiform cirrus clouds, counteracting the well-known net warming from BC's direct scattering and absorption of radiation. Our best estimates indicate that BC INPs generally thin cirrus by indirectly inhibiting the freezing of solution aerosol, with a global net radiative impact of -0.13 ± 0.07 W/m2. Sensitivity tests of BC amounts and ice nucleating efficiencies, and uncertainties in the environment where ice crystals form, show a potential range of impacts from -0.30 to +0.02 W/m2.

Differences in directed functional brain connectivity related to age, sex and mental health

Functional interconnections between brain regions define the "connectome" which is of central interest for understanding human brain function. Resting-state functional magnetic resonance (rsfMRI) work has revealed changes in static connectivity related to age, sex, cognitive abilities and psychiatric symptoms, yet little is known how these factors may alter the information flow. The commonly used approach infers functional brain connectivity using stationary coefficients yielding static estimates of the undirected connection strength between brain regions. Dynamic graphical models (DGMs) are a multivariate model with dynamic coefficients reflecting directed temporal associations between nodes, and can yield novel insight into directed functional connectivity. Here, we leveraged this approach to test for associations between edge-wise estimates of direction flow across the functional connectome and age, sex, intellectual abilities and mental health. We applied DGM to investigate patterns of information flow in data from 984 individuals from the Human Connectome Project (HCP) and 10,249 individuals from the UK Biobank. Our analysis yielded patterns of directed connectivity in independent HCP and UK Biobank data similar to those previously reported, including that the cerebellum consistently receives information from other networks. We show robust associations between information flow and age and sex for several connections, with strongest effects of age observed in the sensorimotor network. Visual, auditory and sensorimotor nodes were also linked to mental health. Our findings support the use of DGM as a measure of directed connectivity in rsfMRI data and provide new insight into the shaping of the connectome during aging.

Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles

The shape and size of self-assembled structures upon local organization of their molecular building blocks are hard to predict in the presence of long-range interactions. Combining small-angle X-ray/neutron scattering data, theoretical modelling, and computer simulations, sodium dodecyl sulfate (SDS), over a broad range of concentrations and ionic strengths, was investigated. Computer simulations indicate that micellar shape changes are associated with different binding of the counterions. By employing a toy model based on point charges on a surface, and comparing it to experiments and simulations, it is demonstrated that the observed morphological changes are caused by symmetry breaking of the irreducible building blocks, with the formation of transient surfactant dimers mediated by the counterions that promote the stabilization of cylindrical instead of spherical micelles. The present model is of general applicability and can be extended to all systems controlled by the presence of mobile charges.

The Critical Point and the Supercritical State of Alkali Feldspars: Implications for the Behavior of the Crust During Impacts

The position of the vapor-liquid dome and of the critical point determine the evolution of the outermost parts of the protolunar disk during cooling and condensation after the Giant Impact. The parts of the disk in supercritical or liquid state evolve as a single thermodynamic phase; when the thermal trajectory of the disk reaches the liquid-vapor dome, gas and melt separate leading to heterogeneous convection and phase separation due to friction. Different layers of the proto-Earth behaved differently during the Giant Impact depending on their constituent materials and initial thermodynamic conditions. Here we use first-principles molecular dynamics to determine the position of the critical point for NaAlSi3O8 and KAlSi3O8 feldspars, major minerals of the Earth and Moon crusts. The variations of the pressure calculated at various volumes along isotherms yield the position of the critical points: 0.5-0.8 g cm-3 and 5500-6000 K range for the Na-feldspar, 0.5-0.9 g cm-3 and 5000-5500 K range for the K-feldspar. The simulations suggest that the vaporization is incongruent, with a degassing of O2 starting at 4000 K and gas component made mostly of free Na and K cations, O2, SiO and SiO2 species for densities below 1.5 g cm-3. The Hugoniot equations of state imply that low-velocity impactors (<8.3 km s-1) would at most melt a cold feldspathic crust, whereas large impacts in molten crust would see temperatures raise up to 30000 K.

In-depth characterization of Trichoderma reesei cellobiohydrolase TrCel7A produced in Nicotiana benthamiana reveals limitations of cellulase production in plants by host-specific post-translational modifications

Sustainable production of biofuels from lignocellulose feedstocks depends on cheap enzymes for degradation of such biomass. Plants offer a safe and cost-effective production platform for biopharmaceuticals, vaccines and industrial enzymes boosting biomass conversion to biofuels. Production of intact and functional protein is a prerequisite for large-scale protein production, and extensive host-specific post-translational modifications (PTMs) often affect the catalytic properties and stability of recombinant enzymes. Here we investigated the impact of plant PTMs on enzyme performance and stability of the major cellobiohydrolase TrCel7A from Trichoderma reesei, an industrially relevant enzyme. TrCel7A was produced in Nicotiana benthamiana using a vacuum-based transient expression technology, and this recombinant enzyme (TrCel7Arec ) was compared with the native fungal enzyme (TrCel7Anat ) in terms of PTMs and catalytic activity on commercial and industrial substrates. We show that the N-terminal glutamate of TrCel7Arec was correctly processed by N. benthamiana to a pyroglutamate, critical for protein structure, while the linker region of TrCel7Arec was vulnerable to proteolytic digestion during protein production due to the absence of O-mannosylation in the plant host as compared with the native protein. In general, the purified full-length TrCel7Arec had 25% lower catalytic activity than TrCel7Anat and impaired substrate-binding properties, which can be attributed to larger N-glycans and lack of O-glycans in TrCel7Arec . All in all, our study reveals that the glycosylation machinery of N. benthamiana needs tailoring to optimize the production of efficient cellulases.

Joint species distribution modelling with the r-package Hmsc

Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analysing data in community ecology. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs. HMSC allows the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships and the spatio-temporal context of the study, providing predictive insights into community assembly processes from non-manipulative observational data of species communities.The full range of functionality of HMSC has remained restricted to Matlab users only. To make HMSC accessible to the wider community of ecologists, we introduce Hmsc 3.0, a user-friendly r implementation.We illustrate the use of the package by applying Hmsc 3.0 to a range of case studies on real and simulated data. The real data consist of bird counts in a spatio-temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. Vignettes on simulated data involve single-species models, models of small communities, models of large species communities and models for large spatial data. We demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. We demonstrate how to construct and fit models with different types of random effects, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates and how to make predictions. We further demonstrate how Hmsc 3.0 can be applied to normally distributed data, count data and presence-absence data.The package, along with the extended vignettes, makes JSDM fitting and post-processing easily accessible to ecologists familiar with r.

Syndecan-4 Protects the Heart From the Profibrotic Effects of Thrombin-Cleaved Osteopontin

Background Pressure overload of the heart occurs in patients with hypertension or valvular stenosis and induces cardiac fibrosis because of excessive production of extracellular matrix by activated cardiac fibroblasts. This initially provides essential mechanical support to the heart, but eventually compromises function. Osteopontin is associated with fibrosis; however, the underlying signaling mechanisms are not well understood. Herein, we examine the effect of thrombin-cleaved osteopontin on fibrosis in the heart and explore the role of syndecan-4 in regulating cleavage of osteopontin. Methods and Results Osteopontin was upregulated and cleaved by thrombin in the pressure-overloaded heart of mice subjected to aortic banding. Cleaved osteopontin was higher in plasma from patients with aortic stenosis receiving crystalloid compared with blood cardioplegia, likely because of less heparin-induced inhibition of thrombin. Cleaved osteopontin and the specific osteopontin peptide sequence RGDSLAYGLR that is exposed after thrombin cleavage both induced collagen production in cardiac fibroblasts. Like osteopontin, the heparan sulfate proteoglycan syndecan-4 was upregulated after aortic banding. Consistent with a heparan sulfate binding domain in the osteopontin cleavage site, syndecan-4 was found to bind to osteopontin in left ventricles and cardiac fibroblasts and protected osteopontin from cleavage by thrombin. Shedding of the extracellular part of syndecan-4 was more prominent at later remodeling phases, at which time levels of cleaved osteopontin were increased. Conclusions Thrombin-cleaved osteopontin induces collagen production by cardiac fibroblasts. Syndecan-4 protects osteopontin from cleavage by thrombin, but this protection is lost when syndecan-4 is shed in later phases of remodeling, contributing to progression of cardiac fibrosis.

Influence of the Thickness of the Overriding Plate on Convergence Zone Dynamics

The important role played by the upper plate in convergence zones dynamics has long been underestimated but is now more and more emphasized. However, the influence of its thickness and/or strength on orogenic systems evolution remains largely unknown. Here we present results from 3D thermo-mechanical numerical simulations of convergence zones (including oceanic subduction followed by continental subduction/collision), in which we vary the rheological profile of the overriding plate (OP). For this, we systematically modify the crustal thickness of the overriding lithosphere and the temperature at the Moho to obtain a thermal thickness of the overriding lithosphere ranging from 80 to 180 km. While all models share a common global evolution (i.e., slab sinking, interaction between slab and the 660 km discontinuity, continental subduction/collision, and slab breakoff), they also highlight first-order differences arising from the variations in the OP strength (thermal thickness). With a thin/weak OP, slab rollback is favored, the slab dip is low, the mantle flow above the slab is vigorous, and the trench migrates at a high rate compared to a thick/strong OP. In addition, slab breakoff and back-arc basin formation events occur significantly earlier than in models involving a thick OP. Our models therefore highlight the major role played by the thickness/strength of the OP on convergence zone dynamics and illustrate its influence in a quantitative way.

Computationally efficient joint species distribution modeling of big spatial data

The ongoing global change and the increased interest in macroecological processes call for the analysis of spatially extensive data on species communities to understand and forecast distributional changes of biodiversity. Recently developed joint species distribution models can deal with numerous species efficiently, while explicitly accounting for spatial structure in the data. However, their applicability is generally limited to relatively small spatial data sets because of their severe computational scaling as the number of spatial locations increases. In this work, we propose a practical alleviation of this scalability constraint for joint species modeling by exploiting two spatial-statistics techniques that facilitate the analysis of large spatial data sets: Gaussian predictive process and nearest-neighbor Gaussian process. We devised an efficient Gibbs posterior sampling algorithm for Bayesian model fitting that allows us to analyze community data sets consisting of hundreds of species sampled from up to hundreds of thousands of spatial units. The performance of these methods is demonstrated using an extensive plant data set of 30,955 spatial units as a case study. We provide an implementation of the presented methods as an extension to the hierarchical modeling of species communities framework.

A 10-year prediagnostic follow-up study shows that serum RNA signals are highly dynamic in lung carcinogenesis

The majority of lung cancer (LC) patients are diagnosed at a late stage, and survival is poor. Circulating RNA molecules are known to have a role in cancer; however, their involvement before diagnosis remains an open question. In this study, we investigated circulating RNA dynamics in prediagnostic LC samples, focusing on smokers, to identify if and when disease-related signals can be detected in serum. We sequenced small RNAs in 542 serum LC samples donated up to 10 years before diagnosis and 519 matched cancer-free controls coming from 905 individuals in the Janus Serum Bank. This sample size provided sufficient statistical power to independently analyze time to diagnosis, stage, and histology. The results showed dynamic changes in differentially expressed circulating RNAs specific to LC histology and stage. The greatest number of differentially expressed RNAs was identified around 7 years before diagnosis for early-stage LC and 1-4 years prior to diagnosis for locally advanced and advanced-stage LC, regardless of LC histology. Furthermore, NSCLC and SCLC histologies have distinct prediagnostic signals. The majority of differentially expressed RNAs were associated with cancer-related pathways. The dynamic RNA signals pinpointed different phases of tumor development over time. Stage-specific RNA profiles may be associated with tumor aggressiveness. Our results improve the molecular understanding of carcinogenesis. They indicate substantial opportunity for screening and improved treatment and will guide further research on early detection of LC. However, the dynamic nature of the RNA signals also suggests challenges for prediagnostic biomarker discovery.

Development of a targeted client communication intervention to women using an electronic maternal and child health registry: a qualitative study

BACKGROUND

Targeted client communication (TCC) using text messages can inform, motivate and remind pregnant and postpartum women of timely utilization of care. The mixed results of the effectiveness of TCC interventions points to the importance of theory based interventions that are co-design with users. The aim of this paper is to describe the planning, development, and evaluation of a theory led TCC intervention, tailored to pregnant and postpartum women and automated from the Palestinian electronic maternal and child health registry.

METHODS

We used the Health Belief Model to develop interview guides to explore women's perceptions of antenatal care (ANC), with a focus on high-risk pregnancy conditions (anemia, hypertensive disorders in pregnancy, gestational diabetes mellitus, and fetal growth restriction), and untimely ANC attendance, issues predefined by a national expert panel as being of high interest. We performed 18 in-depth interviews with women, and eight with healthcare providers in public primary healthcare clinics in the West Bank and Gaza. Grounding on the results of the in-depth interviews, we used concepts from the Model of Actionable Feedback, social nudging and Enhanced Active Choice to compose the TCC content to be sent as text messages. We assessed the acceptability and understandability of the draft text messages through unstructured interviews with local health promotion experts, healthcare providers, and pregnant women.

RESULTS

We found low awareness of the importance of timely attendance to ANC, and the benefits of ANC for pregnancy outcomes. We identified knowledge gaps and beliefs in the domains of low awareness of susceptibility to, and severity of, anemia, hypertension, and diabetes complications in pregnancy. To increase the utilization of ANC and bridge the identified gaps, we iteratively composed actionable text messages with users, using recommended message framing models. We developed algorithms to trigger tailored text messages with higher intensity for women with a higher risk profile documented in the electronic health registry.

CONCLUSIONS

We developed an optimized TCC intervention underpinned by behavior change theory and concepts, and co-designed with users following an iterative process. The electronic maternal and child health registry can serve as a unique platform for TCC interventions using text messages.

Polyaromatic hydrocarbons in pollution: a heart-breaking matter

Air pollution is associated with detrimental effects on human health, including decreased cardiovascular function. However, the causative mechanisms behind these effects have yet to be fully elucidated. Here we review the current epidemiological, clinical and experimental evidence linking pollution with cardiovascular dysfunction. Our focus is on particulate matter (PM) and the associated low molecular weight polycyclic aromatic hydrocarbons (PAHs) as key mediators of cardiotoxicity. We begin by reviewing the growing epidemiological evidence linking air pollution to cardiovascular dysfunction in humans. We next address the pollution-based cardiotoxic mechanisms first identified in fish following the release of large quantities of PAHs into the marine environment from point oil spills (e.g. Deepwater Horizon). We finish by discussing the current state of mechanistic knowledge linking PM and PAH exposure to mammalian cardiovascular patho-physiologies such as atherosclerosis, cardiac hypertrophy, arrhythmias, contractile dysfunction and the underlying alterations in gene regulation. Our aim is to show conservation of toxicant pathways and cellular targets across vertebrate hearts to allow a broad framework of the global problem of cardiotoxic pollution to be established. AhR; Aryl hydrocarbon receptor. Dark lines indicate topics discussed in this review. Grey lines indicate topics reviewed elsewhere.

Efficacy of Climate Forcings in PDRMIP Models

Quantifying the efficacy of different climate forcings is important for understanding the real-world climate sensitivity. This study presents a systematic multimodel analysis of different climate driver efficacies using simulations from the Precipitation Driver and Response Model Intercomparison Project (PDRMIP). Efficacies calculated from instantaneous radiative forcing deviate considerably from unity across forcing agents and models. Effective radiative forcing (ERF) is a better predictor of global mean near-surface air temperature (GSAT) change. Efficacies are closest to one when ERF is computed using fixed sea surface temperature experiments and adjusted for land surface temperature changes using radiative kernels. Multimodel mean efficacies based on ERF are close to one for global perturbations of methane, sulfate, black carbon, and insolation, but there is notable intermodel spread. We do not find robust evidence that the geographic location of sulfate aerosol affects its efficacy. GSAT is found to respond more slowly to aerosol forcing than CO2 in the early stages of simulations. Despite these differences, we find that there is no evidence for an efficacy effect on historical GSAT trend estimates based on simulations with an impulse response model, nor on the resulting estimates of climate sensitivity derived from the historical period. However, the considerable intermodel spread in the computed efficacies means that we cannot rule out an efficacy-induced bias of ±0.4 K in equilibrium climate sensitivity to CO2 doubling when estimated using the historical GSAT trend.

Quantitative and qualitative consequences of reduced pollen loads in a mixed-mating plant

Greater pollination intensity can enhance maternal plant fitness by increasing seed set and seed quality as a result of more intense pollen competition or enhanced genetic sampling. We tested experimentally these effects by varying the pollen load from a single pollen donor on stigmas of female flowers of Dalechampia scandens (Euphorbiaceae) and measuring the effects on seed number and seed mass. Seed set increased rapidly with pollen number at low to moderate pollen loads, and a maximum set of three seeds occurred with a mean pollen load of 19 pollen grains. We did not detect a trade-off between the number of seeds and seed mass within a fruit. Seed mass increased with increasing pollen load, supporting the hypothesis of enhanced seed quality via increased pollen-competition intensity or genetic sampling. These results suggest that maternal fitness increases with larger pollen loads, even when the fertilization success is already high. Our results further highlight the importance of high rates of pollen arrival onto stigmas, as mediated by reliable pollinators. Comparing the pollen-to-seed response curve obtained in this experiment with those observed in natural populations suggests that pollen limitation may be more severe in natural populations than predicted from greenhouse studies. These results also indicate that declines in pollinator abundance may decrease plant fitness through lowered seed quality before an effect on seed set is detected.

The Role of Crustal Buoyancy in the Generation and Emplacement of Magmatism During Continental Collision

During continental collision, considerable amounts of buoyant continental crust subduct to depth and subsequently exhume. Whether various exhumation paths contribute to contrasting styles of magmatism across modern collision zones is unclear. Here we present 2D thermomechanical models of continental collision combined with petrological databases to investigate the effect of the main contrasting buoyancy forces, in the form of continental crustal buoyancy versus oceanic slab age (i.e., its thickness). We specifically focus on the consequences for crustal exhumation mechanisms and magmatism. Results indicate that it is mainly crustal density that determines the degree of steepening of the subducting continent and separates the models' parameter space into two regimes. In the first regime, high buoyancy values (∆ρ > 500 kg/m3) steepen the slab most rapidly (to 45-58°), leading to opening of a gap in the subduction channel through which the subducted crust exhumes ("subduction channel crustal exhumation"). A shift to a second regime ("underplating") occurs when the density contrast is reduced by 50 kg/m3. In this scenario, the slab steepens less (to 37-50°), forcing subducted crust to be placed below the overriding plate. Importantly, the magmatism changes in the two cases: Crustal exhumation through the subduction channel is mainly accompanied by a narrow band of mantle melts, while underplating leads to widespread melting of mixed sources. Finally, we suggest that the amount (or density) of subducted continental crust, and the resulting buoyancy forces, could contribute to contrasting collision styles and magmatism in the Alps and Himalayas/Tibet.

Seasonal shifts in feeding patterns: Individual and population realized specialization in a high Arctic fish

Species with a broad and flexible diet may be at an advantage in a rapidly changing environment such as in today's Arctic ecosystems. Polar cod (Boreogadus saida), an abundant and ecologically important circumpolar Arctic fish, is often described as a zooplankton generalist feeder, which suggests that it may cope successfully with changes in prey composition. This description is justified based on the relatively broad diet of polar cod across sites and seasons. In this case study, we used polar cod dietary data from fall and winter and from two distinct environments, dominated either by Arctic or Atlantic water masses in Svalbard. Our results point to the importance of time and space when drawing conclusions on dietary plasticity and degree of specialization. Polar cod diet differed significantly between fall and the winter and between Arctic and Atlantic domains. Polar cod from Arctic domains displayed a strong realized population specialization on Themisto libellula in fall, and the larger dietary niche width observed in the winter was the product of realized individual specialization, with increased feeding on fish prey. Overall, we did not observe a generalized feeding behavior. If dietary niche width is to inform conservation management, we argue it must be recognized that populations from a single species may adopt seasonally contrasting degrees of dietary specialization and that these populations may differ in their vulnerability to climate-induced changes in prey community composition.

Alternative responses to rare selection events are differentially vulnerable to changes in the frequency, scope, and intensity of environmental extremes

Extreme weather events are becoming more frequent, severe, and/or widespread as a consequence of anthropogenic climate change. While the economic and ecological implications of these changes have received considerable attention, the role of evolutionary processes in determining organismal responses to these critical challenges is currently unknown. Here we develop a novel theoretical framework that explores how alternative pathways for adaptation to rare selection events can influence population-level vulnerabilities to future changes in the frequency, scope, and intensity of environmental extremes. We begin by showing that different life histories and trait expression profiles can shift the balance between additive and multiplicative properties of fitness accumulation, favoring different evolutionary responses to identical environmental phenomena. We then demonstrate that these different adaptive outcomes lead to predictable differences in population-level vulnerabilities to rapid increases in the frequency, intensity, or scope of extreme weather events. Specifically, we show that when the primary mode of fitness accumulation is additive, evolution favors ignoring environmental extremes and lineages become highly vulnerable to extinction if the frequency or scope of extreme weather events suddenly increases. Conversely, when fitness accumulates primarily multiplicatively, evolution favors bet-hedging phenotypes that cope well with historical extremes and are instead vulnerable to sudden increases in extreme event intensity. Our findings address a critical gap in our understanding of the potential consequences of rare selection events and provide a relatively simple rubric for assessing the vulnerabilities of any population of interest to changes in a wide variety of extreme environmental phenomena.

Ethics as ritual: smoothing over moments of dislocation in biomedicine

Applications of biomedical R&D currently imply substantial societal concerns. This paper explores, based on semi-structured interviews with scientists in Norway, how biomedical researchers experience and tackle such concerns in their daily work. It shows how ritualised routine responses to dislocatory moments help maintain order in the daily work of the interviewed scientists; they do not address directly but instead smooth over concerns by a ritualised way of using ethics. This may foreclose substantive reflection and function as a stabiliser for 'business as usual'. Overall, the current way of responding to concerns as described by the interviewees may contribute to a depoliticisation of important issues. The paper contributes to sociological work on ethics by linking it to recent discussions on Responsible Research and Innovation (RRI) and by the empirical research presented. The insights can also help improve science policies such as RRI.

Decreasing incidence of pharmacologically and non-pharmacologically treated type 2 diabetes in Norway: a nationwide study

AIMS/HYPOTHESIS

This study aimed to examine recent time trends in the incidence and prevalence of type 2 diabetes in Norway.

METHODS

In this Norwegian nationwide cohort study, we linked data from national registries with prospectively collected data on diabetes medication and diabetes diagnoses for all residents in Norway aged 30 to 89 years (>3.2 million people). We analysed trends in incidence and prevalence of type 2 diabetes from 2009 to 2014 by type of treatment, sex, age, education level and place of birth.

RESULTS

During 15,463,691 person-years of follow-up from 2009 to 2014, we identified 75,496 individuals with new-onset type 2 diabetes. Of these, 36,334 (48%) were treated with blood-glucose-lowering drugs within 6 months of diagnosis. A low education level and being born in Asia, Africa or South America were significant risk factors for incident type 2 diabetes. While the prevalence of type 2 diabetes increased from 4.9% to 6.1% during the study period, the incidence decreased significantly from 609 cases per 100,000 person-years in 2009 to 398 cases per 100,000 in 2014, an annual reduction of 10.1% (95% CI -10.5, -9.6). A declining incidence was seen for both pharmacologically and non-pharmacologically treated type 2 diabetes, and in all subgroups defined by sex, age group, education level and place of birth.

CONCLUSIONS/INTERPRETATIONS

This nationwide study shows that, despite a decreasing incidence of type 2 diabetes in Norway, the prevalence continues to rise, probably due to diagnosis at a younger age and increased longevity.

An augmented aging process in brain white matter in HIV

OBJECTIVE

HIV infection and aging are both associated with neurodegeneration. However, whether the aging process alone or other factors associated with advanced age account for the progression of neurodegeneration in the aging HIV-positive (HIV+) population remains unclear.

METHODS

HIV+ (n = 70) and HIV-negative (HIV-, n = 34) participants underwent diffusion tensor imaging (DTI) and metrics of microstructural properties were extracted from regions of interest (ROIs). A support vector regression model was trained on two independent datasets of healthy adults across the adult life-span (n = 765, Cam-CAN = 588; UiO = 177) to predict participant age from DTI metrics, and applied to the HIV dataset. Predicted brain age gap (BAG) was computed as the difference between predicted age and chronological age, and statistically compared between HIV groups. Regressions assessed the relationship between BAG and HIV severity/medical comorbidities. Finally, correlation analyses tested for associations between BAG and cognitive performance.

RESULTS

BAG was significantly higher in the HIV+ group than the HIV- group F (1, 103) = 12.408, p = .001). HIV RNA viral load was significantly associated with BAG, particularly in older HIV+ individuals (R2  = 0.29, F(7, 70) = 2.66, p = .021). Further, BAG was negatively correlated with domain-level cognitive function (learning: r = -0.26, p = .008; memory: r = -0.21, p = .034).

CONCLUSIONS

HIV infection is associated with augmented white matter aging, and greater brain aging is associated with worse cognitive performance in multiple domains.

Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome

BACKGROUND

Breast cancer is a heterogeneous disease at the clinical and molecular level. In this study we integrate classifications extracted from five different molecular levels in order to identify integrated subtypes.

METHODS

Tumor tissue from 425 patients with primary breast cancer from the Oslo2 study was cut and blended, and divided into fractions for DNA, RNA and protein isolation and metabolomics, allowing the acquisition of representative and comparable molecular data. Patients were stratified into groups based on their tumor characteristics from five different molecular levels, using various clustering methods. Finally, all previously identified and newly determined subgroups were combined in a multilevel classification using a "cluster-of-clusters" approach with consensus clustering.

RESULTS

Based on DNA copy number data, tumors were categorized into three groups according to the complex arm aberration index. mRNA expression profiles divided tumors into five molecular subgroups according to PAM50 subtyping, and clustering based on microRNA expression revealed four subgroups. Reverse-phase protein array data divided tumors into five subgroups. Hierarchical clustering of tumor metabolic profiles revealed three clusters. Combining DNA copy number and mRNA expression classified tumors into seven clusters based on pathway activity levels, and tumors were classified into ten subtypes using integrative clustering. The final consensus clustering that incorporated all aforementioned subtypes revealed six major groups. Five corresponded well with the mRNA subtypes, while a sixth group resulted from a split of the luminal A subtype; these tumors belonged to distinct microRNA clusters. Gain-of-function studies using MCF-7 cells showed that microRNAs differentially expressed between the luminal A clusters were important for cancer cell survival. These microRNAs were used to validate the split in luminal A tumors in four independent breast cancer cohorts. In two cohorts the microRNAs divided tumors into subgroups with significantly different outcomes, and in another a trend was observed.

CONCLUSIONS

The six integrated subtypes identified confirm the heterogeneity of breast cancer and show that finer subdivisions of subtypes are evident. Increasing knowledge of the heterogeneity of the luminal A subtype may add pivotal information to guide therapeutic choices, evidently bringing us closer to improved treatment for this largest subgroup of breast cancer.