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The study of rare events in molecular and atomic systems such as conformal changes and cluster rearrangements has been one of the most important research themes in chemical physics. Key challenges are associated with long waiting times rendering molecular simulations inefficient, high dimensionality impeding the use of PDE-based approaches, and the complexity or breadth of transition processes limiting the predictive power of asymptotic methods. Diffusion maps are promising algorithms to avoid or mitigate all these issues. We adapt the diffusion map with Mahalanobis kernel proposed by Singer and Coifman (2008) for the SDE describing molecular dynamics in collective variables in which the diffusion matrix is position-dependent and, unlike the case considered by Singer and Coifman, is not associated with a diffeomorphism. We offer an elementary proof showing that one can approximate the generator for this SDE discretized to a point cloud via the Mahalanobis diffusion map. We use it to calculate the committor functions in collective variables for two benchmark systems: alanine dipeptide, and Lennard-Jones-7 in 2D. For validating our committor results, we compare our committor functions to the finite-difference solution or by conducting a "committor analysis" as used by molecular dynamics practitioners. We contrast the outputs of the Mahalanobis diffusion map with those of the standard diffusion map with isotropic kernel and show that the former gives significantly more accurate estimates for the committors than the latter., Comment: Restructured introduction, additional Theorem 3.1 and Appendix A, B

Plant functional traits can greatly influence invasion success on islands. However, interrelationships between traits and invasion success are rarely integrated with the island biogeography theory. Here, we explored relations between functional traits and plant distributions to assess which traits are associated with invasion success (i.e. high island occupancy), test whether non-native richness and seed mass of species with distinct growth forms and dispersal modes vary differently with island characteristics (e.g. area, isolation, exposure to ocean-borne disturbances, distance from the nearest urban area, and whether islands were managed for conservation), and whether results differ from native species. We assembled a database of 264 northern New Zealand offshore islands, amalgamating species lists from field surveys and previously published data, and comprising 822 native and 855 non-native species. Non-native graminoids occurred on islands more frequently than forbs and woody species, and long-distance dispersal modes (wind, animal, unspecialized) more than species with short-distance dispersal modes. Most differences among trait categories of non-native species were associated with human-related variables (i.e. distance from the nearest urban area, and whether islands were conservation areas). Non-native plant species with high island occupancy were less commonly associated with human-related variables than non-native species with low island occupancy. Instead, they were more similar in their distributional patterns to native species within the same trait category, suggesting comparable processes regulate both sets of species. Our results illustrate that integrating trait-based approaches in the island biogeography framework can be a useful tool in understanding and predicting plant invasions.

Spatial modelling of cancer survival is an important tool for identifying geographic disparities and providing an evidence base for resource allocation. Many different approaches have attempted to understand how survival varies geographically. This is the first scoping review to describe different methods and visualization techniques and to assess temporal trends in publications. The review was carried out using the PRISMA guideline using PubMed and Web of Science databases. Two authors independently screened articles. Articles were eligible for review if they measured cancer survival outcomes in small geographical areas by using spatial regression and/or mapping. Thirty-two articles were included, and the number increased over time. Most articles have been conducted in high-income countries using cancer registry databases. Eight different methods of modelling spatial survival were identified, and there were seven different ways of visualizing the results. Increasing the use of spatial modelling through enhanced data availability and knowledge sharing could help inform and motivate efforts to improve cancer outcomes and reduce excess deaths due to geographical inequalities. Efforts to improve the coverage and completeness of population-based cancer registries should continue to be a priority, in addition to encouraging the open sharing of relevant statistical programming syntax and international collaborations.

A polymer network fractures by breaking covalent bonds, but the experimentally measured strength of the polymer network is orders of magnitude lower than the strength of covalent bonds. We investigate the effect of statistical variation of the number of links in polymer chains on strength using a parallel chain model. Each polymer chain is represented by a freely-jointed chain, with a characteristic J-shaped force-extension curve. The chain carries entropic forces for most of the extension and carries covalent forces only for a narrow range of extension. The entropic forces are orders of magnitude lower than the covalent forces. Chains with a statistical distribution of the number of links per chain are pulled between two rigid parallel plates. Chains with fewer links attain covalent forces and rupture at smaller extensions, while chains with more links still carry entropic forces. We compute the applied force on the rigid plates as a function of extension and define the strength of the parallel chain model by the maximum force divided by the total number of chains. With the J-shaped force-extension curve of each chain, even a small scatter in the number of links per chain greatly reduces the strength of the parallel chain model. We further show that the strength of the parallel chain model relates to the scatter in the number of links per chain according to a power law., 17 pages, 5 figures

This version of the article has been accepted for publication, after peer review and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at https://doi.org/10.1007/s13225-021-00493-7. Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The dataset comprises 722,682 fungal operational taxonomic units (OTUs) derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents. The plots are supplied with geographical and edaphic metadata. The OTUs are taxonomically and functionally assigned to guilds and other functional groups. The entire dataset has been corrected by excluding chimeras, index-switch artefacts and potential contamination. The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data. The GSMc dataset is available over the PlutoF repository.

Rare cancers collectively account for around a quarter of cancer diagnoses and deaths. However, epidemiological studies are sparse. We describe spatial and geographical patterns in incidence and survival of rare cancers across Australia using a population-based cancer registry cohort of rare cancer cases diagnosed among Australians aged at least 15 years, 2007 to 2016. Rare cancers were defined using site- and histology-based categories from the European RARECARE study, as individual cancer types having crude annual incidence rates of less than 6/100 000. Incidence and survival patterns were modelled with generalised linear and Bayesian spatial Leroux models. Spatial heterogeneity was tested using the maximised excess events test. Rare cancers (n = 268 070) collectively comprised 22% of all invasive cancer diagnoses and accounted for 27% of all cancer-related deaths in Australia, 2007 to 2016 with an overall 5-year relative survival of around 53%. Males and those living in more remote or more disadvantaged areas had higher incidence but lower survival. There was substantial evidence for spatial variation in both incidence and survival for rare cancers between small geographical areas across Australia, with similar patterns so that those areas with higher incidence tended to have lower survival. Rare cancers are a substantial health burden in Australia. Our study has highlighted the need to better understand the higher burden of these cancers in rural and disadvantaged regions where the logistical challenges in their diagnosis, treatment and support are magnified.

Recent work underscores that ants are highly proficient and ubiquitous scavengers. These tendencies extend to numerically and behaviorally dominant introduced ants, which exhibit a suite of traits that allow them to exploit and monopolize carrion to a greater extent than is widely appreciated. We thus contend that an understanding of how introduced ants fit into food webs remains incomplete. Monopolization of carrion resources by introduced ants could increase worker production, enhance the ability of these species to compete with and prey upon other organisms, and alter the strength of direct and indirect interactions within food webs. Future work should consider how ant invasions influence energy transfer within and between green and brown food webs.

The study of phenomena such as protein folding and conformational changes in molecules is a central theme in chemical physics. Molecular dynamics (MD) simulation is the primary tool for the study of transition processes in biomolecules, but it is hampered by a huge timescale gap between the processes of interest and atomic vibrations which dictate the time step size. Therefore, it is imperative to combine MD simulations with other techniques in order to quantify the transition processes taking place on large timescales. In this work, the diffusion map with Mahalanobis kernel, a meshless approach for approximating the Backward Kolmogorov Operator (BKO) in collective variables, is upgraded to incorporate standard enhanced sampling techniques such as metadynamics. The resulting algorithm, which we call the "target measure Mahalanobis diffusion map" (tm-mmap), is suitable for a moderate number of collective variables in which one can approximate the diffusion tensor and free energy. Imposing appropriate boundary conditions allows use of the approximated BKO to solve for the committor function and utilization of transition path theory to find the reactive current delineating the transition channels and the transition rate. The proposed algorithm, tm-mmap, is tested on the two-dimensional Moro-Cardin two-well system with position-dependent diffusion coefficient and on alanine dipeptide in two collective variables where the committor, the reactive current, and the transition rate are compared to those computed by the finite element method (FEM). Finally, tm-mmap is applied to alanine dipeptide in four collective variables where the use of finite elements is infeasible., Restructured introduction, improved explanation of key algorithms and formulas (Section II.C and III.B,C). Streamlined presentation and proof of Theorem 1

Polychlorinated biphenyls (PCBs) are persistent organic pollutants associated with metabolic disruption and non-alcoholic fatty liver disease (NAFLD). Based on their ability to activate the aryl hydrocarbon receptor (AhR), PCBs are subdivided into two classes: dioxin-like (DL) and non-dioxin-like (NDL) PCBs. Previously, we demonstrated that NDL PCBs compromised the liver to promote more severe diet-induced NAFLD. Here, the hepatic effects and potential mechanisms (by untargeted liver proteomics) of DL PCBs, NDL PCBs or co-exposure to both in diet-induced NAFLD are investigated. Male C57Bl/6 mice were fed a 42% fat diet and exposed to vehicle control; Aroclor1260 (20 mg/kg, NDL PCB mixture); PCB126 (20 μg/kg, DL PCB congener); or a mixture of Aroclor1260 (20 mg/kg)+PCB126 (20 μg/kg) for 12 weeks. Each exposure was associated with a distinct hepatic proteome. Phenotypic and proteomic analyses revealed increased hepatic inflammation and phosphoprotein signaling disruption by Aroclor1260. PCB126 decreased hepatic inflammation and fibrosis at the molecular level; while altering cytoskeletal remodeling, metal homeostasis, and intermediary/xenobiotic metabolism. PCB126 attenuated Aroclor1260-induced hepatic inflammation but increased hepatic free fatty acids in the co-exposure group. Aroclor1260+PCB126 exposure was strongly associated with multiple epigenetic processes, and these could potentially explain the observed non-additive effects of the exposures on the hepatic proteome. Taken together, the results demonstrated that PCB exposures differentially regulated the hepatic proteome and the histologic severity of diet-induced NAFLD. Future research is warranted to determine the AhR-dependence of the observed effects including metal homeostasis and the epigenetic regulation of gene expression.

The impacts of climate change on biodiversity can be modulated by other changing environmental conditions (e.g. induced by land‐use change). The potential interactive effects of climate change and land use have rarely been studied for soil organisms. To test the effects of changing climatic conditions and land use on soil invertebrates, we examined earthworm communities across different seasons in different grassland‐use types (intensively managed grassland, extensively managed meadow and extensively managed sheep pasture). We predicted that the strength of climate change effects would vary with season and land use. Overall, extracted earthworm populations showed the strongest variations in response to the season, indicating major differences in activity patterns and extraction efficiency, whereas climate change and different grassland‐use types had fewer and weaker effects. Future climate, characterized by slightly higher precipitation in spring and autumn but a strong reduction during the summer, had positive effects on the abundance of extracted adult earthworms in spring but then reduced the abundance of active earthworms across the remaining seasons. In contrast, the total biomass of juveniles tended to be consistently lower under future climate conditions. Earthworm species responded differently to the climate change and different grassland management types, and these species‐specific responses further varied strongly across seasons. Intensive grassland management had negative effects, due to plant community composition, whereas sheep grazing favoured earthworm populations, due to dung deposition. There were only limited interactive effects between climate and land use, which thus did not support our main hypothesis. Nevertheless, these results highlight the complex and context‐dependent responses of earthworm communities and activity patterns to climate change, with potential consequences for long‐term population dynamics and crucial ecosystem functions. HIGHLIGHTS: We explored earthworm communities in response to climate change, different grassland‐use types and seasons Climate had species‐specific effects on active earthworms, but few interactions with land‐use type Intensive grassland management decreased, but sheep grazing favoured, active earthworm populations Strong seasonal variations in earthworm activity periods will be modulated by climate change

SummaryHere we introduce the Soil BON Foodweb Team, a cross-continental collaborative network that aims to monitor soil animal communities and food webs using consistent methodology at a global scale. Soil animals support vital soil processes via soil structure modification, direct consumption of dead organic matter, and interactions with microbial and plant communities. Soil animal effects on ecosystem functions have been demonstrated by correlative analyses as well as in laboratory and field experiments, but these studies typically focus on selected animal groups or species at one or few sites with limited variation in environmental conditions. The lack of comprehensive harmonised large-scale soil animal community data including microfauna, mesofauna, and macrofauna, in conjunction with related soil functions, limits our understanding of biological interactions in soil communities and how these interactions affect ecosystem functioning. To provide such data, the Soil BON Foodweb Team invites researchers worldwide to use a common methodology to address six long-term goals: (1) to collect globally representative harmonised data on soil micro-, meso-, and macrofauna communities; (2) to describe key environmental drivers of soil animal communities and food webs; (3) to assess the efficiency of conservation approaches for the protection of soil animal communities; (4) to describe soil food webs and their association with soil functioning globally; (5) to establish a global research network for soil biodiversity monitoring and collaborative projects in related topics; (6) to reinforce local collaboration networks and expertise and support capacity building for soil animal research around the world. In this paper, we describe the vision of the global research network and the common sampling protocol to assess soil animal communities and advocate for the use of standard methodologies across observational and experimental soil animal studies. We will use this protocol to conduct soil animal assessments and reconstruct soil food webs on the sites included in the global soil biodiversity monitoring network, Soil BON, allowing us to assess linkages among soil biodiversity, vegetation, soil physico-chemical properties, and ecosystem functions. In the present paper, we call for researchers especially from countries and ecoregions that remain underrepresented in the majority of soil biodiversity assessments to join us. Together we will be able to provide science-based evidence to support soil biodiversity conservation and functioning of terrestrial ecosystems.

A growing body of work examines the direct and indirect effects of climate change on ecosystems, typically by using manipulative experiments at a single site or performing meta-analyses across many independent experiments. However, results from single-site studies tend to have limited generality. Although meta-analytic approaches can help overcome this by exploring trends across sites, the inherent limitations in combining disparate datasets from independent approaches remain a major challenge. In this paper, we present a globally distributed experimental network that can be used to disentangle the direct and indirect effects of climate change. We discuss how natural gradients, experimental approaches, and statistical techniques can be combined to best inform predictions about responses to climate change, and we present a globally distributed experiment that utilizes natural environmental gradients to better understand long-term community and ecosystem responses to environmental change. The warming and (species) removal in mountains (WaRM) network employs experimental warming and plant species removals at high- and low-elevation sites in a factorial design to examine the combined and relative effects of climatic warming and the loss of dominant species on community structure and ecosystem function, both above- and belowground. The experimental design of the network allows for increasingly common statistical approaches to further elucidate the direct and indirect effects of warming. We argue that combining ecological observations and experiments along gradients is a powerful approach to make stronger predictions of how ecosystems will function in a warming world as species are lost, or gained, in local communities., Ecology and Evolution, 12 (10), ISSN:2045-7758

We present algorithms for solving high-frequency acoustic scattering problems in complex domains. The eikonal and transport partial differential equations from the WKB/geometric optic approximation of the Helmholtz equation are solved recursively to generate boundary conditions for a tree of eikonal/transport equation pairs, describing the phase and amplitude of a geometric optic wave propagating in a complicated domain, including reflection and diffraction. Edge diffraction is modeled using the uniform theory of diffraction. For simplicity, we limit our attention to domains with piecewise linear boundaries and a constant speed of sound. The domain is discretized into a conforming tetrahedron mesh. For the eikonal equation, we extend the jet marching method to tetrahedron meshes. Hermite interpolation enables second order accuracy for the eikonal and its gradient and first order accuracy for its Hessian, computed using cell averaging. To march the eikonal on an unstructured mesh, we introduce a new method of rejecting unphysical updates by considering Lagrange multipliers and local visibility. To handle accuracy degradation near caustics, we introduce several fast Lagrangian initialization algorithms. We store the dynamic programming plan uncovered by the marcher in order to propagate auxiliary quantities along characteristics. We introduce an approximate origin function which is computed using the dynamic programming plan, and whose 1/2-level set approximates the geometric optic shadow and reflection boundaries. We also use it to propagate geometric spreading factors and unit tangent vector fields needed to compute the amplitude and evaluate the high-frequency edge diffraction coefficient. We conduct numerical tests on a semi-infinite planar wedge to evaluate the accuracy of our method. We also show an example with a more realistic building model with challenging architectural features., Comment: 47 pages, 17 figures

15 páginas.- 6 figuras.- 93 referencias, Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms., The bulk of the funding is derived from the Estonian Science Foundation (grants PRG632, PRG1170, PRG1615, MOBTP198), EEA Financial Mechanism Baltic Research Programme (EMP442), and Novo Nordisk Fonden (NNF20OC0059948).

Polychlorinated biphenyls (PCBs) have been associated with abnormal liver enzymes and suspected nonalcoholic fatty liver disease (NAFLD) in cohort studies. NAFLD affects greater than 25% of the global population and may result in liver-related mortality. Both dioxin-like and non-dioxin-like PCBs have been associated with NAFLD, but their effects and mechanisms differ. Dioxin-like PCBs altered the gut:liver axis and microbiome and caused hepatic steatosis by disrupting hepatic lipid metabolism. In contrast, NDL PCBs reduced the liver's protective responses to promote diet-induced NAFLD. Mechanisms included the disruption of phosphoprotein signaling resulting in altered nuclear receptor function.

Non-alcoholic fatty liver disease (NAFLD), the most common form of liver disease, affects over 30% of the US population. Our group and others have previously demonstrated that low-level environmental pollutant exposures were associated with increased odds ratios for unexplained alanine aminotransferase (ALT) elevation, a surrogate biomarker for NAFLD, in the adult National Health and Nutrition Examination Survey (NHANES). However, recently, more sensitive and lower ALT cut-offs have been proposed. The objective of this observational study is to utilize these ALT cut-offs to determine new associations between environmental chemicals and the surrogate NAFLD biomarker. Adult NHANES 2003–2004 participants without viral hepatitis, hemochromatosis, or alcoholic liver disease were analyzed in this cross-sectional study. ALT elevation was defined as >30 IU/L in men and >19 IU/L in women. Odds ratios adjusted for potential confounders for ALT elevation were determined across exposure quartiles for 17 pollutant subclasses comprised of 111 individual pollutants. The overall prevalence of ALT elevation was 37.6%. Heavy metal and organochlorine insecticide subclasses were associated with dose-dependent increased adjusted odds ratios for ALT elevation of 1.6 (95% CI 1.2–2.3) and 3.5 (95% CI 2.3–5.5) respectively, for the highest vs. lowest exposure quartiles (p(trend)

PURPOSE: Fatty liver disease (FLD) affects over 25% of the global population and may lead to liver-related mortality due to cirrhosis and liver cancer. FLD caused by occupational and environmental chemical exposures is termed ‘toxicant associated steatohepatitis’ (TASH). The current review addresses the scientific progress made in the mechanistic understanding of TASH since its initial description in 2010. RECENT FINDINGS: Recently discovered modes of actions for volatile organic compounds and persistent organic pollutants include: (i) the endocrine, metabolism, and signaling disrupting chemical hypotheses; (ii) chemical-nutrient interactions and the two ‘hit’ hypothesis. These key hypotheses were then reviewed in the context of the steatosis adverse outcome pathway (AOP) proposed by the US Environmental Protection Agency. SUMMARY: The conceptual understanding of the contribution of environmental exposures to FLD has progressed significantly. However, because this is a new research area, more studies including mechanistic human data are required to address current knowledge gaps.

For decades, scientists have known where the highest numbers of species that live aboveground are found. So, they made maps of the world showing these patterns. For most of the aboveground groups, the highest numbers of species occur in the tropics and numbers decrease toward the poles. However, until recently, we did not understand such global patterns for many organisms living in the soil. We decided to create global maps of earthworm species richness. Earthworms provide humans with many useful services, such as moving the soils and improving their quality, which can increase the amount of food that is grown. If we want to protect earthworms and the services they provide, these global maps of earthworms are important because we need to understand where they are and why they live there.

Have you ever wanted to conduct scientific research? Citizen, or community science involves non-scientists in assisting scientists with research. The term covers a huge variety of projects: from online-only where you can classify galaxies, to practical outdoor activities, and even helping with scientific expeditions. Ideally, citizen science benefits everyone—scientists collect more data, and over larger geographic areas than they could on their own. Non-scientists benefit by learning something new and experiencing how science works, and hopefully having fun! The small size of most soil organisms is challenging for citizen science. However, earthworms are easy to recognize and relatively large, so there have been several citizen science projects focused on them. In this article, we discuss earthworm citizen science from its origins with 18th and 19th century natural historians, to the modern day. Discover what non-scientists have contributed to earthworm science and how you can design your own earthworm investigations.

James et al . claim that there are areas of concern in our work. We believe that they have misunderstood the methods behind our paper and that differences in scale have been overlooked. Once those misunderstandings have been resolved, their remaining criticisms are either not sustained or agree with our statements. To advance the field, we recommend additional sampling using comparable methodologies in underrepresented areas.

Land snails are one of the most diverse groups of terrestrial animals and are commonly used as model organisms in ecology, biogeography and conservation biology. Despite being poor dispersers, they form crucial components of island faunas and exhibit high percentages of endemism. Insular land snails are also among the most threatened animals on Earth, already having suffered extensive human-caused extinctions. However, current estimates of global insular land snail diversity are basedon sporadic records published at the scale of individual islands and/or archipelagos. To tackle this shortfall, we herein present the major features of a global inventory of island snails. We recovered full species lists from existing literature and available species checklists for 727 islands across the globe and collated a database which currently includes the occurrence of 11,139 species, that is approximately 48% of all known land snail species (of which there are an estimated 23,000). Seventy-five percent of the species are single-island endemics, underlining the exceptional nature of islands as global biodiversity hotspots. Overall, our attempt is one of few to examine insular invertebrate diversity at coarser scales and a crucial step to the study of global patterns in island biodiversity. © the authors, CC-BY 4.0 license

1. Polychlorinated biphenyls (PCBs) are persistent environmental pollutants that disrupt hepatic xenobiotic and intermediary metabolism, leading to metabolic syndrome and nonalcoholic steatohepatitis (NASH). 2. Since phenobarbital indirectly activates Constitutive Androstane Receptor (CAR) by antagonizing growth factor binding to the epidermal growth factor receptor (EGFR), we hypothesized that PCBs may also diminish EGFR signaling. 3. The effects of the PCB mixture Aroclor 1260 on the protein phosphorylation cascade triggered by EGFR activation were determined in murine (in vitro and in vivo) and human models (in vitro). EGFR tyrosine residue phosphorylation was decreased by PCBs in all models tested. 4. The IC50 values for Aroclor 1260 concentrations that decreased Y1173 phosphorylation of EGFR were similar in murine AML-12 and human HepG2 cells (∼2–4 μg/mL). Both dioxin and non-dioxin-like PCB congeners decreased EGFR phosphorylation in cell culture. 5. PCB treatment reduced phosphorylation of downstream EGFR effectors including Akt and mTOR, as well as other phosphoprotein targets including STAT3 and c-RAF in vivo. 6. PCBs diminish EGFR signaling in human and murine hepatocyte models and may dysregulate critical phosphoprotein regulators of energy metabolism and nutrition, providing a new mechanism of action in environmental diseases.

Long-term monitoring of host-parasite interactions is important for understanding the consequences of infection on host fitness and population dynamics. In an eight-year survey of the loggerhead sea turtle (Caretta caretta) population nesting in Cabo Verde, we determined the spatiotemporal variation of Ozobranchus margoi, a sanguivorous leech best known as a vector for sea turtle fibropapilloma virus. We quantified O. margoi association with turtles’ δ15N and δ13C stable isotopes to identify where infection occurs. We then measured the influence of infection on reproduction and offspring fitness. We found that parasite prevalence has increased from 10% of the population in 2010, to 33% in 2017. Stable isotope analysis of host skin samples suggests transmission occurs within the host’s feeding grounds. Interestingly, we found a significant interaction between individual size and infection on the reproductive success of turtles. Specifically, small, infected females produced fewer offspring of poorer condition, while in contrast, large, infected turtles produced greater clutch sizes and larger offspring. We interpret this interaction as evidence, upon infection, for a size-dependent shift in reproductive strategy from bet hedging to terminal investment, altering population dynamics. This link between infection and reproduction underscores the importance of using long-term monitoring to quantify the impact of disease dynamics over time.

The endocrine disrupting chemicals, polychlorinated biphenyls (PCBs), have been associated with nonalcoholic steatohepatitis (NASH) and diabetes. However, an integrative analysis of the effects of PCBs on the liver and pancreas has never been performed for the two major PCB subtypes, dioxin-like (DL) and nondioxin-like (NDL), and a mixture of NDL/DL PCBs. Therefore, male C57BL/6 J mice fed a control synthetic diet were treated with either a NDL PCB mixture, Aroclor 1260 (20 mg/kg); a single DL PCB congener, PCB 126 (20 μg/kg); a NDL/DL mixture, Aroclor 1260 plus PCB 126; or vehicle control for 2 weeks. PCB126 had the greatest impact on hepatic lipid metabolism. It caused steatosis due to increased hepatic lipid import with associated hypolipidemia. However, all PCB exposures impacted expression of hepatic lipid metabolism genes in different manners. The ‘NASH gene’, Pnpla3, was elevated by Aroclor 1260, but decreased by all other exposures. The expression of hepatokines implicated in metabolic syndrome (Fgf21, Igf1, and betatrophin) were differentially regulated. The NDL/DL PCB mixture had the greatest effects on pancreatic histology, including acinar cell atrophy, mild steatosis, and fibrosis without ductal changes or immune cell infiltration. It decreased expression of insulin and altered the expression of genes regulating islet identity. None of these exposures was associated with altered HOMA-IR or HOMA-B. In summary, PCB exposures differentially regulated liver and pancreas structure and function. Novel mechanisms for PCB-induced endocrine/metabolic disruption included altered hepatokines and Pnpla3 as well as ‘PCB pancreatopathy’ that was associated with altered expression of pancreatic islet identity factors. More research is required to understand fully these findings in the context of human NASH and diabetes.

Understanding the processes that underlie the current distribution of genetic diversity in endangered species is a goal of modern conservation biology. Specifically, the role of colonization and dispersal events throughout a species’ evolutionary history often remains elusive. The loggerhead sea turtle (Caretta caretta) faces multiple conservation challenges due to its migratory nature and philopatric behaviour. Here, using 4207 mtDNA sequences, we analysed the colonisation patterns and distribution of genetic diversity within a major ocean basin (the Atlantic), a regional rookery (Cabo Verde Archipelago) and a local island (Island of Boa Vista, Cabo Verde). Data analysis using hypothesis-driven population genetic models suggests the colonization of the Atlantic has occurred in two distinct waves, each corresponding to a major mtDNA lineage. We propose the oldest lineage entered the basin via the isthmus of Panama and sequentially established aggregations in Brazil, Cabo Verde and in the area of USA and Mexico. The second lineage entered the Atlantic via the Cape of Good Hope, establishing colonies in the Mediterranean Sea, and from then on, re-colonized the already existing rookeries of the Atlantic. At the Cabo Verde level, we reveal an asymmetric gene flow maintaining links across island-specific nesting groups, despite significant genetic structure. This structure stems from female philopatric behaviours, which could further be detected by weak but significant differentiation amongst beaches separated by only a few kilometres on the island of Boa Vista. Exploring biogeographic processes at diverse geographic scales improves our understanding of the complex evolutionary history of highly migratory philopatric species. Unveiling the past facilitates the design of conservation programmes targeting the right management scale to maintain a species’ evolutionary potential.

BACKGROUND: Environmental pollution contributes to fatty liver disease pathogenesis. Polychlorinated biphenyl (PCB) exposures have been associated with liver enzyme elevation and suspected steatohepatitis in cohort studies. Male mice treated with the commercial PCB mixture, Aroclor 1260 (20 mg/kg), and fed high fat diet (HFD) for 12 weeks developed steatohepatitis. Receptor-based modes of action including inhibition of the epidermal growth factor (EGF) receptor were previously proposed, but other mechanisms likely exist. OBJECTIVES: To identify and validate the pathways, transcription factors, and mechanisms responsible for the steatohepatitis associated with PCB and HFD co-exposures. METHODS: Comparative proteomics analysis was performed in archived mouse liver samples from the aforementioned chronic exposure study. Pathway and transcription factor analysis (TFA) was performed, and selected results were validated. RESULTS: Liver proteomics detected 1103 unique proteins. Aroclor 1260 upregulated 154 and downregulated 93 of these. Aroclor 1260+HFD co-exposures affected 55 pathways including glutathione metabolism, intermediary metabolism, and cytoskeletal remodeling. TFA of Aroclor 1260 treatment demonstrated alterations in the function of 42 transcription factors including downregulation of NRF2 and key nuclear receptors previously demonstrated to protect against steatohepatitis (e.g., HNF4α, FXR, PPARα/δ/γ, etc.). Validation studies demonstrated that Aroclor 1260 significantly reduced HNF4α protein levels; while Aroclor 1260+HFD reduced expression of the HNF4α target gene, albumin, in vivo. Aroclor 1260 attenuated EGF-dependent HNF4α phosphorylation and target gene activation in vitro. Aroclor 1260 reduced levels of NRF2, its target genes, and glutathione in vivo. Aroclor 1260 attenuated EGF-dependent NRF2 upregulation, in vitro. Aroclor 1260 indirectly activated hepatic stellate cells in vitro via induction of hepatocyte-derived TGFβ. CONCLUSION: PCB exposures adversely impacted transcription factors regulating liver protection, function, and fibrosis. PCBs, thus, compromised the liver by reducing its protective responses against nutritional stress to promote diet-induced steatohepatitis. The identified mechanisms by which environmental pollutants influence fatty liver disease pathogenesis require confirmation in humans.

In this age of computer gaming, portable device video and high definition entertainment, students are exposed to sophisticated graphics and virtual reality every day. As a result, students arrive at universities with a high level of expectation and experience in visualization and 3D graphics. Traditional materials for education and outreach rely predominantly on two-dimensional displays of maps, photographs, data graphs/histograms and conceptual diagrams. Advances in geospatial technologies, including unmanned aerial systems and virtual/ augmented reality devices can be used to enhance and innovate instructional materials in classrooms from pre-K to graduate degree programs. This work reports on these technologies and the integration of the 3D Immersion and Geovisualization (3DIG) system at the Center for Geospatial Research at the University of Georgia, USA. We present system components, lessons learned during design and implementation of the system, and the incorporation of 3DIG into teaching, learning and research. Data flow is used as a multi-component system integrator and shows how interconnected and complementary technologies can provide hands-on and immersive experiential learning to students in the geosciences. System evaluation shows increased student interest/engagement and indicates that 3DIG facilitates the understanding of complex concepts.

AimUnderstanding the processes that underlie the distribution of genetic diversity in endangered species is a goal of modern conservation biology. Specifically, how population structure affects genetic diversity and contributes to a species’ adaptive potential remain elusive. The loggerhead sea turtle (Caretta caretta) faces multiple conservation challenges due to its migratory nature and philopatric behaviour.LocationsAtlantic Ocean, Cabo Verde, island of BoavistaMethodsHere, using 4207 mtDNA sequences, we analysed the colonisation patterns and distribution of genetic diversity within a major ocean basin (the Atlantic), a regional rookery (Cabo Verde Archipelago) and a local island (Island of Boavista, Cabo Verde).ResultsHypothesis-driven population genetic models suggest the colonization of the Atlantic has occurred in two distinct waves, each corresponding to major mtDNA lineages. We propose the oldest lineage entered the basin via the isthmus of Panama and sequentially established aggregations in Brazil, Cabo Verde and in the area of USA and Mexico. The second lineage entered the Atlantic via the Cape of Good Hope, establishing colonies in the Mediterranean Sea, and from then on, re-colonized the already existing rookeries of the Atlantic. At the Cabo Verde level, we reveal an asymmetric gene flow maintaining links across nesting groups despite significant genetic structure amongst nesting groups. This structure stems from female philopatric behaviour which could further be detected by weak but significant structure amongst beaches separated by only a few kilometres on the island of Boavista.Main conclusionTo explore demographic processes at diverse geographic scales improves understanding the complex evolutionary history of highly migratory philopatric species. Unveiling the past facilitates the design of conservation programmes targeting the right management scale to maintain a species’ adaptive potential and putative response to human-induced selection.

Deejaying, emceeing, graffiti writing, and breakdancing. Together, these artistic expressions combined to form the foundation of one of the most significant cultural phenomena of the late 20th century — Hip-Hop. Rooted in African American culture and experience, the music, fashion, art, and attitude that is Hip-Hop crossed both racial boundaries and international borders. The Foundations of Hip-Hop Encyclopedia is a general reference work for students, scholars, and virtually anyone interested in Hip-Hop’s formative years. In thirty-six entries, it covers the key developments, practices, personalities, and products that mark the history of Hip-Hop from the 1970s through the early ‘90s. All entries are written by students at Virginia Tech who enthusiastically enrolled in a course on Hip-Hop taught by Dr. Anthony Kwame Harrison, author of Hip Hop Underground, and co-taught by Craig E. Arthur. Because they are students writing about issues and events that took place well before most of them were born, their entries capture the distinct character of young people reflecting back on how a music and culture that has profoundly shaped their lives came to be. Future editions are planned as more students take the class, making this a living, evolving work.

Motivation and aim: Soil biodiversity is central to ecosystem function and services. It represents most of terrestrial biodiversity and at least a quarter of all biodiversity on Earth. Yet, research into broad, generalizable spatial and temporal patterns of soil biota has been limited compared to aboveground systems due to complexities of the soil system. We review the literature and identify key considerations necessary to expand soil macroecology beyond the recent surge of global maps of soil taxa, so that we can gain greater insight into the mechanisms and processes shaping soil biodiversity. We focus primarily on three groups of soil taxa (earthworms, mycorrhizal fungi and soil bacteria) that represent a range of body sizes and ecologies, and, therefore, interact with their environment at different spatial scales. Results: The complexities of soil, including fine-scale heterogeneity, 3-D habitat structure, difficulties with taxonomic delimitation, and the wide-ranging ecologies of its inhabitants, require the classical macroecological toolbox to be expanded to consider novel sampling, molecular identification, functional approaches, environmental variables, and modelling techniques. Main conclusions: Soil provides a complex system within which to apply macroecological research, yet, it is this property that itself makes soil macroecology a field ripe for innovative methodologies and approaches. To achieve this, soil-specific data, spatio-temporal, biotic, and abiotic considerations are necessary at all stages of research, from sampling design to statistical analyses. Insights into whole ecosystems and new approaches to link genes, functions and diversity across spatial and temporal scales, alongside methodologies already applied in aboveground macroecology, invasion ecology and aquatic ecology, will facilitate the investigation of macroecological processes in soil biota, which is key to understanding the link between biodiversity and ecosystem functioning in terrestrial ecosystems.

Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research., Soil organism biodiversity contributes to ecosystem function, but biodiversity and function have not been equivalently studied across the globe. Here the authors identify locations, environment types, and taxonomic groups for which there is currently a lack of biodiversity and ecosystem function data in the existing literature.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide., 677232 to N.E.). K.S.R. and W.H.v.d.P. were supported by ERC-ADV grant 323020 to W.H.v.d.P. Also supported by iDiv (DFG FZT118) Flexpool proposal 34600850 (C.A.G. and N.E.); the Academy of Finland (285882) and the Natural Sciences and Engineering Research Council of Canada (postdoctoral fellowship and RGPIN-2019-05758) (E.K.C.); DOB Ecology (T.W.C., J.v.d.H., and D.R.); ERC-AdG 694368 (M.R.); and the TULIP Laboratory of Excellence (ANR-10-LABX-41) (M.L.). In addition, data collection was funded by the Russian Foundation for Basic Research (12-04-01538-a, 12-04-01734-a, 14-44-03666-r_center_a, 15-29-02724-ofi_m, 16-04-01878-a 19-05-00245); Tarbiat Modares University; Aurora Organic Dairy; UGC(NERO) (F. 1-6/Acctt./NERO/2007-08/1485); Natural Sciences and Engineering Research Council (RGPIN-2017-05391); Slovak Research and Development Agency (APVV-0098-12); Science for Global Development through Wageningen University; Norman Borlaug LEAP Programme and International Atomic Energy Agency (IAEA); São Paulo Research Foundation - FAPESP (12/22510-8); Oklahoma Agricultural Experiment Station; INIA - Spanish Agency (SUM 2006-00012-00-0); Royal Canadian Geographical Society; Environmental Protection Agency (Ireland) (2005-S-LS-8); University of Hawai‘i at Mānoa (HAW01127H; HAW01123M); European Union FP7 (FunDivEurope, 265171); U.S. Department of the Navy, Commander Pacific Fleet (W9126G-13-2-0047); Science and Engineering Research Board (SB/SO/AS-030/2013) Department of Science and Technology, New Delhi, India; Strategic Environmental Research and Development Program (SERDP) of the U.S. Department of Defense (RC-1542); Maranhão State Research Foundation (FAPEMA); Coordination for the Improvement of Higher Education Personnel (CAPES); Ministry of Education, Youth and Sports of the Czech Republic (LTT17033); Colorado Wheat Research Foundation; Zone Atelier Alpes, French National Research Agency (ANR-11-BSV7-020-01, ANR-09-STRA-02-01, ANR 06 BIODIV 009-01); Austrian Science Fund (P16027, T441); Landwirtschaftliche Rentenbank Frankfurt am Main; Welsh Government and the European Agricultural Fund for Rural Development (Project Ref. A AAB 62 03 qA731606); SÉPAQ; Ministry of Agriculture and Forestry of Finland; Science Foundation Ireland (EEB0061); University of Toronto (Faculty of Forestry); National Science and Engineering Research Council of Canada; Haliburton Forest and Wildlife Reserve; NKU College of Arts and Sciences Grant; Österreichische Forschungsförderungsgesellschaft (837393 and 837426); Mountain Agriculture Research Unit of the University of Innsbruck; Higher Education Commission of Pakistan; Kerala Forest Research Institute, Peechi, Kerala; UNEP/GEF/TSBF-CIAT Project on Conservation and Sustainable Management of Belowground Biodiversity; Ministry of Agriculture and Forestry of Finland; Complutense University of Madrid/European Union FP7 project BioBio (FPU UCM 613520); GRDC; AWI; LWRRDC; DRDC; CONICET (National Scientific and Technical Research Council) and FONCyT (National Agency of Scientific and Technological Promotion) (PICT, PAE, PIP), Universidad Nacional de Luján y FONCyT [PICT 2293 (2006)], Fonds de recherche sur la nature et les technologies du Québec (131894), Deutsche Forschungsgemeinschaft [SCHR1000/3-1, SCHR1000/6-1, 6-2 (FOR 1598), WO 670/7-1, WO 670/7-2, and SCHA 1719/1-2], CONACYT (FONDOS MIXTOS TABASCO/PROYECTO11316); NSF (DGE-0549245, DGE-0549245, DEB-BE-0909452, NSF1241932); Institute for Environmental Science and Policy at the University of Illinois at Chicago; Dean’s Scholar Program at UIC; Garden Club of America Zone VI Fellowship in Urban Forestry from the Casey Tree Endowment Fund; J. E. Weaver Competitive Grant from the Nebraska Chapter of The Nature Conservancy; the College of Liberal Arts and Sciences at DePaul University; Elmore Hadley Award for Research in Ecology and Evolution from the UIC Dept. of Biological Sciences; Spanish CICYT (AMB96-1161; REN2000-0783/GLO; REN2003-05553/GLO; REN2003-03989/GLO; CGL2007-60661/BOS); Yokohama National University; MEXT KAKENHI (25220104); Japan Society for the Promotion of Science KAKENHI (25281053, 17KT0074, 25252026); ADEME (0775C0035); Ministry of Science, Innovation and Universities of Spain (CGL2017-86926-P); Syngenta Philippines; UPSTREAM; LTSER (Val Mazia/Matschertal); Marie Sklodowska Curie Postdoctoral Fellowship (747607); National Science and Technology Base Resource Survey Project of China (2018FY100306); McKnight Foundation (14-168); Program of Fundamental Researches of Presidium of Russian Academy of Sciences (AAAA-A18-118021490070-5); Brazilian National Council of Research CNPq; and French Ministry of Foreign and European Affairs. Author contributions: H.R.P.P. led the analysis, data curation, and writing of the original manuscript draft. C.A.G. assisted in analyses and writing of the original manuscript draft. E.K.C. and N.E. revised subsequent manuscript drafts. J.v.d.H., D.R., and T.W.C. provided additional analyses. E.K.C., N.E., and M.P.T. acquired funding for the project. J.K., K.B.G., B.S., M.L.C.B., M.J.I.B., and G.B. contributed to data curation. H.R.P.P., C.A.G., M.L.C.B., M.J.I.B., G.B., O.F., A.O., E.M.B., J.B., U.B., T.D., F.T.d.V., B.K.-R., M.L., J.M., C.M., W.H.v.d.P., K.S.R., M.C.R., D.R., M.R., M.P.T., D.H.W., D.A.W., E.K.C., and N.E. contributed to the project conceptualization. All authors reviewed and edited the final draft manuscript. The majority of the authors provided data for the analyses. Competing interests: The authors declare no competing interests. Data and materials availability: Data and analysis code are available on the iDiv Data repository (DOI: 10.25829/idiv.1804-5-2593) and GitHub (https://github.com/helenphillips/GlobalEWDiversity; DOI: 10.5281/zenodo.3386456).

As biodiversity worldwide is decreasing, to preserve adaptive potential, the importance of maintaining species’ genetic and trait diversities is increasing. An efficient foraging strategy is a critical trait for an organism’s fitness, as it affects its physiology and reproduction. Understanding such strategies is especially relevant for species with long feeding migrations such as sea turtles. Using carbon and nitrogen stable isotopes combined with mitochondrial sequencing, we explored the diversity of feeding strategies in genetically differentiated nesting groups of loggerhead sea turtles (Caretta caretta) within the Cape Verde Archipelago. Here, we reveal a pattern where turtles from most islands use two distinct oceanic feeding strategies, including one putatively linked to a15N-enriched zone of the West African upwelling area. On the Eastern island of Boavista, an additional third strategy exists used by turtles feeding mostly neritically. Contrary to previous paradoxical assumptions, oceanic turtles, that represent the vast majority of the population, are not smaller than neritic turtles and therefore do not seem to feed in a suboptimal environment. Our results also suggest that the number of feeding strategies may correlate with demography, whereby a greater feeding strategy diversity matches demographic signs of recent expansion after a population bottleneck for turtles nesting on the island of Boavista. Overall, the feeding ecology of Cape Verde loggerhead turtles is complex and likely shaped by an interaction between environmental and population parameters. Our results stress the importance of conservation efforts to prevent loss of critical diversity in endangered species.

Salicylic acid (SA)-mediated innate immune responses are activated in plants perceiving volatile monoterpenes. Here, we show that monoterpene-associated responses are propagated in feed-forward loops involving the systemic acquired resistance (SAR) signaling components pipecolic acid, glycerol-3-phosphate, and LEGUME LECTIN-LIKE PROTEIN1 (LLP1). In this cascade, LLP1 forms a key regulatory unit in both within-plant and between-plant propagation of immunity. The data integrate molecular components of SAR into systemic signaling networks that are separate from conventional, SA-associated innate immune mechanisms. These networks are central to plant-to-plant propagation of immunity, potentially raising SAR to the population level. In this process, monoterpenes act as microbe-inducible plant volatiles, which as part of plant-derived volatile blends have the potential to promote the generation of a wave of innate immune signaling within canopies or plant stands. Hence, plant-to-plant propagation of SAR holds significant potential to fortify future durable crop protection strategies following a single volatile trigger., Plants immune responses are triggered upon perception of volatile monoterpenes. Here, Wenig et al. show that a feed-forward loop featuring LEGUME LECTIN-LIKE PROTEIN1 propagates monoterpene-associated cues both within and between plants, illustrating how systemic immunity could act at a population level.