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Abstract Six different configurations, a mixture of grids and atmospheric dynamical cores available in the Community Earth System Model, version 2.2 (CESM2.2), are evaluated for their skill in representing the climate of the Arctic and the surface mass balance of the Greenland Ice Sheet (GrIS). The finite‐volume dynamical core uses structured, latitude‐longitude grids, whereas the spectral‐element dynamical core is built on unstructured meshes, permitting grid flexibility such as quasi‐uniform grid spacing globally. The 1°–2° latitude‐longitude and quasi‐uniform unstructured grids systematically overestimate both accumulation and ablation over the GrIS. Of these 1°–2° grids, the latitude‐longitude grids outperform the quasi‐uniform unstructured grids because they have more degrees of freedom to represent the GrIS. Two Arctic‐refined meshes, with 1/4° and 1/8° refinement over Greenland, were developed for the spectral‐element dynamical core and are documented here as newly supported configurations in CESM2.2. The Arctic meshes substantially improve the simulated clouds and precipitation rates in the Arctic. Over Greenland, these meshes skillfully represent accumulation and ablation processes, leading to a more realistic GrIS surface mass balance. As CESM is in the process of transitioning away from conventional latitude‐longitude grids, these new Arctic‐refined meshes improve the representation of polar processes in CESM by recovering resolution lost in the transition to quasi‐uniform grids, albeit at increased computational cost.

Identifying genetic variation underlying human diseases establishes targets for therapeutic development and helps tailor treatments to individual patients. Large-scale transcriptomic profiling has extended the study of such molecular heterogeneity between patients to somatic tissues. However, the lower resolution of bulk RNA profiling, especially in a complex, composite tissue such as the skin, has limited its success. Here we demonstrate approaches to interrogate patient-level molecular variance in a chronic skin inflammatory disease, psoriasis vulgaris, leveraging single-cell RNA-sequencing of CD45+ cells isolated from active lesions. Highly psoriasis-specific transcriptional abnormalities display greater than average inter-individual variance, nominating them as potential sources of clinical heterogeneity. We find that one of these chemokines, CXCL13, demonstrates significant correlation with severity of lesions within our patient series. Our analyses also establish that genes elevated in psoriatic skin-resident memory T cells are enriched for programs orchestrating chromatin and CDC42-dependent cytoskeleton remodeling, specific components of which are distinctly correlated with and against Th17 identity on a single-cell level. Collectively, these analyses describe systematic means to dissect cell type- and patient-level differences in cutaneous psoriasis using high-resolution transcriptional profiles of human inflammatory disease.

Abstract. Background:. Acute thrombosis of the superior mesenteric vein (SMV) is a rare but potentially catastrophic condition. Clinically separate from portal venous thrombosis due to a higher proportion of associated thrombophilic disorders and intestinal infarction, SMV thrombosis warrants a distinct approach to management. The aim of this review is to report the evidence for current practice. Methods:. A systematic review was carried out in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Four clinical trials databases and 4 trial registries were searched. This search was not limited by language or study type, but was limited to an adult population (18 years and above). The search period was between January 1, 2000 and February 28, 2019. The review was registered in the PROSPERO database: CRD42018116825. Bias was assessed using the ROBINS-I tool. Results:. A total of 7989 studies were identified, resulting in 19 observational studies being analyzed. Eighteen studies reported on anti-coagulation, 1 reported on anti-coagulation plus endovascular thrombectomy, 9 reported on thrombolysis, and 10 reported on the role of surgery. Bias assessment showed that confounding was a significant area of potential bias. This review has reported that the management of SMV thrombosis is centered around a patients’ perceived hemodynamic stability. If there is evidence of perforation or peritonism then surgical intervention is advocated. Otherwise, anti-coagulation or thrombolysis is preferred. Conclusions:. The data reported were compared with, and added to, that presented by the European Society for Vascular Surgery 2017 guidelines. Overall the source data were heterogenous, with multiple sources of bias and statistical comparison was not achievable.

Abstract This study provides an overview of the coupled high‐resolution Version 1 of the Energy Exascale Earth System Model (E3SMv1) and documents the characteristics of a 50‐year‐long high‐resolution control simulation with time‐invariant 1950 forcings following the HighResMIP protocol. In terms of global root‐mean‐squared error metrics, this high‐resolution simulation is generally superior to results from the low‐resolution configuration of E3SMv1 (due to resolution, tuning changes, and possibly initialization procedure) and compares favorably to models in the CMIP5 ensemble. Ocean and sea ice simulation is particularly improved, due to better resolution of bathymetry, the ability to capture more variability and extremes in winds and currents, and the ability to resolve mesoscale ocean eddies. The largest improvement in this regard is an ice‐free Labrador Sea, which is a major problem at low resolution. Interestingly, several features found to improve with resolution in previous studies are insensitive to resolution or even degrade in E3SMv1. Most notable in this regard are warm bias and associated stratocumulus deficiency in eastern subtropical oceans and lack of improvement in El Niño. Another major finding of this study is that resolution increase had negligible impact on climate sensitivity (measured by net feedback determined through uniform +4K prescribed sea surface temperature increase) and aerosol sensitivity. Cloud response to resolution increase consisted of very minor decrease at all levels. Large‐scale patterns of precipitation bias were also relatively unaffected by grid spacing.

Abstract This work documents the first version of the U.S. Department of Energy (DOE) new Energy Exascale Earth System Model (E3SMv1). We focus on the standard resolution of the fully coupled physical model designed to address DOE mission‐relevant water cycle questions. Its components include atmosphere and land (110‐km grid spacing), ocean and sea ice (60 km in the midlatitudes and 30 km at the equator and poles), and river transport (55 km) models. This base configuration will also serve as a foundation for additional configurations exploring higher horizontal resolution as well as augmented capabilities in the form of biogeochemistry and cryosphere configurations. The performance of E3SMv1 is evaluated by means of a standard set of Coupled Model Intercomparison Project Phase 6 (CMIP6) Diagnosis, Evaluation, and Characterization of Klima simulations consisting of a long preindustrial control, historical simulations (ensembles of fully coupled and prescribed SSTs) as well as idealized CO2 forcing simulations. The model performs well overall with biases typical of other CMIP‐class models, although the simulated Atlantic Meridional Overturning Circulation is weaker than many CMIP‐class models. While the E3SMv1 historical ensemble captures the bulk of the observed warming between preindustrial (1850) and present day, the trajectory of the warming diverges from observations in the second half of the twentieth century with a period of delayed warming followed by an excessive warming trend. Using a two‐layer energy balance model, we attribute this divergence to the model's strong aerosol‐related effective radiative forcing (ERFari+aci = −1.65 W/m2) and high equilibrium climate sensitivity (ECS = 5.3 K).

Abstract Supported by the U.S. Department of Energy (DOE), the Energy Exascale Earth System Model (E3SM) project aims to optimize the use of DOE resources to address the grand challenge of actionable predictions of Earth system variability and change. This requires sustained advancement to (1) integrate model development with leading‐edge computational advances toward ultra‐high‐resolution modeling; (2) represent the coupled human‐Earth system to address energy sector vulnerability to variability and change; and (3) address uncertainty in model simulations and projections. Scientific development of the E3SM modeling system is driven by the simulation requirements in three overarching science areas centering on understanding the Earth's water cycle, biogeochemistry, and cryosphere systems and their future changes. This paper serves as an introduction to the E3SM special collection, which includes 50 papers published in several AGU journals. It provides an overview of the E3SM project, including its goals and science drivers. It also provides a brief history of the development of E3SM version 1 and highlights some key findings from papers included in the special collection.

Summary: Inflammatory response heterogeneity has impeded high-resolution dissection of diverse immune cell populations during activation. We characterize mouse cutaneous immune cells by single-cell RNA sequencing, after inducing inflammation using imiquimod and oxazolone dermatitis models. We identify 13 CD45+ subpopulations, which broadly represent most functionally characterized immune cell types. Oxazolone pervasively upregulates Jak2/Stat3 expression across T cells and antigen-presenting cells (APCs). Oxazolone also induces Il4/Il13 expression in newly infiltrating basophils, and Il4ra and Ccl24, most prominently in APCs. In contrast, imiquimod broadly upregulates Il17/Il22 and Ccl4/Ccl5. A comparative analysis of single-cell inflammatory transcriptional responses reveals that APC response to oxazolone is tightly restricted by cell identity, whereas imiquimod enforces shared programs on multiple APC populations in parallel. These global molecular patterns not only contrast immune responses on a systems level but also suggest that the mechanisms of new sources of inflammation can eventually be deduced by comparison to known signatures.

Potato, S. tuberosum, is one of the most important global crops, but has high levels of waste due to tuber greening under light, which is associated with the accumulation of neurotoxic glycoalkaloids. However, unlike the situation in de-etiolating seedlings, the mechanisms underlying tuber greening are not well understood. Here, we have investigated the effect of monochromatic blue, red, and far-red light on the regulation of chlorophyll and glycoalkaloid accumulation in potato tubers. Blue and red wavelengths were effective for induction and accumulation of chlorophyll, carotenoids and the two major potato glycoalkaloids, α-solanine and α-chaconine, whereas none of these accumulated in darkness or under far-red light. Key genes in chlorophyll biosynthesis (HEMA1, encoding the rate-limiting enzyme glutamyl-tRNA reductase, GSA, CHLH and GUN4) and six genes (HMG1, SQS, CAS1, SSR2, SGT1 and SGT2) required for glycoalkaloid synthesis were also induced under white, blue, and red light but not in darkness or under far-red light. These data suggest a role for both cryptochrome and phytochrome photoreceptors in chlorophyll and glycoalkaloid accumulation. The contribution of phytochrome was further supported by the observation that far-red light could inhibit white light-induced chlorophyll and glycoalkaloid accumulation and associated gene expression. Transcriptomic analysis of tubers exposed to white, blue, and red light showed that light induction of photosynthesis and tetrapyrrole-related genes grouped into three distinct groups with one group showing a generally progressive induction by light at both 6 h and 24 h, a second group showing induction at 6 h in all light treatments, but induction only by red and white light at 24 h and a third showing just a very moderate light induction at 6 h which was reduced to the dark control level at 24 h. All glycoalkaloid synthesis genes showed a group one profile consistent with what was seen for the most light regulated chlorophyll synthesis genes. Our data provide a molecular framework for developing new approaches to reducing waste due to potato greening.

Potato production is often constrained by abiotic stresses such as drought and high temperatures which are often present in combination. In the present work, we aimed to identify key mechanisms and processes underlying single and combined abiotic stress tolerance by comparative analysis of tolerant and susceptible cultivars. Physiological data indicated that the cultivars Desiree and Unica were stress tolerant while Agria and Russett Burbank were stress susceptible. Abiotic stress caused a greater reduction of photosynthetic carbon assimilation in the susceptible cultivars which was associated with a lower leaf transpiration rate. Oxidative stress, as estimated by the accumulation of malondialdehyde was not induced by stress treatments in any of the genotypes with the exception of drought stress in Russett Burbank. Stress treatment resulted in increases in ascorbate peroxidase activity in all cultivars except Agria which increased catalase activity in response to stress. Transcript profiling highlighted a decrease in the abundance of transcripts encoding proteins associated with PSII light harvesting complex in stress tolerant cultivars. Furthermore, stress tolerant cultivars accumulated fewer transcripts encoding a type-1 metacaspase implicated in programmed cell death. Stress tolerant cultivars exhibited stronger expression of genes associated with plant growth and development, hormone metabolism and primary and secondary metabolism than stress susceptible cultivars. Metabolite profiling revealed accumulation of proline in all genotypes following drought stress that was partially suppressed in combined heat and drought. On the contrary, the sugar alcohols inositol and mannitol were strongly accumulated under heat and combined heat and drought stress while galactinol was most strongly accumulated under drought. Combined heat and drought also resulted in the accumulation of Valine, isoleucine, and lysine in all genotypes. These data indicate that single and multiple abiotic stress tolerance in potato is associated with a maintenance of CO2 assimilation and protection of PSII by a reduction of light harvesting capacity. The data further suggests that stress tolerant cultivars suppress cell death and maintain growth and development via fine tuning of hormone signaling, and primary and secondary metabolism. This study highlights potential targets for the development of stress tolerant potato cultivars.

Abstract We derive a formulation of the nonhydrostatic equations in spherical geometry with a Lorenz staggered vertical discretization. The combination conserves a discrete energy in exact time integration when coupled with a mimetic horizontal discretization. The formulation is a version of Dubos and Tort (2014, https://doi.org/10.1175/MWR-D-14-00069.1) rewritten in terms of primitive variables. It is valid for terrain following mass or height coordinates and for both Eulerian or vertically Lagrangian discretizations. The discretization relies on an extension to Simmons and Burridge (1981, https://doi.org/10.1175/1520-0493(1981)1092.0.CO;2) vertical differencing, which we show obeys a discrete derivative product rule. This product rule allows us to simplify the treatment of the vertical transport terms. Energy conservation is obtained via a term‐by‐term balance in the kinetic, internal, and potential energy budgets, ensuring an energy‐consistent discretization up to time truncation error with no spurious sources of energy. We demonstrate convergence with respect to time truncation error in a spectral element code with a horizontal explicit vertically implicit implicit‐explicit time stepping algorithm.

Abstract It is the purpose of this paper to provide a comprehensive documentation of the new NCAR (National Center for Atmospheric Research) version of the spectral element (SE) dynamical core as part of the Community Earth System Model (CESM2.0) release. This version differs from previous releases of the SE dynamical core in several ways. Most notably the hybrid sigma vertical coordinate is based on dry air mass, the condensates are dynamically active in the thermodynamic and momentum equations (also referred to as condensate loading), and the continuous equations of motion conserve a more comprehensive total energy that includes condensates. Not related to the vertical coordinate change, the hyperviscosity operators and the vertical remapping algorithms have been modified. The code base has been significantly reduced, sped up, and cleaned up as part of integrating SE as a dynamical core in the CAM (Community Atmosphere Model) repository rather than importing the SE dynamical core from High‐Order Methods Modeling environment as an external code.

Chemoprophylactic prevention of veterinary heartworm disease in companion animals, caused by the vector-borne nematode parasite Dirofilaria immitis, is a multi-billion-dollar global market. Experimental use of cats and dogs in preclinical heartworm drug testing is increasing due to evolving drug-resistance to frontline macrocyclic lactones and renewed investment in alternative preventative drug research. We and others recently published data demonstrating proof-of-concept of utilising lymphopenic severe-combined immunodeficient (SCID) or Recombination Activating Gene (RAG)2 deficient mice with additional knockout of the IL-2/7 receptor gamma chain (γc) as alternative preventative drug screening research models of dirofilariasis. Here we summarise the current knowledge of candidate immunodeficient mouse models tested, including a comparison of susceptibility using different background strains of mice, different D. immitis isolates, following use of anti-inflammatory treatments to further suppress residual innate immunity, and efficacies achieved against different reference anthelmintics. We supplement this precis with new data on treatment response to the veterinary anthelmintic, oxfendazole, and initial evaluation of D. immitis susceptibility in CB.17 SCID and C57BL/6 RAG2 -/-γc -/- mice. We conclude that in addition to NSG and NXG mice, RAG2 -/-γc -/- mice on either a BALB/c or C57BL/6 background offer an alternative screening model option, widening access to academic and commercial laboratories wishing to pursue initial rapid in vivo drug screening whilst avoiding potentially unnecessary cat or dog testing.

Chemoprophylactic prevention of veterinary heartworm disease in companion animals, caused by the vector-borne nematode parasite Dirofilaria immitis, is a multi-billion-dollar global market. Experimental use of cats and dogs in preclinical heartworm drug testing is increasing due to evolving drug-resistance to frontline macrocyclic lactones and renewed investment in alternative preventative drug research. We and others recently published data demonstrating proof-of-concept of utilising lymphopenic severe-combined immunodeficient (SCID) or Recombination Activating Gene (RAG)2 deficient mice with additional knockout of the IL-2/7 receptor gamma chain (γc) as alternative preventative drug screening research models of dirofilariasis. Here we summarise the current knowledge of candidate immunodeficient mouse models tested, including a comparison of susceptibility using different background strains of mice, different D. immitis isolates, following use of anti-inflammatory treatments to further suppress residual innate immunity, and efficacies achieved against different reference anthelmintics. We supplement this precis with new data on treatment response to the veterinary anthelmintic, oxfendazole, and initial evaluation of D. immitis susceptibility in CB.17 SCID and C57BL/6 RAG2 -/-γc -/- mice. We conclude that in addition to NSG and NXG mice, RAG2 -/-γc -/- mice on either a BALB/c or C57BL/6 background offer an alternative screening model option, widening access to academic and commercial laboratories wishing to pursue initial rapid in vivo drug screening whilst avoiding potentially unnecessary cat or dog testing.