The Atmospheric Response to Meridional Shifts of the Gulf Stream SST Front and Its Dependence on Model Resolution

The Gulf Stream (GS) plays a key role in shaping the North Atlantic climate. Moreover, the associated sea surface temperature (SST) front undergoes interannual-to-decadal variability that is thought to force significant atmospheric circulation anomalies. However, general circulation models do not accurately reproduce the atmospheric response to SST front variability as estimated from observations. In this work we analyze the atmospheric response to the GS SST front (GSF) shifts in a multimodel ensemble of atmosphere-only simulations forced with observed SSTs (1950-2014). The atmospheric response is found to be resolution dependent. Only the high-resolution simulations produce a wintertime response similar to observed anomalies. More specifically, (i) analysis of the atmospheric thermodynamic balance close to the GSF showed that the anomalous diabatic heating associated to the GSF displacement is mainly balanced by vertical motion and by meridional transient eddy heat transport (not the case for low-resolution models), while (ii) the large-scale response includes a meridional shift of the North Atlantic eddy-driven jet and storm track homodirectional to the GSF displacement. This atmospheric response is accompanied by changes in low-level baroclinicity close to and north of the GSF, resulting from the oceanic forcing and the zonal atmospheric circulation anomalies respectively. The low-level baroclinicity anomalies lead to changes in baroclinic eddy activity and, ultimately, in the jet via eddy-mean flow interaction. Considering the two-way nature of air-sea interactions, using historical atmosphere-only simulations is a powerful way to isolate the impact of realistic oceanic variability on the atmosphere. Our results suggest that interannual-to-decadal predictability may be higher than what low-resolution models currently indicate

Improving predictive performance on survival in dairy cattle using an ensemble learning approach

Cow survival is a complex trait that combines traits like milk production, fertility, health and environmental factors such as farm management. This complexity makes survival difficult to predict accurately. This is probably the reason why few studies attempted to address this problem and no studies are published that use ensemble methods for this purpose. We explored if we could improve prediction of cow survival to second lactation, when predicted at five different moments in a cow's life, by combining the predictions of multiple (weak) methods in an ensemble method. We tested four ensemble methods: majority voting rule, multiple logistic regression, random forest and naive Bayes. Precision, recall, balanced accuracy, area under the curve (AUC) and gains in proportion of surviving cows in a scenario where the best 50% were selected were used to evaluate the ensemble model performance. We also calculated correlations between the ensemble models and obtained McNemar's test statistics. We compared the performance of the ensemble methods against those of the individual methods. We also tested if there was a difference in performance metrics when continuous (from 0 to 1) and binary (0 or 1) prediction outcomes were used. In general, using continuous prediction output resulted in higher performance metrics than binary ones. AUCs for models ranged from 0.561 to 0.731, with generally increasing performance at moments later in life. Precision, AUC and balanced accuracy values improved significantly for the naive Bayes and multiple logistic regression ensembles in at least one data set, although performance metrics did remain low overall. The multiple logistic regression ensemble method resulted in equal or better precision, AUC, balanced accuracy and proportion of animals surviving on all datasets and was significantly different from the other ensembles in three out of five moments. The random forest ensemble method resulted in the least significant improvement over the individual methods

WASOS: An Ontology for Modelling Traditional Knowledge of Sustainable Water Stewardship

Recent work and publications concerning sustainable water stewardship in Rajasthan (India) highlight how contemporary challenges are eroding traditional, communal approaches to water stewardship through mechanised extraction beyond the renewable capacities of ecosystems. Our work is focused on developing a formal ontology for modelling the knowledge of traditional water stewardship in India’s drylands by capturing the key constitutional elements of regenerative methods. Our method follows an iterative evolving prototype process for delivering the first version of the Ontology for Sustainable Water Stewardship (WASOS). The ontology contains a moderate number of high-level classes and properties that represent the water management decisionmaking process. By making key relationships visible, we aim to support decision-making in complex catchments particularly where there are contested urban and rural claims on water

Northern Hemisphere blocking simulation in current climate models: evaluating progress from the Climate Model Intercomparison Project Phase 5 to 6 and sensitivity to resolution

Global climate models (GCMs) are known to suffer from biases in the simulation of atmospheric blocking, and this study provides an assessment of how blocking is represented by the latest generation of GCMs. It is evaluated (i) how historical CMIP6 (Climate Model Intercomparison Project Phase 6) simulations perform compared to CMIP5 simulations and (ii) how horizontal model resolution affects the simulation of blocking in the CMIP6-HighResMIP (PRIMAVERA – PRocess-based climate sIMulation: AdVances in high-resolution modelling and European climate Risk Assessment) model ensemble, which is designed to address this type of question. Two blocking indices are used to evaluate the simulated mean blocking frequency and blocking persistence for the Euro-Atlantic and Pacific regions in winter and summer against the corresponding estimates from atmospheric reanalysis data. There is robust evidence that CMIP6 models simulate blocking frequency and persistence better than CMIP5 models in the Atlantic and Pacific and during winter and summer. This improvement is sizeable so that, for example, winter blocking frequency in the median CMIP5 model in a large Euro-Atlantic domain is underestimated by 33 % using the absolute geopotential height (AGP) blocking index, whereas the same number is 18 % for the median CMIP6 model. As for the sensitivity of simulated blocking to resolution, it is found that the resolution increase, from typically 100 to 20 km grid spacing, in most of the PRIMAVERA models, which are not re-tuned at the higher resolutions, benefits the mean blocking frequency in the Atlantic in winter and summer and in the Pacific in summer. Simulated blocking persistence, however, is not seen to improve with resolution. Our results are consistent with previous studies suggesting that resolution is one of a number of interacting factors necessary for an adequate simulation of blocking in GCMs. The improvements reported in this study hold promise for further reductions in blocking biases as model development continues

Mitigating Climate Biases in the Midlatitude North Atlantic by Increasing Model Resolution: SST Gradients and Their Relation to Blocking and the Jet

Starting to resolve the oceanic mesoscale in climate models is a step change in model fidelity. This study examines how certain obstinate biases in the midlatitude North Atlantic respond to increasing resolution (from 18 to 0.258 in the ocean) and how such biases in sea surface temperature (SST) affect the atmosphere. Using a multimodel ensemble of historical climate simulations run at different horizontal resolutions, it is shown that a severe cold SST bias in the central North Atlantic, common to many ocean models, is significantly reduced with increasing resolution. The associated bias in the time-mean meridional SST gradient is shown to relate to a positive bias in low-level baroclinicity, while the cold SST bias causes biases also in static stability and diabatic heating in the interior of the atmosphere. The changes in baroclinicity and diabatic heating brought by increasing resolution lead to improvements in European blocking and eddy-driven jet variability. Across the multimodel ensemble a clear relationship is found between the climatological meridional SST gradients in the broader Gulf Stream Extension area and two aspects of the atmospheric circulation: the frequency of high-latitude blocking and the southern-jet regime. This relationship is thought to reflect the two-way interaction (with a positive feedback) between the respective oceanic and atmospheric anomalies. These North Atlantic SST anomalies are shown to be important in forcing significant responses in the midlatitude atmospheric circulation, including jet variability and the storm track. Further increases in oceanic and atmospheric resolution are expected to lead to additional improvements in the representation of Euro-Atlantic climate

Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network

The ongoing coronavirus disease 2019 (COVID-19) pandemic has highlighted the need to better understand virus-host interactions. We developed a network-based method that expands the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-host protein interaction network and identifies host targets that modulate viral infection. To disrupt the SARS-CoV-2 interactome, we systematically probed for potent compounds that selectively target the identified host proteins with high expression in cells relevant to COVID-19. We experimentally tested seven chemical inhibitors of the identified host proteins for modulation of SARS-CoV-2 infection in human cells that express ACE2 and TMPRSS2. Inhibition of the epigenetic regulators bromodomain-containing protein 4 (BRD4) and histone deacetylase 2 (HDAC2), along with ubiquitin-specific peptidase (USP10), enhanced SARS-CoV-2 infection. Such proviral effect was observed upon treatment with compounds JQ1, vorinostat, romidepsin and spautin-1, when measured by cytopathic effect and validated by viral RNA assays, suggesting that the host proteins HDAC2, BRD4 and USP10 have antiviral functions. We observed marked differences in antiviral effects across cell lines, which may have consequences for identification of selective modulators of viral infection or potential antiviral therapeutics. While network-based approaches enable systematic identification of host targets and selective compounds that may modulate the SARS-CoV-2 interactome, further developments are warranted to increase their accuracy and cell-context specificity.Peer reviewe

RNA editing signature during myeloid leukemia cell differentiation

Adenosine deaminases acting on RNA (ADARs) are key proteins for hematopoietic stem cell self-renewal and for survival of differentiating progenitor cells. However, their specific role in myeloid cell maturation has been poorly investigated. Here we show that ADAR1 is present at basal level in the primary myeloid leukemia cells obtained from patients at diagnosis as well as in myeloid U-937 and THP1 cell lines and its expression correlates with the editing levels. Upon phorbol-myristate acetate or Vitamin D3/granulocyte macrophage colony-stimulating factor (GM-CSF)-driven differentiation, both ADAR1 and ADAR2 enzymes are upregulated, with a concomitant global increase of A-to-I RNA editing. ADAR1 silencing caused an editing decrease at specific ADAR1 target genes, without, however, interfering with cell differentiation or with ADAR2 activity. Remarkably, ADAR2 is absent in the undifferentiated cell stage, due to its elimination through the ubiquitin–proteasome pathway, being strongly upregulated at the end of the differentiation process. Of note, peripheral blood monocytes display editing events at the selected targets similar to those found in differentiated cell lines. Taken together, the data indicate that ADAR enzymes play important and distinct roles in myeloid cells

Eight grand challenges in socio-environmental systems modeling

Modeling is essential to characterize and explore complex societal and environmental issues in systematic and collaborative ways. Socio-environmental systems (SES) modeling integrates knowledge and perspectives into conceptual and computational tools that explicitly recognize how human decisions affect the environment. Depending on the modeling purpose, many SES modelers also realize that involvement of stakeholders and experts is fundamental to support social learning and decision-making processes for achieving improved environmental and social outcomes. The contribution of this paper lies in identifying and formulating grand challenges that need to be overcome to accelerate the development and adaptation of SES modeling. Eight challenges are delineated: bridging epistemologies across disciplines; multi-dimensional uncertainty assessment and management; scales and scaling issues; combining qualitative and quantitative methods and data; furthering the adoption and impacts of SES modeling on policy; capturing structural changes; representing human dimensions in SES; and leveraging new data types and sources. These challenges limit our ability to effectively use SES modeling to provide the knowledge and information essential for supporting decision making. Whereas some of these challenges are not unique to SES modeling and may be pervasive in other scientific fields, they still act as barriers as well as research opportunities for the SES modeling community. For each challenge, we outline basic steps that can be taken to surmount the underpinning barriers. Thus, the paper identifies priority research areas in SES modeling, chiefly related to progressing modeling products, processes and practices

Hybrid Equation/Agent-Based Model of Ischemia-Induced Hyperemia and Pressure Ulcer Formation Predicts Greater Propensity to Ulcerate in Subjects with Spinal Cord Injury

Pressure ulcers are costly and life-threatening complications for people with spinal cord injury (SCI). People with SCI also exhibit differential blood flow properties in non-ulcerated skin. We hypothesized that a computer simulation of the pressure ulcer formation process, informed by data regarding skin blood flow and reactive hyperemia in response to pressure, could provide insights into the pathogenesis and effective treatment of post-SCI pressure ulcers. Agent-Based Models (ABM) are useful in settings such as pressure ulcers, in which spatial realism is important. Ordinary Differential Equation-based (ODE) models are useful when modeling physiological phenomena such as reactive hyperemia. Accordingly, we constructed a hybrid model that combines ODEs related to blood flow along with an ABM of skin injury, inflammation, and ulcer formation. The relationship between pressure and the course of ulcer formation, as well as several other important characteristic patterns of pressure ulcer formation, was demonstrated in this model. The ODE portion of this model was calibrated to data related to blood flow following experimental pressure responses in non-injured human subjects or to data from people with SCI. This model predicted a higher propensity to form ulcers in response to pressure in people with SCI vs. non-injured control subjects, and thus may serve as novel diagnostic platform for post-SCI ulcer formation. © 2013 Solovyev et al

Unimodality Problems in Ehrhart Theory

Ehrhart theory is the study of sequences recording the number of integer points in non-negative integral dilates of rational polytopes. For a given lattice polytope, this sequence is encoded in a finite vector called the Ehrhart $h^*$-vector. Ehrhart $h^*$-vectors have connections to many areas of mathematics, including commutative algebra and enumerative combinatorics. In this survey we discuss what is known about unimodality for Ehrhart $h^*$-vectors and highlight open questions and problems.Comment: Published in Recent Trends in Combinatorics, Beveridge, A., et al. (eds), Springer, 2016, pp 687-711, doi 10.1007/978-3-319-24298-9_27. This version updated October 2017 to correct an error in the original versio