Ab-initio study of the energy competition between \Gamma and K valleys in bilayer transition metal dichalcogenides

Moir\'e engineering in two-dimensional van der Waals bilayer crystals has emerged as a flexible platform for controlling strongly correlated electron systems. The competition between valleys for the band extremum energy position in the parent layers is crucial in deciding the qualitative nature of the moir\'e Hamiltonian since it controls the physics of the moir\'e minibands. Here we use density functional theory to examine the competition between K and $\Gamma$ for the valence band maximum in homo- and hetero-bilayers formed from the transition metal dichalcogenides (TMD), MX\{_2} where M=Mo,W and X=S,Se,Te. We shed light on how the competition is influenced by interlayer separation, which can be modified by applying pressure, by external gate-defined electric fields, and by transition metal atom d-orbital correlations. Our findings are related to several recent experiments, and contribute to the development of design rules for moir\'{e} materials

Estimating the Global Influence of Cover Crops on Ecosystem Service Indicators in Croplands With the LPJ‐GUESS Model

Cover crops (CCs) can improve soil nutrient retention and crop production while providing climate change mitigation co-benefits. However, quantifying these ecosystem services across global agricultural lands remains inadequate. Here, we assess how the use of herbaceous CCs with and without biological nitrogen (N) fixation affects agricultural soil carbon stocks, N leaching, and crop yields, using the dynamic global vegetation model LPJ-GUESS. The model performance is evaluated with observations from worldwide field trials and modeled output further compared against previously published large-scale estimates. LPJ-GUESS broadly captures the enhanced soil carbon, reduced N leaching, and yield changes that are observed in the field. Globally, we found that combining N-fixing CCs with no-tillage technique could potentially increase soil carbon levels by 7% (+0.32 Pg C yr$^{−1}$ in global croplands) while reducing N leaching loss by 41% (−7.3 Tg N yr$^{−1}$) compared with fallow controls after 36 years of simulation since 2015. This integrated practice is accompanied by a 2% of increase in total crop production (+37 million tonnes yr$^{−1}$ including wheat, maize, rice, and soybean) in the last decade of the simulation. The identified effects of CCs on crop productivity vary widely among main crop types and N fertilizer applications, with small yield changes found in soybean systems and highly fertilized agricultural soils. Our results demonstrate the possibility of conservation agriculture when targeting long-term environmental sustainability without compromising crop production in global croplands

Assessing the impacts of agricultural managements on soil carbon stocks, nitrogen loss, and crop production – a modelling study in eastern Africa

Improved agricultural management plays a vital role in protecting soils from degradation in eastern Africa. Changing practices such as reducing tillage, fertilizer use, or cover crops are expected to enhance soil organic carbon (SOC) storage, with climate change mitigation co-benefits, while increasing crop production. However, the quantification of cropland management effects on agricultural ecosystems remains inadequate in this region. Here, we explored seven management practices and their potential effects on soil carbon (C) pools, nitrogen (N) losses, and crop yields under different climate scenarios, using the dynamic vegetation model LPJ-GUESS. The model performance is evaluated against observations from two long-term maize field trials in western Kenya and reported estimates from published sources. LPJ-GUESS generally produces soil C stocks and maize productivity comparable with measurements and mostly captures the SOC decline under some management practices that is observed in the field experiments. We found that for large parts of Kenya and Ethiopia, an integrated conservation agriculture practice (no-tillage, residue and manure application, and cover crops) increases SOC levels in the long term (+11 % on average), accompanied by increased crop yields (+22 %) in comparison to the conventional management. Planting nitrogen-fixing cover crops in our simulations is also identified as a promising individual practice in eastern Africa to increase soil C storage (+4 %) and crop production (+18 %), with low environmental cost of N losses (+24 %). These management impacts are also sustained in simulations of three future climate pathways. This study highlights the possibilities of conservation agriculture when targeting long-term environmental sustainability and food security in crop ecosystems, particularly for those with poor soil conditions in tropical climates

Enterovirus D68 outbreak detection through a syndromic disease epidemiology network

BACKGROUND: In 2014, enterovirus D68 (EV-D68) was responsible for an outbreak of severe respiratory illness in children, with 1,153 EV-D68 cases reported across 49 states. Despite this, there is no commercial assay for its detection in routine clinical care. BioFire® Syndromic Trends (Trend) is an epidemiological network that collects, in near real-time, deidentified. BioFire test results worldwide, including data from the BioFire® Respiratory Panel (RP). OBJECTIVES: Using the RP version 1.7 (which was not explicitly designed to differentiate EV-D68 from other picornaviruses), we formulate a model, Pathogen Extended Resolution (PER), to distinguish EV-D68 from other human rhinoviruses/enteroviruses (RV/EV) tested for in the panel. Using PER in conjunction with Trend, we survey for historical evidence of EVD68 positivity and demonstrate a method for prospective real-time outbreak monitoring within the network. STUDY DESIGN: PER incorporates real-time polymerase chain reaction metrics from the RPRV/EV assays. Six institutions in the United States and Europe contributed to the model creation, providing data from 1,619 samples spanning two years, confirmed by EV-D68 gold-standard molecular methods. We estimate outbreak periods by applying PER to over 600,000 historical Trend RP tests since 2014. Additionally, we used PER as a prospective monitoring tool during the 2018 outbreak. RESULTS: The final PER algorithm demonstrated an overall sensitivity and specificity of 87.1% and 86.1%, respectively, among the gold-standard dataset. During the 2018 outbreak monitoring period, PER alerted the research network of EV-D68 emergence in July. One of the first sites to experience a significant increase, Nationwide Children's Hospital, confirmed the outbreak and implemented EV-D68 testing at the institution in response. Applying PER to the historical Trend dataset to determine rates among RP tests, we find three potential outbreaks with predicted regional EV-D68 rates as high as 37% in 2014, 16% in 2016, and 29% in 2018. CONCLUSIONS: Using PER within the Trend network was shown to both accurately predict outbreaks of EV-D68 and to provide timely notifications of its circulation to participating clinical laboratories

ECLAIRE: Effects of Climate Change on Air Pollution Impacts and Response Strategies for European Ecosystems. Project final report

The central goal of ECLAIRE is to assess how climate change will alter the extent to which air pollutants threaten terrestrial ecosystems. Particular attention has been given to nitrogen compounds, especially nitrogen oxides (NOx) and ammonia (NH3), as well as Biogenic Volatile Organic Compounds (BVOCs) in relation to tropospheric ozone (O3) formation, including their interactions with aerosol components. ECLAIRE has combined a broad program of field and laboratory experimentation and modelling of pollution fluxes and ecosystem impacts, advancing both mechanistic understanding and providing support to European policy makers. The central finding of ECLAIRE is that future climate change is expected to worsen the threat of air pollutants on Europe’s ecosystems. Firstly, climate warming is expected to increase the emissions of many trace gases, such as agricultural NH3, the soil component of NOx emissions and key BVOCs. Experimental data and numerical models show how these effects will tend to increase atmospheric N deposition in future. By contrast, the net effect on tropospheric O3 is less clear. This is because parallel increases in atmospheric CO2 concentrations will offset the temperature-driven increase for some BVOCs, such as isoprene. By contrast, there is currently insufficient evidence to be confident that CO2 will offset anticipated climate increases in monoterpene emissions. Secondly, climate warming is found to be likely to increase the vulnerability of ecosystems towards air pollutant exposure or atmospheric deposition. Such effects may occur as a consequence of combined perturbation, as well as through specific interactions, such as between drought, O3, N and aerosol exposure. These combined effects of climate change are expected to offset part of the benefit of current emissions control policies. Unless decisive mitigation actions are taken, it is anticipated that ongoing climate warming will increase agricultural and other biogenic emissions, posing a challenge for national emissions ceilings and air quality objectives related to nitrogen and ozone pollution. The O3 effects will be further worsened if progress is not made to curb increases in methane (CH4) emissions in the northern hemisphere. Other key findings of ECLAIRE are that: 1) N deposition and O3 have adverse synergistic effects. Exposure to ambient O3 concentrations was shown to reduce the Nitrogen Use Efficiency of plants, both decreasing agricultural production and posing an increased risk of other forms of nitrogen pollution, such as nitrate leaching (NO3-) and the greenhouse gas nitrous oxide (N2O); 2) within-canopy dynamics for volatile aerosol can increase dry deposition and shorten atmospheric lifetimes; 3) ambient aerosol levels reduce the ability of plants to conserve water under drought conditions; 4) low-resolution mapping studies tend to underestimate the extent of local critical loads exceedance; 5) new dose-response functions can be used to improve the assessment of costs, including estimation of the value of damage due to air pollution effects on ecosystems, 6) scenarios can be constructed that combine technical mitigation measures with dietary change options (reducing livestock products in food down to recommended levels for health criteria), with the balance between the two strategies being a matter for future societal discussion. ECLAIRE has supported the revision process for the National Emissions Ceilings Directive and will continue to deliver scientific underpinning into the future for the UNECE Convention on Long-range Transboundary Air Pollution

ECLAIRE third periodic report

The ÉCLAIRE project (Effects of Climate Change on Air Pollution Impacts and Response Strategies for European Ecosystems) is a four year (2011-2015) project funded by the EU's Seventh Framework Programme for Research and Technological Development (FP7)

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Estimating the Global Influence of Cover Crops on Ecosystem Service Indicators in Croplands With the LPJ-GUESS Model

Cover crops (CCs) can improve soil nutrient retention and crop production while providing climate change mitigation co-benefits. However, quantifying these ecosystem services across global agricultural lands remains inadequate. Here, we assess how the use of herbaceous CCs with and without biological nitrogen (N) fixation affects agricultural soil carbon stocks, N leaching, and crop yields, using the dynamic global vegetation model LPJ-GUESS. The model performance is evaluated with observations from worldwide field trials and modeled output further compared against previously published large-scale estimates. LPJ-GUESS broadly captures the enhanced soil carbon, reduced N leaching, and yield changes that are observed in the field. Globally, we found that combining N-fixing CCs with no-tillage technique could potentially increase soil carbon levels by 7% (+0.32 Pg C yr−1 in global croplands) while reducing N leaching loss by 41% (−7.3 Tg N yr−1) compared with fallow controls after 36 years of simulation since 2015. This integrated practice is accompanied by a 2% of increase in total crop production (+37 million tonnes yr−1 including wheat, maize, rice, and soybean) in the last decade of the simulation. The identified effects of CCs on crop productivity vary widely among main crop types and N fertilizer applications, with small yield changes found in soybean systems and highly fertilized agricultural soils. Our results demonstrate the possibility of conservation agriculture when targeting long-term environmental sustainability without compromising crop production in global croplands

BNF in grain legumes in LPJ-GUESS

This file contains the input data for model runs on global scale and the measured results for BNF evaluation at site scales presented in Geoscientific Model Development (GMD) pape