Drivers of the decadal variability of the North Ionian Gyre upper layer circulation during 1910-2010: a regional modelling study

A long simulation over the period 1901–2010 with an eddy-permitting ocean circulation model is used to study the variability of the upper layer circulation in the North Ionian Gyre (NIG) in the Eastern Mediterranean Sea (EMed). The model is driven by the atmospheric forcing from the twentieth century reanalysis data set ERA-20C, ensuring a consistent performance of the model over the entire simulation period. The main modes of variability known in the EMed, in particular the decadal reversals of the NIG upper layer circulation observed since the late 1980s are well reproduced. We find that the simulated NIG upper layer circulation prior to the observational period is characterized by long-lasting cyclonic phases with weak variability during years 1910–1940 and 1960–1985, while in the in-between period (1940–1960) quasi-decadal NIG circulation reversals occur with similar characteristics to those observed in the recent decades. Our simulation indicates that the NIG upper layer circulation is rather prone to the cyclonic mode with occasional kicks to the anticyclonic mode. The coherent variability of the NIG upper layer circulation mode and of the Adriatic Deep Water (AdDW) outflow implies that atmospheric forcing triggering strong AdDW formation is required to kick the NIG into an anticyclonic circulation 1–2 years later. A sensitivity experiment mimicking a cold winter event over the Adriatic Sea supports this hypothesis. Our simulation shows that it is the multi-decadal variability of the salinity in the Adriatic Sea that leads to periods where low salinity prevents strong AdDW formation events. This explains the absence of quasi-decadal NIG reversals during 1910–1940 and 1960–198

Lombardi Drawings of Graphs

We introduce the notion of Lombardi graph drawings, named after the American abstract artist Mark Lombardi. In these drawings, edges are represented as circular arcs rather than as line segments or polylines, and the vertices have perfect angular resolution: the edges are equally spaced around each vertex. We describe algorithms for finding Lombardi drawings of regular graphs, graphs of bounded degeneracy, and certain families of planar graphs.Comment: Expanded version of paper appearing in the 18th International Symposium on Graph Drawing (GD 2010). 13 pages, 7 figure

GiViP: A Visual Profiler for Distributed Graph Processing Systems

Analyzing large-scale graphs provides valuable insights in different application scenarios. While many graph processing systems working on top of distributed infrastructures have been proposed to deal with big graphs, the tasks of profiling and debugging their massive computations remain time consuming and error-prone. This paper presents GiViP, a visual profiler for distributed graph processing systems based on a Pregel-like computation model. GiViP captures the huge amount of messages exchanged throughout a computation and provides an interactive user interface for the visual analysis of the collected data. We show how to take advantage of GiViP to detect anomalies related to the computation and to the infrastructure, such as slow computing units and anomalous message patterns.Comment: Appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria.

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton

Fertilizer and Soil Health in Africa The Role of Fertilizer in Building Soil Health to Sustain Farming and Address Climate Change

Summary Soil health is commonly defined as the ability to generate sufficient crop yields while maintaining the future productive capacity of soils and the ecosystem services soils regulate and deliver. However, less consensus exists on indicators to assess soil health and its changes over time and space, although soil organic carbon (SOC) is generally acknowledged as a key indicator. In the context of this paper, soil health status is equated with SOC status. Current SOC conditions are influenced by soil properties and climate. Under smallholder farming conditions, SOC is variable and affected by past crop and soil management practices, which are influenced by farmer typology. Although SOC content under cropland is a maximum of 60-70% of that under natural vegetation, there is substantial scope to increase it in smallholder farming conditions. A conceptual framework relating to fertilizer, crop productivity, and soil health is presented here. While fertilizer application commonly results in a substantial increase in crop yield at various scales, a key indicator of fertilizer use, agronomic efficiency (AE), is often observed to be lower than relatively easily achievable values under well-managed conditions, caused by a diversity of factors. Low AE values do not necessarily result in greater greenhouse gas (GHG) emissions because of the low fertilizer application rates in sub-Saharan Africa (SSA), though increases in GHG emissions are likely with increases in fertilizer use. Crop response to organic inputs is substantially lower although organic inputs increase SOC content, which usually results in greater AE values relative to sole application of fertilizer. Increases in crop productivity are associated with increases in SOC, though the relationship is weak and efforts besides fertilizer application itself are required. That said, N(PK) fertilizer has had a positive effect on SOC in most parts of the world except SSA, an observation corroborated by an analysis of past and ongoing long-term experiments, likely related to the low and erratic use of fertilizer in the region. While fertilizer use can be an entry point to increasing soil health, this will not likely happen on degraded soils where responses to fertilizer are limited. In such cases, investments to rehabilitate degraded soils should come first. Several approaches can be followed to determine best fertilizer recommendations, while recognizing nutrients needs by crops and soil-specific properties. Site-specificity commonly requires an assessment of the soil fertility status of a particular field, and analytical tools now allow for the development of locally relevant recommendations at scale with some early successes. While organic inputs do positively impact SOC, attractive options to increase organic inputs in smallholder farming systems are limited and mostly related to in-situ production, with an important emphasis on multi-purpose legumes. Climate adaptation is facilitated by healthy Fertilizer and Soil Health in Africa 2 soils and requires fertilizer to be combined with other crop, soil, and water management practices (Wortmann and Stewart, 2021). While low yields are linked to the ecological yield gap, whereby the potential productivity of crops is set by biological factors, input and output prices determine the economic yield gap, which is usually quite lower than the former because of unfavourable ratio of fertilizer prices to crop product prices. Even though profitability is a key driver of impact, many other factors affect the adoption of appropriate fertilizer and soil health recommendations, including farmers’ production objectives, resource endowment, land tenure, and access to markets. A main bottleneck in engaging smallholder farmers in soil health-restoring practices is the relatively large amount of time such practices take to deliver benefits that are visible to farmers. In the absence of incentive programs, farmers require short-term benefits, generated within their farming systems. Furthermore, associated advice on complementary practices to fertilizer use increases the complexity of information to be conveyed to farmers. Scaling models have moved toward the delivery of bundled services, often digitally enabled, to address challenges with communicating complex information and the necessary complementary crop and soil management practices. Targeted policy interventions can support the delivery of broad digitally enabled fertilizer management recommendations and the creation of conditions that enable smallholder farmers to implement these recommendations at scale. A number of recommendations have been generated from the scientific information, covered under the following headings: (1) key elements of a Fertilizer and Soil Health Action Plan; (2) development of quantitative indicators and targets of soil health; (3) addressing climate change requires choices; (4) incentivizing farmers; (5) soil health investments, which require localized actions (think global, act local); and (6) not only fertilizers, but also auxiliary interventions, as defined by the Integrated Soil Fertility Management (ISFM) approach. Action is needed today to reverse the downward spiral of low and inefficient fertilizer use, resulting in low yields and declining soil health

A portable prototype magnetometer to differentiate ischemic and non-ischemic heart disease in patients with chest pain

Background: Magnetocardiography (MCG) is a non-invasive technique used to measure and map cardiac magnetic fields. We describe the predictive performance of a portable prototype magnetometer designed for use in acute and routine clinical settings. We assessed the predictive ability of the measurements derived from the magnetometer for the ruling-out of healthy subjects and patients whose chest pain has a non-ischemic origin from those with ischemic heart disease (IHD). Methods: MCG data were analyzed from a technical performance study, a pilot clinical study, and a young healthy reference group. Participants were grouped to enable differentiation of those with IHD versus non-IHD versus controls: Group A (70 IHD patients); Group B (69 controls); Group C (37 young healthy volunteers). Scans were recorded in an unshielded room. Between-group differences were explored using analysis of variance. The ability of 10 candidate MCG predictors to predict normal/abnormal cases was analyzed using logistic regression. Predictive performance was internally validated using repeated five-fold cross-validation. Results: Three MCG predictors showed a significant difference between patients and age-matched controls (P<0.001); eight predictors showed a significant difference between patients and young healthy volunteers (P<0.001). Logistic regression comparing patients with controls yielded a specificity of 35.0%, sensitivity of 95.4%, and negative predictive value for the ruling-out of IHD of 97.8% (area under the curve 0.78). Conclusion: This analysis represents a preliminary indication that the portable magnetometer can help rule-out healthy subjects and patients whose chest pain has a non-ischemic origin from those with IHD

Maximum Entropy Reconstructions of Dynamic Signaling Networks from Quantitative Proteomics Data

Advances in mass spectrometry among other technologies have allowed for quantitative, reproducible, proteome-wide measurements of levels of phosphorylation as signals propagate through complex networks in response to external stimuli under different conditions. However, computational approaches to infer elements of the signaling network strictly from the quantitative aspects of proteomics data are not well established. We considered a method using the principle of maximum entropy to infer a network of interacting phosphotyrosine sites from pairwise correlations in a mass spectrometry data set and derive a phosphorylation-dependent interaction network solely from quantitative proteomics data. We first investigated the applicability of this approach by using a simulation of a model biochemical signaling network whose dynamics are governed by a large set of coupled differential equations. We found that in a simulated signaling system, the method detects interactions with significant accuracy. We then analyzed a growth factor mediated signaling network in a human mammary epithelial cell line that we inferred from mass spectrometry data and observe a biologically interpretable, small-world structure of signaling nodes, as well as a catalog of predictions regarding the interactions among previously uncharacterized phosphotyrosine sites. For example, the calculation places a recently identified tumor suppressor pathway through ARHGEF7 and Scribble, in the context of growth factor signaling. Our findings suggest that maximum entropy derived network models are an important tool for interpreting quantitative proteomics data

Light and Heavy Fractions of Soil Organic Matter in Response to Climate Warming and Increased Precipitation in a Temperate Steppe

Soil is one of the most important carbon (C) and nitrogen (N) pools and plays a crucial role in ecosystem C and N cycling. Climate change profoundly affects soil C and N storage via changing C and N inputs and outputs. However, the influences of climate warming and changing precipitation regime on labile and recalcitrant fractions of soil organic C and N remain unclear. Here, we investigated soil labile and recalcitrant C and N under 6 years' treatments of experimental warming and increased precipitation in a temperate steppe in Northern China. We measured soil light fraction C (LFC) and N (LFN), microbial biomass C (MBC) and N (MBN), dissolved organic C (DOC) and heavy fraction C (HFC) and N (HFN). The results showed that increased precipitation significantly stimulated soil LFC and LFN by 16.1% and 18.5%, respectively, and increased LFC∶HFC ratio and LFN∶HFN ratio, suggesting that increased precipitation transferred more soil organic carbon into the quick-decayed carbon pool. Experimental warming reduced soil labile C (LFC, MBC, and DOC). In contrast, soil heavy fraction C and N, and total C and N were not significantly impacted by increased precipitation or warming. Soil labile C significantly correlated with gross ecosystem productivity, ecosystem respiration and soil respiration, but not with soil moisture and temperature, suggesting that biotic processes rather than abiotic factors determine variations in soil labile C. Our results indicate that certain soil carbon fraction is sensitive to climate change in the temperate steppe, which may in turn impact ecosystem carbon fluxes in response and feedback to climate change