Control of the Dust Vertical Distribution over Western Africa by Convection and Scavenging

Saharan dust represents more than 50%of the total desert dust emitted around the globe and its radiative effect significantly affects the atmospheric circulation at a continental scale.Previous studies on dust vertical distribution and the Saharan Air Layer(SAL)showed some shortcomings that could be attributed to imperfect representation of the effects of deep convection and scavenging.The authors investigate here the role of deep convective transport and scavenging on the vertical distribution of mineral dust over Western Africa.Using multi-year(2006-2010)simulations performed with the variable-resolution(zoomed)version of the LMDZ climate model.Simulations are compared with aerosol amounts recorded by the Aerosol Robotic Network(AERONET)and with vertical profiles of the Cloud-Aerosol Lidar with Orthogonal Polarization(CALIOP)measurements.LMDZ allows a thorough examination of the respective roles of deep convective transport,convective and stratiform scavenging,boundary layer transport,and advection processes on the vertical mineral dust distribution over Western Africa.The comparison of simulated dust Aerosol Optical Depth(AOD)and distribution with measurements suggest that scavenging in deep convection and subsequent re-evaporation of dusty rainfall in the lower troposphere are critical processes for explaining the vertical distribution of desert dust.These processes play a key role in maintaining a well-defined dust layer with a sharp transition at the top of the SAL and in establishing the seasonal cycle of dust distribution.This vertical distribution is further reshaped offshore in the Inter-Tropical Convergence Zone(ITCZ)over the Atlantic Ocean by marine boundary layer turbulent and convective transport and wet deposition at the surface.

Meteorological and Climate Modelling Services Tailored to Viticulturists

Grape production is likewise inherently interconnected to climate and weather, and, although grapes may grow worldwide, premium wine-grape production occurs in Mediterranean-like climate ranges. Changes in climate and weather patterns are threatening premium wine-grapes, directly affecting the European wine industry. This is because grapevines are extremely sensitive to their surrounding environment, with seasonal variations in yield much higher than other common crops, such as cereals. With a view to making South European wine industry resilient to climate change, VISCA (Vineyards Integrated Smart Climate Application) project has deployed a Climate Service (CS) Decision Support System (DSS) tool that provides to wine producers with well-founded information to be able to apply correctly adaptation strategies on specific grape varieties and locations, and to achieve optimum production results (e.g., yield and quantity). In this paper we show the meteorological, seasonal and climatic models and data sets used to answer the viticulturist needs;from short-term and mid-term forecast to seasonal forecast and climate projections.

Air Quality Trends in Metropolitan Zones in Veracruz, México

Mexico and currently in Veracruz state, there are metropolitan zones (MZ) growing. Therefore, main objective in this paper is to analyze new data and AQ trends during 01.09.2013 to 30.06.2015 of two new AQ monitoring stations installed in Xalapa and Minatitlan MZ in 2013-year. The methodology applied used quality criteria to the datasets, followed by data validation and statistics for further analysis to determine the hourly, weekly and yearly trends of NO2, O3, SO2, PM10 and PM2.5. Indicators were compared with Mexican standards, CAI-LAC report, WHO guidelines, EU and USA standards to evaluate the AQ in both sites. We observed AQ trends from moderate to bad in Xalapa and Minatitlan MZ where the PM10 and PM2.5 surpassed the WHO guidelines and Mexican standards. O3 and SO2 in Xalapa presented a quality from good to moderate and in Minatitlan sometimes were from moderate to bad. NO2 did not exceed the value limits of Mexican standards, only Xalapa has exceeded the WHO guidelines. In Minatitlan, the Mexican limits were not exceeded. Concluding, PM10 and PM2.5 concentrations were the main problem. Others pollutants that influenced the AQ were O3, NO2 and SO2 in Minatitlan MZ due probably to meteorology, site conditions, location and oil and petrochemical industries. In Xalapa, MZ NO2 and SO2 are attributed mainly to road transport.

Circulation-Type Classification over Mexico by the Era-Interim Database and Cost733

In this paper an approach of a synoptic classification by cluster k-means (CKM) and the European Gro&#223wettertypes (GWT) was performed and executed in COST733 package. The methodology used a CKM with nine clusters and GWT with 16. The COST733 evaluated a dataset of 30-years since 1986 to 2015. The variables selected were mean sea level pressure (mslp), geopotential height (z500 and z850), wind speed and direction (u10, v10 and u, v at 850 hPa) and relative vorticity (vo) with a 0.75° × 0.75° resolution of the data grid at 00:00, 06:00, 12:00 and 18:00 UTC and 0 steps. These results were evaluated using COST733 to find the quality of measurements by the explained variance (EV) or reduction ratio in error and pseudo F value (PF) to determine the certainty of the results. GWT-16 showed better yearly values in the evaluation with 32.7 (EV) and 354.3 (PF) against the CKM-9 of 54.2 (EV) and 1621.8 (PF). Finally, it was concluded that GWT-16 could be used for classification of synoptic systems over Mexico and the analysis of meteorological phenomena triggers on increases or decreases of atmospheric pollution in areas over Mexico.

Automated Metadata Annotation:What Is and Is Not Possible with Machine Learning

Automated metadata annotation is only as good as training dataset,or rules that are available for the domain.It's important to learn what type of data content a pre-trained machine learning algorithm has been trained on to understand its limitations and potential biases.Consider what type of content is readily available to train an algorithm-what's popular and what's available.However,scholarly and historical content is often not available in consumable,homogenized,and interoperable formats at the large volume that is required for machine learning.There are exceptions such as science and medicine,where large,well documented collections are available.This paper presents the current state of automated metadata annotation in cultural heritage and research data,discusses challenges identified from use cases,and proposes solutions.

Wnt genes in colonic polyposis predisposition

Much of the genetic predisposition to polyposis,and particularly to serrated polyposis(SP),remains unknown.Only germline pathogenic variants in RNF43,a tumor suppressor that exerts negative feedback in the Wnt/β-catenin signaling pathway,have been causally linked to some SP cases(<2%),a disease associated with increased risk of colorectal cancer(CRC).^(1) Most known hereditary CRC and polyposis genes affect DNA repair,BMP/TGF-β,or Wnt signaling,being the latter associated with adenomatous and serrated polyposis phenotypes.2 Based on this observation,we evaluated the presence and role of germline variants in those pathways in unsolved polyposis patients.

Recent advances in seasonal and multi-annual tropical cyclone forecasting

Seasonal tropical cyclone(TC)forecasting has evolved substantially since its commencement in the early 1980s.However,present operational seasonal TC forecasting services still do not meet the requirements of society and stakeholders:current operational products are mainly basin-scale information,while more detailed sub-basin scale information such as potential risks of TC landfall is anticipated for decision making.To fill this gap and make the TC science and services move forward,this paper reviews recent research and development in seasonal tropical cyclone(TC)forecasting.In particular,this paper features new research topics on seasonal TC predictability in neutral conditions of El Ni˜no–Southern Oscillation(ENSO),emerging forecasting techniques of seasonal TC activity including Machine Learning/Artificial Intelligence,and multi-annual TC predictions.We also review the skill of forecast systems at predicting landfalling statistics for certain regions of the North Atlantic,Western North Pacific and South Indian oceans and discuss the gap that remains between current products and potential user's expectations.New knowledge and advanced forecasting techniques are expected to further enhance the capability of seasonal TC forecasting and lead to more actionable and fit-for-purpose products.

Towards efficient data exchange and sharing for big-data driven materials science:metadata and data formats

With big-data driven materials research,the new paradigm of materials science,sharing and wide accessibility of data are becoming crucial aspects.Obviously,a prerequisite for data exchange and big-data analytics is standardization,which means using consistent and unique conventions for,e.g.,units,zero base lines,and file formats.There are two main strategies to achieve this goal.One accepts the heterogeneous nature of the community,which comprises scientists from physics,chemistry,bio-physics,and materials science,by complying with the diverse ecosystem of computer codes and thus develops“converters”for the input and output files of all important codes.These converters then translate the data of each code into a standardized,codeindependent format.The other strategy is to provide standardized open libraries that code developers can adopt for shaping their inputs,outputs,and restart files,directly into the same code-independent format.In this perspective paper,we present both strategies and argue that they can and should be regarded as complementary,if not even synergetic.The represented appropriate format and conventions were agreed upon by two teams,the Electronic Structure Library(ESL)of the European Center for Atomic and Molecular Computations(CECAM)and the NOvel MAterials Discovery(NOMAD)Laboratory,a European Centre of Excellence(CoE).A key element of this work is the definition of hierarchical metadata describing state-of-the-art electronic-structure calculations.

GekkoFS—A Temporary Burst Buffer File System for HPC Applications

Many scientific fields increasingly use high-performance computing(HPC)to process and analyze massive amounts of experimental data while storage systems in today's HPC environments have to cope with new access patterns.These patterns include many metadata operations,small I/O requests,or randomized file I/O,while general-purpose parallel file systems have been optimized for sequential shared access to large files.Burst buffer file systems create a separate file system that applications can use to store temporary data.They aggregate node-local storage available within the compute nodes or use dedicated SSD clusters and offer a peak bandwidth higher than that of the backend parallel file system without interfering with it.However,burst buffer file systems typically offer many features that a scientific application,running in isolation for a limited amount of time,does not require.We present GekkoFS,a temporary,highly-scalable file system which has been specifically optimized for the aforementioned use cases.GekkoFS provides relaxed POSIX semantics which only offers features which are actually required by most(not all)applications.GekkoFS is,therefore,able to provide scalable I/O performance and reaches millions of metadata operations already for a small number of nodes,significantly outperforming the capabilities of common parallel file systems.

On/Off-Line Prediction Applied to Job Scheduling on Non-Dedicated NOWs

This paper proposes a prediction engine designed for non-dedicated clusters, which is able to estimate the turnaround time for parallel applications, even in the presence of serial workload of the workstation owner. The prediction engine can be configured to work with three different estimation kernels： a Historical kernel, a Simulation kernel based on analytical models and an integration of both, named Hybrid kernel. These estimation proposals were integrated into a scheduling system, named CISNE, which can be executed in an on-line or off-line mode. The accuracy of the proposed estimation methods was evaluated in relation to different job scheduling policies in a real and a simulated cluster environment. In both environments, we observed that the Hybrid system gives the best results because it combines the ability of a simulation engine to capture the dynamism of a non-dedicated environment together with the accuracy of the historical methods to estimate the application runtime considering the state of the resources.

Ad Hoc File Systems for High-Performance Computing

Storage backends of parallel compute clusters are still based mostly on magnetic disks,while newer and faster storage technologies such as flash-based SSDs or non-volatile random access memory(NVRAM)are deployed within compute nodes.Including these new storage technologies into scientific workflows is unfortunately today a mostly manual task,and most scientists therefore do not take advantage of the faster storage media.One approach to systematically include nodelocal SSDs or NVRAMs into scientific workflows is to deploy ad hoc file systems over a set of compute nodes,which serve as temporary storage systems for single applications or longer-running campaigns.This paper presents results from the Dagstuhl Seminar 17202"Challenges and Opportunities of User-Level File Systems for HPC"and discusses application scenarios as well as design strategies for ad hoc file systems using node-local storage media.The discussion includes open research questions,such as how to couple ad hoc file systems with the batch scheduling environment and how to schedule stage-in and stage-out processes of data between the storage backend and the ad hoc file systems.Also presented are strategies to build ad hoc file systems by using reusable components for networking and how to improve storage device compatibility.Various interfaces and semantics are presented,for example those used by the three ad hoc file systems BeeOND,GekkoFS,and BurstFS.Their presentation covers a range from file systems running in production to cutting-edge research focusing on reaching the performance limits of the underlying devices.

A Finite Element Method Solver for Time-Dependent and Stationary Schrodinger Equations with a Generic Potential

A general finite element solution of the Schrodinger equation for a onedimensional problem is presented.The solver is applicable to both stationary and time-dependent cases with a general user-selected potential term.Furthermore,it is possible to include external magnetic or electric fields,as well as spin-orbital and spinmagnetic interactions.We use analytically soluble problems to validate the solver.The predicted numerical auto-states are compared with the analytical ones,and selected mean values are used to validate the auto-functions.In order to analyze the performance of the time-dependent Schrodinger equation,a traveling wave package benchmark was reproduced.In addition,a problem involving the scattering of a wave packet over a double potential barrier shows the performance of the solver in cases of transmission and reflection of packages.Other general problems,related to periodic potentials,are treated with the same general solver and a Lagrange multiplier method to introduce periodic boundary conditions.Some simple cases of known periodic potential solutions are reported.

Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

We introduce the concept of Canonical Workflow Building Blocks(CWBB),a methodology of describing and wrapping computational tools,in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms.The concept is implemented and demonstrated with the BioExcel Building Blocks library(BioBB),a collection of tool wrappers in the field of computational biomolecular simulation.Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow,built using this library and run with 5 different Workflow Manager Systems(WfMS).We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research(CWFR)in order to improve widespread adoption and reuse of computational methods across workflow language barriers.

SARS-CoV-2 interaction with Siglec-1 mediates trans-infection by dendritic cells

Antigen-presenting cells(APCs)may be resistant to SARS-CoV-2 infection but still contribute to viral pathogenesis.Lectins such as sialic acid-binding Ig-like lectin 1(Siglec-1/CD169)mediate the attachment of viruses to APCs.Here,we show that APCs effectively capture SARS-CoV-2 within compartments via recognition of Siglec-1.This receptor interacts with sialylated gangliosides on membranes of SARS-CoV-2 variants.