Towards an end-to-end analysis and prediction system for weather, climate, and marine applications in the Red Sea

Author Posting. © American Meteorological Society, 2021. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 102(1), (2021): E99-E122, https://doi.org/10.1175/BAMS-D-19-0005.1.The Red Sea, home to the second-longest coral reef system in the world, is a vital resource for the Kingdom of Saudi Arabia. The Red Sea provides 90% of the Kingdom’s potable water by desalinization, supporting tourism, shipping, aquaculture, and fishing industries, which together contribute about 10%–20% of the country’s GDP. All these activities, and those elsewhere in the Red Sea region, critically depend on oceanic and atmospheric conditions. At a time of mega-development projects along the Red Sea coast, and global warming, authorities are working on optimizing the harnessing of environmental resources, including renewable energy and rainwater harvesting. All these require high-resolution weather and climate information. Toward this end, we have undertaken a multipronged research and development activity in which we are developing an integrated data-driven regional coupled modeling system. The telescopically nested components include 5-km- to 600-m-resolution atmospheric models to address weather and climate challenges, 4-km- to 50-m-resolution ocean models with regional and coastal configurations to simulate and predict the general and mesoscale circulation, 4-km- to 100-m-resolution ecosystem models to simulate the biogeochemistry, and 1-km- to 50-m-resolution wave models. In addition, a complementary probabilistic transport modeling system predicts dispersion of contaminant plumes, oil spill, and marine ecosystem connectivity. Advanced ensemble data assimilation capabilities have also been implemented for accurate forecasting. Resulting achievements include significant advancement in our understanding of the regional circulation and its connection to the global climate, development, and validation of long-term Red Sea regional atmospheric–oceanic–wave reanalyses and forecasting capacities. These products are being extensively used by academia, government, and industry in various weather and marine studies and operations, environmental policies, renewable energy applications, impact assessment, flood forecasting, and more.The development of the Red Sea modeling system is being supported by the Virtual Red Sea Initiative and the Competitive Research Grants (CRG) program from the Office of Sponsored Research at KAUST, Saudi Aramco Company through the Saudi ARAMCO Marine Environmental Center at KAUST, and by funds from KAEC, NEOM, and RSP through Beacon Development Company at KAUST

Physical forcing and physical/biochemical variability of the Mediterranean Sea: a review of unresolved issues and directions for future research

This paper is the outcome of a workshop held in Rome in November 2011 on the occasion of the 25th anniversary of the POEM (Physical Oceanography of the Eastern Mediterranean) program. In the workshop discussions, a number of unresolved issues were identified for the physical and biogeochemical properties of the Mediterranean Sea as a whole, i.e., comprising the Western and Eastern sub-basins. Over the successive two years, the related ideas were discussed among the group of scientists who participated in the workshop and who have contributed to the writing of this paper. Three major topics were identified, each of them being the object of a section divided into a number of different sub-sections, each addressing a specific physical, chemical or biological issue: 1. Assessment of basin-wide physical/biochemical properties, of their variability and interactions. 2. Relative importance of external forcing functions (wind stress, heat/moisture fluxes, forcing through straits) vs. internal variability. 3. Shelf/deep sea interactions and exchanges of physical/biogeochemical properties and how they affect the sub-basin circulation and property distribution. Furthermore, a number of unresolved scientific/methodological issues were also identified and are reported in each sub-section after a short discussion of the present knowledge. They represent the collegial consensus of the scientists contributing to the paper. Naturally, the unresolved issues presented here constitute the choice of the authors and therefore they may not be exhaustive and/or complete. The overall goal is to stimulate a broader interdisciplinary discussion among the scientists of the Mediterranean oceanographic community, leading to enhanced collaborative efforts and exciting future discoveries

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Seasonal variability of Red Sea mixed layer depth: the influence of atmospheric buoyancy and momentum forcing

The seasonal and spatial evolution of the mixed layer (ML) in the Red Sea (RS) and the influence of atmospheric buoyancy and momentum forcing are analyzed for the 2001–2015 period using a high-resolution (1/100°, 50 vertical layers) ocean circulation model. The simulation reveals a strong spatiotemporal variability reflecting the complex patterns associated with the air–sea buoyancy flux and wind forcing, as well as the significant impact of the basin’s general and mesoscale circulation. During the spring and summer months, buoyancy forcing intensifies stratification, resulting in a generally shallow ML throughout the basin. Nevertheless, the results reveal local maxima associated with the influence of mesoscale circulation and regular wind induced mixing. Under the influence of surface buoyancy loss, the process of deepening of the ML commences in early September, reaching its maximum depth in January and February. The northern Gulf of Aqaba and the western parts of the northern RS, exhibit the deepest ML, with a gradual shoaling toward the south, primarily due to the surface advection of relatively fresh water that enters the basin from the Gulf of Aden. The mixed layer depth (MLD) variability is primarily driven by atmospheric buoyancy forcing, especially its heat flux component. Although evaporative fluxes dominate the annually averaged surface buoyancy forcing, they exhibit weak seasonal and spatial variability. Wind induced mixing exerts a significant impact on the MLD only locally, especially during summer. Of particular importance are strong winds channeled by topography, such as those in the vicinity of the Strait of Bab-Al-Mandeb and the straits connecting the two gulfs in the north, as well as lateral jets venting through mountain gaps, such as the Tokar Jet in the central RS. The analysis highlights the complex patterns of air-sea interactions, thermohaline circulation, and mesoscale activity, all of them strongly imprinted on the MLD distribution

Interannual Variability of the Exchange Flow Through the Strait of Bab-al-Mandeb

The interannual variability of the exchange flow between the Red Sea and the Gulf of Aden through the Bab-al-Mandeb strait is examined based on a high-resolution, nonhydrostatic hindcast model simulation covering a 19-year period (1995-2013), using the MITgcm (MIT general circulation model). The model is validated against moored profiles and along-strait cruise observations collected during the period from June 1995 to November 1996 and 19-year sea surface temperature satellite observations. The model well reproduces the properties of the water masses at the strait over a wide range of spatiotemporal scales, including the typical two- and three-layer seasonal patterns and the related intraseasonal-to-interannual cycles. The seasonality of the exchange flow is predominately determined by the time-varying surface winds, with a higher correlation over the Gulf of Aden, reflecting the importance of local Gulf of Aden processes for the exchanges at the strait. The alternation of the two seasonal patterns is driven by a combination of the buoyancy-driven mean circulation with the wind-induced transport. The onset/offset of the two patterns is estimated to take place one-to-two weeks after the respective monsoon-driven wind reversal. Model results indicate that the onset dates and durations of both patterns exhibit a considerable interannual variability. Additionally, the duration of the summer (winter) exchange pattern presents a significant increasing (decreasing) trend of similar to 1.45day/year (similar to 1.22day/year) over the 19-year period. Significant interannual variabilities and trends are observed in terms of the total volume of water, salt mass, and stored heat of the exchanges. Budget analysis of these trends suggests that the duration of the two exchange patterns is more important in determining the interannual variability and the related trends than the intensity of the exchange, or the variations in mean salinity or temperature of the exchanged water masses. Plain Language Summary The interannual variability of exchange flow through the poorly sampled strait of Bab-al-Mandeb is examined based on a high-resolution, nonhydrostatic hindcast model simulation covering a 19-year period (1995-2013), using the MITgcm model. The simulation successfully reproduces the properties of water masses at the strait over a wide range of spatiotemporal scales, including the typical two- and three-layer seasonal patterns and the related intraseasonal-to-interannual cycles. We show that the seasonality of the exchange flow is predominately determined by the time-varying surface winds, and the alteration of the two seasonal patterns is driven by a combination of the buoyancy-driven mean circulation with the wind-induced transport. The simulation results reveal that the onset dates and durations of both patterns exhibit a considerable interannual variability. The duration of the summer (winter) exchange pattern presents a significant increasing (decreasing) trend of 1.45day/year (1.22day/year) over the 19-year period. Significant interannual variability and trends are also observed with respect to the exchanged total volume of water, salt mass, and stored heat. Based on a budget analysis of these trends, we demonstrate that the duration of the two exchange patterns is more important in determining the interannual variability and the related trends

Translation into Greek, cross-cultural adaptation and validation of the Disabilities of the Arm, Shoulder, and Hand Questionnaire (DASH)

The purpose of this study was to translate, adapt, and validate a Greek version of the Disabilities of the Arm, Shoulder, and Hand (DASH) Questionnaire. The English version of DASH was translated into Greek (DASH-GR) and cultural adaptation was performed. Subsequently, psychometric properties and validity were assessed in 106 consecutive eligible patients presenting with a variety of unilateral upper limb disorders. All patients completed the Short Form 36 Health Survey questionnaire and the DASH-GR. Test-retest reliability was assessed in a subgroup of 35 patients who filled in the questionnaire seven days later. The internal consistency of the 30 items of the DASH-GR, estimated by the internal consistency coefficient (Cronbach’s alpha) was 0.96. The difference between the individual scores of the initial assessment and reassessment of the DASH ranged from -6.5 to 14.5 (mean difference was 3.74 (SD +/- 6.1)). The correlation coefficient between total scores of the initial assessment and reassessment was high (Pearson’s r = 0.918, p < 0.0005) (Kentall tau-b = 0.72, p < 0.001). The correlation coefficient between the DASH-GR and SF-36 total scores was 0.625 (p < 0.001), showing a strong correlation between the two questionnaires. The Greek version of the DASH retains the characteristics of the English original and is a reliable and valid instrument that can provide a standardized measure of patient-centered outcomes in Greek-speaking patients with unilateral disorders of the upper limb

<i>In situ</i> nutrient an velocity observations and model outputs of temperature and salinity

<p><b><i>a)</i></b><i>In situ</i> measurements of nutrient concentrations and mean velocity vectors at ~66m depth during September 2011; reprinted and adapted with permission from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168440#pone.0168440.ref018" target="_blank">18</a>]. <b><i>b)</i></b> <i>and</i> <b><i>c)</i></b> September climatological salinity and temperature at 65m depth, calculated from the MITgcm circulation model.</p

Southern Red Sea simulated minimum salinity between 0m and 100m depth.

<p><b><i>a)</i></b> September climatology of the lowest salinity values observed between 0m and 100m depth—calculated from the MITgcm circulation model, and <b><i>b)</i></b> the depth at which these minimum salinity values occur.</p