Offline parameter estimation using EnKF and maximum likelihood error covariance estimates: Application to a subgrid-scale orography parameterization

International audienceRecent works show that the parameters controlling the parameterizations of the physical processes in climate models can be estimated from observations using filtering techniques. In this paper, we propose an offline parameter estimation approach, without estimating the state of the climate model. It is based on the Ensemble Kalman Filter (EnKF) and an iterative estimation of the error covariance matrices and of the background state using a maximum likelihood algorithm. The technique is implemented in a subgrid-scale orography (SSO) parameterization scheme that works in a single vertical column. First, the parameter estimation technique is evaluated using twin experiments. Then, the technique is used with synthetic observations to estimate how the parameters of the SSO scheme should change when the resolution of the input orography dataset of a general circulation model is increased. Our analysis reveals that when the resolution of the orography dataset increases, the scheme should take into account the dynamical sheltering that can occur at low levels between mountain peaks located within the same gridbox area

AtlantOS fitness for HAB Bulletins

Assessment of the observing system fitness for HAB warning bulletin in the Atlanti

A review of innovation-based methods to jointly estimate model and observation error covariance matrices in ensemble data assimilation

Data assimilation combines forecasts from a numerical model with observations. Most of the current data assimilation algorithms consider the model and observation error terms as additive Gaussian noise, specified by their covariance matrices Q and R, respectively. These error covariances, and specifically their respective amplitudes, determine the weights given to the background (i.e., the model forecasts) and to the observations in the solution of data assimilation algorithms (i.e., the analysis). Consequently, Q and R matrices significantly impact the accuracy of the analysis. This review aims to present and to discuss, with a unified framework, different methods to jointly estimate the Q and R matrices using ensemble-based data assimilation techniques. Most of the methodologies developed to date use the innovations, defined as differences between the observations and the projection of the forecasts onto the observation space. These methodologies are based on two main statistical criteria: (i) the method of moments, in which the theoretical and empirical moments of the innovations are assumed to be equal, and (ii) methods that use the likelihood of the observations, themselves contained in the innovations. The reviewed methods assume that innovations are Gaussian random variables, although extension to other distributions is possible for likelihood-based methods. The methods also show some differences in terms of levels of complexity and applicability to high-dimensional systems. The conclusion of the review discusses the key challenges to further develop estimation methods for Q and R. These challenges include taking into account time-varying error covariances, using limited observational coverage, estimating additional deterministic error terms, or accounting for correlated noise

Author Correction: Ecology, evolution and spillover of coronaviruses from bats.

In the past two decades, three coronaviruses with ancestral origins in bats have emerged and caused widespread outbreaks in humans, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the first SARS epidemic in 2002–2003, the appreciation of bats as key hosts of zoonotic coronaviruses has advanced rapidly. More than 4,000 coronavirus sequences from 14 bat families have been identified, yet the true diversity of bat coronaviruses is probably much greater. Given that bats are the likely evolutionary source for several human coronaviruses, including strains that cause mild upper respiratory tract disease, their role in historic and future pandemics requires ongoing investigation. We review and integrate information on bat–coronavirus interactions at the molecular, tissue, host and population levels. We identify critical gaps in knowledge of bat coronaviruses, which relate to spillover and pandemic risk, including the pathways to zoonotic spillover, the infection dynamics within bat reservoir hosts, the role of prior adaptation in intermediate hosts for zoonotic transmission and the viral genotypes or traits that predict zoonotic capacity and pandemic potential. Filling these knowledge gaps may help prevent the next pandemic

Definition of a temporal distribution index for high temporal resolution precipitation data over Peninsular Spain and the Balearic Islands: the fractal dimension; and its synoptic implications

Precipitation on the Spanish mainland and in the Balearic archipelago exhibits a high degree of spatial and temporal variability, regardless of the temporal resolution of the data considered. The fractal dimension indicates the property of self-similarity, and in the case of this study, wherein it is applied to the temporal behaviour of rainfall at a fine (10-min) resolution from a total of 48 observatories, it provides insights into its more or less convective nature. The methodology of Jenkinson & Collison which automatically classifies synoptic situations at the surface, as well as an adaptation of this methodology at 500 hPa, was applied in order to gain insights into the synoptic implications of extreme values of the fractal dimension. The highest fractal dimension values in the study area were observed in places with precipitation that has a more random behaviour over time with generally high totals. Four different regions in which the atmospheric mechanisms giving rise to precipitation at the surface differ from the corresponding above-ground mechanisms have been identified in the study area based on the fractal dimension. In the north of the Iberian Peninsula, high fractal dimension values are linked to a lower frequency of anticyclonic situations, whereas the opposite occurs in the central region. In the Mediterranean, higher fractal dimension values are associated with a higher frequency of the anticyclonic type and a lower frequency of the advective type from the east. In the south, lower fractal dimension values indicate higher frequency with respect to the anticyclonic type from the east and lower frequency with respect to the cyclonic type

Evaluation of two treatment strategies for the prevention of preterm birth in women identified as at risk by ultrasound (PESAPRO Trial): Study protocol for a randomized controlled trial

Background: Premature birth is considered one of the main problems in modern Obstetrics. It causes more than 50 % of neonatal mortality; it is responsible for a large proportion of infant morbidity and incurs very high economic costs. Cervical length, which can be accurately measured by ultrasound, has an inverse relationship with the risk of preterm birth. As a result, having an effective intervention for asymptomatic patients with short cervix could reduce the prematurity. Although recently published data demonstrates the effectiveness of vaginal progesterone and cervical pessary, these treatments have never been compared to one another. Methods/Design: The PESAPRO study is a noncommercial, multicenter, open-label, randomized clinical trial (RCT) in pregnant women with a short cervix as identified by transvaginal ultrasonography at 19 to 22 weeks of gestation. Patients are randomized (1:1) to either daily vaginal progesterone or cervical pessary until the 37th week of gestation or delivery; whichever comes first. During the trial, women visit every 4 weeks for routine questions and tests. The primary outcome is the proportion of spontaneous preterm deliveries before 34 weeks of gestation. A sample size of 254 pregnant women will be included at 29 participating hospitals in order to demonstrate noninferiority of placing a pessary versus vaginal progesterone. The first patient was randomized in August 2012, and recruitment of study subjects will continue until the end of December 2015. Discussion: This trial assesses the comparative efficacy and safety between two accepted treatments, cervical pessary versus vaginal progesterone, and it will provide evidence in order to establish clinical recommendationsThe study has been funded by two national grants from the Spanish Ministry of Health and ISCIII

Mechanisms for a nutrient-conserving carbon pump in a seasonally stratified, temperate continental shelf sea

Continental shelf seas may have a significant role in oceanic uptake and storage of carbon dioxide (CO2) from the atmosphere, through a ‘continental shelf pump’ mechanism. The northwest European continental shelf, in particular the Celtic Sea (50°N 8°W), was the target of extensive biogeochemical sampling from March 2014 to September 2015, as part of the UK Shelf Sea Biogeochemistry research programme (UK-SSB). Here, we use the UK-SSB carbonate chemistry and macronutrient measurements to investigate the biogeochemical seasonality in this temperate, seasonally stratified system. Following the onset of stratification, near-surface biological primary production during spring and summer removed dissolved inorganic carbon and nutrients, and a fraction of the sinking particulate organic matter was subsequently remineralised beneath the thermocline. Water column inventories of these variables throughout 1.5 seasonal cycles, corrected for air-sea CO2 exchange and sedimentary denitrification and anammox, isolated the combined effect of net community production (NCP) and remineralisation on the inorganic macronutrient inventories. Overall inorganic inventory changes suggested that a significant fraction (>50%) of the annual NCP of around 3 mol-C m–2 yr–1 appeared to be stored within a long-lived organic matter (OM) pool with a lifetime of several months or more. Moreover, transfers into and out of this pool appeared not to be in steady state over the one full seasonal cycle sampled. Accumulation of such a long-lived and potentially C-rich OM pool is suggested to be at least partially responsible for the estimated net air-to-sea CO2 flux of ∼1.3 mol-C m–2 yr–1 at our study site, while providing a mechanism through which a nutrient-conserving continental shelf pump for CO2 could potentially operate in this and other similar regions

Observations of vertical mixing in autumn and its effect on the autumn phytoplankton bloom

This work examines the seasonal cycle of density structure and its influence on primary production in a temperate shelf sea, with a particular focus on the breakdown of stratification in autumn. We do this by combining new, high resolution observations of water column structure, meteorological forcing, nitrate and chlorophyll fluorescence collected between March 2014 and July 2015 on the North West European Shelf. Our results challenge the generally accepted assumption that convection dominates over wind driven mixing resulting in seasonal breakdown of stratification. Furthermore we found, that vertical mixing in autumn not only transformed the vertical density structure but also the vertical structure of chlorophyll biomass and surface nutrients. The subsurface chlorophyll maximum was eroded and a vertically homogeneous profile of chlorophyll biomass established itself above the pycnocline. This increased mixing also led to replenishment of surface nitrate concentrations, which supported an autumn phytoplankton bloom. While the significance of phytoplankton blooms in autumn has previously not been well quantified, we argue that these can act as a significant contributor to the seasonal drawdown of carbon