An Introduction to Ensemble-Based Data Assimilation Method in the Earth Sciences

In this chapter, the ensemble-based data assimilation methods are introduced, including their developments, applications and existing concerns. These methods include both traditional methods such as Kalman filter and its derivatives and some advanced algorithms such as sigma-point Kalman filters and particle filters. Emphasis is placed on the challenges of applying these methods onto high-dimensional systems in the earth sciences

A method on estimating time-varying vertical eddy viscosity for an Ekman layer model with data assimilation

Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 36(9), (2019): 1789-1812, doi:10.1175/JTECH-D-18-0223.1.Temporal vertical eddy viscosity coefficient (VEVC) in an Ekman layer model is estimated using an adjoint method. Twin experiments are carried out to investigate the influences of several factors on inversion results, and the conclusions of twin experiments are 1) the adjoint method is a capable method to estimate different kinds of temporal distributions of VEVCs; 2) the gradient descent algorithm is better than CONMIN and L-BFGS for the present problem, although the posterior two algorithms perform better on convergence efficiency; 3) inversion results are sensitive to initial guesses; 4) the model is applicable to different wind conditions; 5) the inversion result with thick boundary layer depth (BLD) is slightly better than thin BLD; 6) inversion results are more sensitive to observations in upper layers than those in lower layers; 7) inversion results are still acceptable when data noise exists, indicating the method can sustain noise to a certain degree; 8) a regularization method is proved to be useful to improve the results for present problem; and 9) the present method can tolerate the existence of balance errors due to the imperfection of governing equations. The methodology is further validated in practical experiments where Ekman currents are derived from Bermuda Testbed Mooring data and assimilated. Modeled Ekman currents coincide well with observed ones, especially for upper layers. The results demonstrate that the assumptions of depth dependence and time dependence are equally important for VEVCs. The feasibility of the typical Ekman model, the imperfection of Ekman balance equations, and the deficiencies of the present method are discussed. This method provides a potential way to realize the time variations of VEVCs in ocean models.The authors thank the seven reviewers for the constructive suggestions which have greatly improved the manuscript. Financial support is provided by the National Key Research and Development Plan of China (Grants 2017YFA0604100 and 2017YFC1404000), the National Natural Science Foundation of China (Grants 41876086 and 41806012), Scientific Research Fund of the Second Institute of Oceanography, MNR (Grant JG1819), and the Fundamental Research Funds for the Central Universities of China. Jicai thanks the support of China Scholarship Council for the visiting research in WHOI, and he also thanks the host of WHOI. BTM data are provided by Ocean Physics Laboratory, University of California, Santa Barbara (http://opl.ucsb.edu).2020-03-1

SCALE method for single-cell ATAC-seq analysis via latent feature extraction.

Single-cell ATAC-seq (scATAC-seq) profiles the chromatin accessibility landscape at single cell level, thus revealing cell-to-cell variability in gene regulation. However, the high dimensionality and sparsity of scATAC-seq data often complicate the analysis. Here, we introduce a method for analyzing scATAC-seq data, called Single-Cell ATAC-seq analysis via Latent feature Extraction (SCALE). SCALE combines a deep generative framework and a probabilistic Gaussian Mixture Model to learn latent features that accurately characterize scATAC-seq data. We validate SCALE on datasets generated on different platforms with different protocols, and having different overall data qualities. SCALE substantially outperforms the other tools in all aspects of scATAC-seq data analysis, including visualization, clustering, and denoising and imputation. Importantly, SCALE also generates interpretable features that directly link to cell populations, and can potentially reveal batch effects in scATAC-seq experiments

Effects of post-treatment electroacupuncture on ventricular monophasic action potential and cardiac function in a rat model of ischemia/reperfusion injury

Background: To determine the effects of post-treatment electroacupuncture (EA) on the electrophysiological properties of ventricular muscle in rats with ischemia/reperfusion (IR) injury. Methods: Male Sprague–Dawley (SD) rats were randomly assigned into sham-operated (SH), IR and IR + EA groups (n = 8 each). The IR model was generated by ligation of the left anterior descending (LAD) coronary artery for 30 min. After establishing the IR model, EA was administered at PC6 for 30 min while opening the coronary artery and allowing reperfusion for 30 min. Heart rate (HR), mean arterial pressure and monophasic action potential (MAP)of cardiac muscle in the outer membrane of the antetheca of the left ventricle before coronary artery ligation (T0),after coronary artery ligation for 30 min (T1) and after reperfusion for 30 min (T2) were recorded. At the same time, ventricular electrophysiological parameters including ventricular effective refractory period (ERP), conduction velocity (CV) and ventricular fibrillation threshold (VFT) were measured. Then, the cardiac function and the levels of creatine kinase-muscle/brain (CK-MB) and cardiac troponin I (cTnI) were monitored. Based on these data,monophasic action potential amplitude (MAPA), the maximum depolarization velocity (Vmax) and the MAP durations at 50% and 90% repolarization (MAPD50 and MAPD90) were calculated to determine the incidence of arrhythmia during reperfusion. Results: Compared with the SH group, the IR group showed an obviously decreased HR as well as reduced mean arterial pressure, Vmax, CV, ERP and MAPA. All indices of cardiac function except left ventricular end-diastolic pressure (LVEDP) decreased (i.e. ventricular systolic pressure (LVSP), left ventricular ejection fraction (LVEF), fractional shortening (FS) and rate of the ventricular pressure rise/drop (±dp/dt)). Furthermore, the MAPD50 and MAPD90 were prolonged, and the levels of CK-MB and cTnI increased (p 0.05). Conclusion: EA post-treatment can relieve prolongation of repolarization and slowed depolarization of ventricular muscle during IR, thus decreasing the rate of incidence of reperfusion arrhythmia

Trajectory Estimation of Aircraft in a Double-Satellite Passive Positioning System with the Adjoint Method

A double-satellite passive positioning system is constructed based on the theory of space geometry, where two observation coordinate systems and a fundamental coordinate system exist. In each observation coordinate system, there exists a ray from the observation satellite to the aircraft. One difficulty lies in that these two rays may not intersect due to the existence of various errors. Under this situation, this work assumes that the middle point of common perpendicular between two rays is the actual position of aircraft. Based on the theory of space geometry, the coordinates of aircraft in the fundamental coordinate system can be determined. A dynamic model with the adjoint method is developed to estimate the trajectory of aircraft during the process of rocket propulsion. By assimilating observations, the trajectory of aircraft can be calculated. Numerical experiments are designed to validate the reasonability and feasibility of this model. Simulated results indicate that even by assimilating a small number of observations, the trajectory of aircraft can be estimated. In addition, the trajectory estimation can become more accurate when more observations are assimilated to the model

Structural defects in 2D MoS2 nanosheets and their roles in the adsorption of airborne elemental mercury

In this research, ab initio calculations and experimental approach were adopted to reveal the mechanism of Hg0 adsorption on MoS2 nanosheets that contain various types of defects. The ab initio calculation showed that, among different structural defects, S vacancies (Vs) in the MoS2 nanosheets exhibited outstanding potential to strongly adsorb Hg0. The MoS2 material was then prepared in a controlled manner under conditions, such as temperature, concentration of precursors, etc., that were determined by adopting the new method developed in this study. Characterisation confirmed that the MoS2 material is of graphene-like layered structure with abundant structural defects. The integrated dynamic and steady state (IDSS) testing demonstrated that the Vs-rich nanosheets showed excellent Hg0 adsorption capability. In addition, ab initial calculation on charge density difference, PDOS, and adsorption pathways revealed that the adsorption of Hg0 on the Vs-rich MoS2 surface is non-activated chemisorption

Progress and challenges in maternal health in western China:a Countdown to 2015 national case study

Background China is one of the few Countdown countries to have achieved Millennium Development Goal 5 (75% reduction in maternal mortality ratio between 1990 and 2015). We aimed to examine the health systems and contextual factors that might have contributed to the substantial decline in maternal mortality between 1997 and 2014. We chose to focus on western China because poverty, ethnic diversity, and geographical access represent particular challenges to ensuring universal access to maternal care in the region. Methods In this systematic assessment, we used data from national census reports, National Statistical Yearbooks, the National Maternal and Child Health Routine Reporting System, the China National Health Accounts report, and National Health Statistical Yearbooks to describe changes in policies, health financing, health workforce, health infrastructure, coverage of maternal care, and maternal mortality by region between 1997 and 2014. We used a multivariate linear regression model to examine which contextual and health systems factors contributed to the regional variation in maternal mortality ratio in the same period. Using data from a cross-sectional survey in 2011, we also examined equity in access to maternity care in 42 poor counties in western China. Findings Maternal mortality declined by 8·9% per year between 1997 and 2014 (geometric mean ratio for each year 0·91, 95% CI 0·91–0·92). After adjusting for GDP per capita, length of highways, female illiteracy, the number of licensed doctors per 1000 population, and the proportion of ethnic minorities, the maternal mortality ratio was 118% higher in the western region (2·18, 1·44–3·28) and 41% higher in the central region (1·41, 0·99–2·01) than in the eastern region. In the rural western region, the proportion of births in health facilities rose from 41·9% in 1997 to 98·4% in 2014. Underpinning such progress was the Government’s strong commitment to long-term strategies to ensure access to delivery care in health facilities—eg, professionalisation of maternity care in large hospitals, effective referral systems for women medically or socially at high risk, and financial subsidies for antenatal and delivery care. However, in the poor western counties, substantial disparity by education level of the mother existed in access to health facility births (44% of illiterate women vs 100% of those with college or higher education), antenatal care (17% vs 69%) had at least four visits), and caesarean section (8% vs 44%). Interpretation Despite remarkable progress in maternal survival in China, substantial disparities remain, especially for the poor, less educated, and ethnic minority groups in remote areas in western China. Whether China’s highly medicalised model of maternity care will be an answer for these populations is uncertain. A strategy modelled after China’s immunisation programme, whereby care is provided close to the women’s homes, might need to be explored, with township hospitals taking a more prominent role

DNMTs Play an Important Role in Maintaining the Pluripotency of Leukemia Inhibitory Factor-Dependent Embryonic Stem Cells.

Naive pluripotency can be maintained in medium with two inhibitors plus leukemia inhibitory factor (2i/LIF) supplementation, which primarily affects canonical WNT, FGF/ERK, and JAK/STAT3 signaling. However, whether one of these three supplements alone is sufficient to maintain naive self-renewal remains unclear. Here we show that LIF alone in medium is sufficient for adaptation of 2i/L-ESCs to embryonic stem cells (ESCs) in a hypermethylated state (L-ESCs). Global transcriptomic analysis shows that L-ESCs are close to 2i/L-ESCs and in a stable state between naive and primed pluripotency. Notably, our results demonstrate that DNA methyltransferases (DNMTs) play an important role in LIF-dependent mouse ESC adaptation and self-renewal. LIF-dependent ESC adaptation efficiency is significantly increased in serum treatment and reduced in Dnmt3a or Dnmt3l knockout ESCs. Importantly, unlike epiblast stem cells, L-ESCs contribute to somatic tissues and germ cells in chimeras. L-ESCs cultured under such simple conditions as in this study would provide a more conducive platform to clarify the molecular mechanism of ESCs in in vitro culture

Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation

Rhizoctonia solani AG1 IA is a soil-borne fungal phytopathogen that can significantly harm crops resulting in economic loss. This species overwinters in grass roots and diseased plants, and produces sclerotia that infect future crops. R. solani AG1 IA does not produce spores; therefore, understanding the molecular mechanism of sclerotia formation is important for crop disease control. To identify the genes involved in this process for the development of disease control targets, the transcriptomes of this species were determined at three important developmental stages (mycelium, sclerotial initiation, and sclerotial maturation) using an RNA-sequencing approach. A total of 5,016, 6,433, and 5,004 differentially expressed genes (DEGs) were identified in the sclerotial initiation vs. mycelial, sclerotial maturation vs. mycelial, and sclerotial maturation vs. sclerotial initiation stages, respectively. Moreover, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses showed that these DEGs were enriched in diverse categories, including oxidoreductase activity, carbohydrate metabolic process, and oxidation-reduction processes. A total of 12 DEGs were further verified using reverse transcription quantitative PCR. Among the genes examined, NADPH oxidase 1 (NOX1) and superoxide dismutase (SOD) were highly induced in the stages of sclerotial initiation and maturation. In addition, the highest reactive oxygen species (ROS) production levels were detected during sclerotial initiation, and enzyme activities of NOX1, SOD, and catalase (CAT) matched with the gene expression profiles. To further evaluate the role of ROS in sclerotial formation, R. solani AG1 IA was treated with the CAT inhibitor aminotriazole and H2O2, resulting in the early differentiation of sclerotia. Taken together, this study provides useful information toward understanding the molecular basis of R. solani AG1 IA sclerotial formation and maturation, and identified the important role of ROS in these processes

Critical roles of edge turbulent transport in the formation of high-field-side high-density front and density limit disruption in J-TEXT tokamak

This article presents an in-depth study of the sequence of events leading to density limit disruption in J-TEXT tokamak plasmas, with an emphasis on boudary turbulent transport and the high-field-side high-density (HFSHD) front. These phenomena were extensively investigated by using Langmuir probe and Polarimeter-interferometer diagnostics