Passive tracer reconstruction as a least-squares problem with a semi-Lagrangian constraint: An application to fish eggs and larvae

A variational, data assimilation, algorithm was developed for reconstruction of a two-dimensional, nonstationary, passive tracer field in the ocean with open boundaries and a known velocity field. The observations, spatial smoothing terms and passive tracer conservation equation were included as weak constraints. The algorithm was tested with simulated, nonstationary, pseudo-oceanographic data integrated for a 7-day period. Simulations were run to determine the robustness of the algorithm and the effect of theoretical, simulated \u27sampling events,\u27 mimicking the standard oceanographic survey. We explored the sensitivity of the reconstructed tracer fields to the distribution of the pseudo-oceanographic sampling strategy, essentially an antenna problem, and to errors in the velocity field and the observations. The algorithm was applied to observations of silver hake ( Merluccius bilinearis) eggs and larvae obtained in August 1998 on the Scotian Shelf. Finally, the evolution of fish eggs and larvae concentration was found. The corresponding mortality rate of fish eggs and larvae was determined to be 0.28 day-1, with errors of 0.03 day-1. The approach, which is quite general and could be applied to many different problems requiring minimization subject to constraints, allows for error analysis of the results

Assimilation of High-Frequency Radar Data in the East Chukchi Sea

The maximum-likelihood ensemble filter (MLEF) is an eficient technique of data assimilation related to both 3D-variational (3Dvar) and Ensemble Kalman Filter (EnKF) methods. We demonstrate the utility of MLEF by assimilating high-frequency radar (HFR) data into a realistic model of the east Chukchi Sea. A set of three radar stations in Wainwright, Point Lay, and Barrow provide two-dimensional resolution of the sea-surface velocity. We use MLEF to incorporate this HFR data into a numerical model constructed using the Regional Ocean Modelling System (ROMS) for the ice-free months of 2012. The resulting analysis can be used as a benchmark for future operational forecasting, allowing for better real-time monitoring and decision-making as this biologically rich region is influenced by industry and commerce

Model-data synthesis and high resolution simulation of the Bering Sea

The Bering Sea is the source of over 50% of the total US fish catch and the home to immense populations of birds and marine mammals. This extraordinarily productive ecosystem is vulnerable to climate regime shifts that have occurred over the past decades. These regime shifts are closely linked to warming and cooling of the atmosphere and ocean, and the coincident retreat or expansion of the sea ice cover with strong interannual and decadal variability. Here we investigate changes in the Bering ice/ocean system in recent years. One of key tools for this investigation is the Bering Ecosystem STudy ice-ocean Modeling and Assimilation System (BESTMAS) for synthesis and modeling of the Bering ice/ocean system

Volume, Heat and Salt Transport in the North-Eastern Bering Sea During 2007-2010 Derived Through the 4dvar Data Assimilation of In-Situ and Satellite Observations

The rich collection of BEST-BSIERP observations and other sources of data provide an excellent opportunity for synthesis through modeling and data assimilation to improve our understanding of changes in physical forcings of the Bering ecosystem in response to climate change. Assimilating data of different origins, which may be sparse in space and time, is difficult using simple algorithms (traditional optimal interpolation, correlation analysis etc.). The 4Dvar approach is effective for performing spatiotemporal interpolation of sparse data via interpolation (covariance) functions with scales based on ocean dynamics (Bennett, 2002).NSF Arctic Progra

Клинико-этиологическая характеристика смешанных инфекций у детей в стационаре г. Ижевска

Aim: to study the structure, features of the findings and treatment of mixed infections in children at the present stage.Materials and methods. 85 case histories of children aged 5 months to 17 years and 10 months were examined, the final diagnosis of which included 2 or more infections on the basis of the children's infectious diseases department City Clinical Hospital № 7 of Izhevsk. Children with acute infectious pathology (acute intestinal infections, acute respiratory infections, herpes infections) are hospitalized in this hospital. Diagnostic methods: polymerase chain reaction, ELISA, bacteriological.Results. Mixed infections are equally common in both boys and girls, while there is a predominance of mixed infections in young children (up to 1 year and from 1 year to 3 years) 62.4%. The structure of infectious morbidity is consistently dominated by acute enteric infection – 83.5% cases and acute respiratory infections – 53.0% cases. The progression of SARS-CoV-2-associated and herpes-associated mixed infections is characterized by a pronounced polymorphism of clinical manifestations. The etiological factor for each nosology was deciphered only in 17.7%; in 43.5% of cases, only one etiological factor was verified in the laboratory; in 38.8% of cases, no etiological factor was confirmed in the laboratory.Цель: изучить структуру, особенности клинического течения и лечения смешанных инфекций у детей на современном этапе.Материалы и методы. На базе детского инфекционного отделения БУЗ УР «ГКБ №7 МЗ УР» г. Ижевска нами были исследованы 85 историй болезни детей в возрасте от 5 месяцев до 17 лет 10 месяцев, заключительный диагноз которых включал 2 и более инфекции. В данный стационар госпитализируются дети с острой инфекционной патологией: острые респираторные инфекции (ОРИ), острые кишечные инфекции (ОКИ), герпесвирусные инфекции. Диагностические методы: ПЦР, ИФА, бактериологический.Результаты. Микст-инфекции одинаково часто встречаются как у мальчиков, так и у девочек, при этом отмечается преобладание микст-инфекций у детей младшего возраста (до 1 года и от 1 года до 3-х лет) – в 62,4%. В структуре инфекционной заболеваемости стабильно доминируют ОКИ – 83,5% случаев и ОРИ – 53% случаев. Течение SARS-CoV-2-ассоциированных и герпесвирусных-ассоциированных микст-инфекций характеризуется выраженным полиморфизмом клинических проявлений. Этиологический фактор для каждой нозологии был расшифрован только в 17,7%; в 43,5% случаев лабораторно был верифицирован только один этиологический фактор; в 38,8% случаев ни один этиологический фактор не был подтвержден лабораторно

On Propagation of Excitation Waves in Moving Media: The FitzHugh-Nagumo Model

BACKGROUND: Existence of flows and convection is an essential and integral feature of many excitable media with wave propagation modes, such as blood coagulation or bioreactors. METHODS/RESULTS: Here, propagation of two-dimensional waves is studied in parabolic channel flow of excitable medium of the FitzHugh-Nagumo type. Even if the stream velocity is hundreds of times higher that the wave velocity in motionless medium (), steady propagation of an excitation wave is eventually established. At high stream velocities, the wave does not span the channel from wall to wall, forming isolated excited regions, which we called "restrictons". They are especially easy to observe when the model parameters are close to critical ones, at which waves disappear in still medium. In the subcritical region of parameters, a sufficiently fast stream can result in the survival of excitation moving, as a rule, in the form of "restrictons". For downstream excitation waves, the axial portion of the channel is the most important one in determining their behavior. For upstream waves, the most important region of the channel is the near-wall boundary layers. The roles of transversal diffusion, and of approximate similarity with respect to stream velocity are discussed. CONCLUSIONS: These findings clarify mechanisms of wave propagation and survival in flow

Healthcare delivery for HIV-positive people with tuberculosis in Europe

Background In a 2013 survey, we reported distinct discrepancies in delivery of tuberculosis (TB) and HIV services in eastern Europe (EE) vs. western Europe (WE). Objectives To verify the differences in TB and HIV services in EE vs. WE. Methods Twenty-three sites completed a survey in 2018 (EE, 14; WE, nine; 88% response rate). Results were compared across as well as within the two regions. When possible, results were compared with the 2013 survey. Results Delivery of healthcare was significantly less integrated in EE: provision of TB and HIV services at one site (36% in EE vs. 89% in WE; P = 0.034), and continued TB follow-up in one location (42% vs. 100%; P = 0.007). Although access to TB diagnostics, standard TB and HIV drugs was generally good, fewer sites in EE reported unlimited access to rifabutin/multi-drug-resistant TB (MDR-TB) drugs, HIV integrase inhibitors and opioid substitution therapy (OST). Compared with 2013, routine usage of GeneXpert was more common in EE in 2018 (54% vs. 92%; P = 0.073), as was access to moxifloxacin (46% vs. 91%; P = 0.033), linezolid (31% vs. 64%; P = 0.217), and bedaquiline (0% vs. 25%; P = 0.217). Integration of TB and HIV services (46% vs. 39%; P = 1.000) and provision of OST to patients with opioid dependency (54% vs. 46%; P = 0.695) remained unchanged. Conclusion Delivery of TB and HIV healthcare, including integration of TB and HIV care and access to MDR-TB drugs, still differs between WE and EE, as well as between individual EE sites

QM/MM description of newly selected catalytic bioscavengers against organophosphorus compounds revealed reactivation stimulus mediated by histidine residue in the acyl-binding loop

© 2018 Zlobin, Mokrushina, Terekhov, Zalevsky, Bobik, Stepanova, Aliseychik, Kartseva, Panteleev, Golovin, Belogurov, Gabibov and Smirnov. Butyrylcholinesterase (BChE) is considered as an efficient stoichiometric antidote against organophosphorus (OP) poisons. Recently we utilized combination of calculations and ultrahigh-throughput screening (uHTS) to select BChE variants capable of catalytic destruction of OP pesticide paraoxon. The purpose of this study was to elucidate the molecular mechanism underlying enzymatic hydrolysis of paraoxon by BChE variants using hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. Detailed analysis of accomplished QM/MM runs revealed that histidine residues introduced into the acyl-binding loop are always located in close proximity with aspartate residue at position 70. Histidine residue acts as general base thus leading to attacking water molecule activation and subsequent SN2 inline hydrolysis resulting in BChE reactivation. This combination resembles canonical catalytic triad found in active centers of various proteases. Carboxyl group activates histidine residue by altering its pKa, which in turn promotes the activation of water molecule in terms of its nucleophilicity. Observed re-protonation of catalytic serine residue at position 198 from histidine residue at position 438 recovers initial configuration of the enzyme's active center, facilitating next catalytic cycle. We therefore suggest that utilization of uHTS platform in combination with deciphering of molecular mechanisms by QM/MM calculations may significantly improve our knowledge of enzyme function, propose new strategies for enzyme design and open new horizons in generation of catalytic bioscavengers against OP poisons

Характеристика осложнений после операций по поводу туберкулеза легких у больных ВИЧ-инфекцией с разным уровнем CD4+-лимфоцитов и вирусной нагрузки

The objective: to study postoperative complications in pulmonary tuberculosis HIV positive patients with the relevance to CD4+ count and viral load before surgery.Subjects and methods. The results of planned lung resections of various extent for tuberculosis in 139 HIV positive patients were analyzed.Results. There was no statistically significant correlation between baseline CD4+ count and viral load and the development of postoperative complications in the investigated cases.Цель исследования: изучение послеоперационных осложнений при туберкулезе легких у больных с ВИЧ-инфекцией в зависимости от уровня CD4+-лимфоцитов и вирусной нагрузки перед операцией.Материалы и методы. Проанализированы результаты плановых резекций легких различного объема по поводу туберкулеза у 139 ВИЧ-позитивных пациентов.Результаты. Не выявлено статистически значимой взаимосвязи между исходным уровнем CD4+-лимфоцитов и вирусной нагрузкой с развитием послеоперационных осложнений у пациентов

Defining the Boundaries of Normal Thrombin Generation: Investigations into Hemostasis

In terms of its soluble precursors, the coagulation proteome varies quantitatively among apparently healthy individuals. The significance of this variability remains obscure, in part because it is the backdrop against which the hemostatic consequences of more dramatic composition differences are studied. In this study we have defined the consequences of normal range variation of components of the coagulation proteome by using a mechanism-based computational approach that translates coagulation factor concentration data into a representation of an individual's thrombin generation potential. A novel graphical method is used to integrate standard measures that characterize thrombin generation in both empirical and computational models (e.g max rate, max level, total thrombin, time to 2 nM thrombin (“clot time”)) to visualize how normal range variation in coagulation factors results in unique thrombin generation phenotypes. Unique ensembles of the 8 coagulation factors encompassing the limits of normal range variation were used as initial conditions for the computational modeling, each ensemble representing “an individual” in a theoretical healthy population. These “individuals” with unremarkable proteome composition was then compared to actual normal and “abnormal” individuals, i.e. factor ensembles measured in apparently healthy individuals, actual coagulopathic individuals or artificially constructed factor ensembles representing individuals with specific factor deficiencies. A sensitivity analysis was performed to rank either individual factors or all possible pairs of factors in terms of their contribution to the overall distribution of thrombin generation phenotypes. Key findings of these analyses include: normal range variation of coagulation factors yields thrombin generation phenotypes indistinguishable from individuals with some, but not all, coagulopathies examined; coordinate variation of certain pairs of factors within their normal ranges disproportionately results in extreme thrombin generation phenotypes, implying that measurement of a smaller set of factors may be sufficient to identify individuals with aberrant thrombin generation potential despite normal coagulation proteome composition