Mass Conservation Analysis For The Lower St. Johns River Using Continuous And Discontinuous Galerkin Finite Element Methods

This thesis provides a mass conservation analysis of the Lower St. Johns River for the purpose of providing basis for future salinity transport modeling. The analysis provides an assessment of the continuous (CG) and discontinuous (DG) Galerkin finite element methods with respect to their mass conservation properties. The following thesis also presents a rigorous literature review pertaining to salinity transport in the Lower St. Johns River, from which this effort generates the data used to initialize and validate numerical simulations. Two research questions are posed and studied in this thesis: can a DG-based modeling approach produce mass conservative numerical solutions; and what are the flow interactions between the river and the marshes within the coastal region of the Lower St. Johns River? Reviewing the available data provides an initial perspective of the ecosystem. For this, salinity data are obtained and assembled for three modeling scenarios. Each scenario, High Extreme, Most Variable, and Low Extreme, is 30 days long (taken from year 1999) and represents a unique salinity regime in the Lower St. Johns River. Time-series of salinity data is collected at four stations in the lower and middle reaches of the Lower St. Johns River, which provides a vantage point for assessing longitudinal variation of salinity. As an aside, precipitation and evaporation data is presented for seven stations along the entire St. Johns River, which provides added insight into salinity transport in the river. A mass conservation analysis is conducted for the Lower St. Johns River. The analysis utilizes a segmentation of the Lower St. Johns River, which divides the domain into sections iv based on physical characteristics. Mass errors are then calculated for the CG and DG finite element methods to determine mass conservative abilities. Also, the flow interactions (i.e., volume exchange) between the river and marshes are evaluated through the use of tidal prisms. The CG- and DG- finite element methods are then tested in tidal simulation performance, which the results are then compared to observed tides and tidal currents at four stations within the lower portion of the Lower St. Johns River. Since the results show that the DG model outperforms the CG model, the DG model is used in the tidally driven salinity transport simulations. Using four stations within the lower and middle part of the Lower St. Johns River, simulated and observed water levels and salinity concentrations are compared

Thromboxane A2 is a key regulator of pathogenesis during Trypanosoma cruzi infection

Chagas' disease is caused by infection with the parasite Trypanosoma cruzi. We report that infected, but not uninfected, human endothelial cells (ECs) released thromboxane A2 (TXA2). Physical chromatography and liquid chromatography-tandem mass spectrometry revealed that TXA2 is the predominant eicosanoid present in all life stages of T. cruzi. Parasite-derived TXA2 accounts for up to 90% of the circulating levels of TXA2 in infected wild-type mice, and perturbs host physiology. Mice in which the gene for the TXA2 receptor (TP) has been deleted, exhibited higher mortality and more severe cardiac pathology and parasitism (fourfold) than WT mice after infection. Conversely, deletion of the TXA2 synthase gene had no effect on survival or disease severity. TP expression on somatic cells, but not cells involved in either acquired or innate immunity, was the primary determinant of disease progression. The higher intracellular parasitism observed in TP-null ECs was ablated upon restoration of TP expression. We conclude that the host response to parasite-derived TXA2 in T. cruzi infection is possibly an important determinant of mortality and parasitism. A deeper understanding of the role of TXA2 may result in novel therapeutic targets for a disease with limited treatment options

Early Use of Adjunctive Therapies for Pediatric Acute Respiratory Distress Syndrome:A PARDIE Study

Rationale: Few data exist to guide early adjunctive therapy use in pediatric acute respiratory distress syndrome (PARDS). Objectives: To describe contemporary use of adjunctive therapies for early PARDS as a framework for future investigations. Methods: This was a preplanned substudy of a prospective, international, cross-sectional observational study of children with PARDS from 100 centers over 10 study weeks. Measurements and Main Results: We investigated six adjunctive therapies for PARDS: continuous neuromuscular blockade, corticosteroids, inhaled nitric oxide (iNO), prone positioning, high-frequency oscillatory ventilation (HFOV), and extracorporeal membrane oxygenation. Almost half (45%) of children with PARDS received at least one therapy. Variability was noted in the median starting oxygenation index of each therapy; corticosteroids started at the lowest oxygenation index (13.0; interquartile range, 7.6–22.0) and HFOV at the highest (25.7; interquartile range, 16.7–37.3). Continuous neuromuscular blockade was the most common, used in 31%, followed by iNO (13%), corticosteroids (10%), prone positioning (10%), HFOV (9%), and extracorporeal membrane oxygenation (3%). Steroids, iNO, and HFOV were associated with comorbidities. Prone positioning and HFOV were more common in middle-income countries and less frequently used in North America. The use of multiple ancillary therapies increased over the first 3 days of PARDS, but there was not an easily identifiable pattern of combination or order of use. Conclusions: The contemporary description of prevalence, combinations of therapies, and oxygenation threshold for which the therapies are applied is important for design of future studies. Region of the world, income, and comorbidities influence adjunctive therapy use and are important variables to include in PARDS investigations

Simplified Models for LHC New Physics Searches

This document proposes a collection of simplified models relevant to the design of new-physics searches at the LHC and the characterization of their results. Both ATLAS and CMS have already presented some results in terms of simplified models, and we encourage them to continue and expand this effort, which supplements both signature-based results and benchmark model interpretations. A simplified model is defined by an effective Lagrangian describing the interactions of a small number of new particles. Simplified models can equally well be described by a small number of masses and cross-sections. These parameters are directly related to collider physics observables, making simplified models a particularly effective framework for evaluating searches and a useful starting point for characterizing positive signals of new physics. This document serves as an official summary of the results from the "Topologies for Early LHC Searches" workshop, held at SLAC in September of 2010, the purpose of which was to develop a set of representative models that can be used to cover all relevant phase space in experimental searches. Particular emphasis is placed on searches relevant for the first ~50-500 pb-1 of data and those motivated by supersymmetric models. This note largely summarizes material posted at http://lhcnewphysics.org/, which includes simplified model definitions, Monte Carlo material, and supporting contacts within the theory community. We also comment on future developments that may be useful as more data is gathered and analyzed by the experiments.Comment: 40 pages, 2 figures. This document is the official summary of results from "Topologies for Early LHC Searches" workshop (SLAC, September 2010). Supplementary material can be found at http://lhcnewphysics.or

Physics searches at the LHC

With the LHC up and running, the focus of experimental and theoretical high energy physics will soon turn to an interpretation of LHC data in terms of the physics of electroweak symmetry breaking and the TeV scale. We present here a broad review of models for new TeV-scale physics and their LHC signatures. In addition, we discuss possible new physics signatures and describe how they can be linked to specific models of physics beyond the Standard Model. Finally, we illustrate how the LHC era could culminate in a detailed understanding of the underlying principles of TeV-scale physics.Comment: 184 pages, 55 figures, 14 tables, hundreds of references; scientific feedback is welcome and encouraged. v2: text, references and Overview Table added; feedback still welcom

Progression of Pathogenic Events in Cynomolgus Macaques Infected with Variola Virus

Smallpox, caused by variola virus (VARV), is a devastating human disease that affected millions worldwide until the virus was eradicated in the 1970 s. Subsequent cessation of vaccination has resulted in an immunologically naive human population that would be at risk should VARV be used as an agent of bioterrorism. The development of antivirals and improved vaccines to counter this threat would be facilitated by the development of animal models using authentic VARV. Towards this end, cynomolgus macaques were identified as adequate hosts for VARV, developing ordinary or hemorrhagic smallpox in a dose-dependent fashion. To further refine this model, we performed a serial sampling study on macaques exposed to doses of VARV strain Harper calibrated to induce ordinary or hemorrhagic disease. Several key differences were noted between these models. In the ordinary smallpox model, lymphoid and myeloid hyperplasias were consistently found whereas lymphocytolysis and hematopoietic necrosis developed in hemorrhagic smallpox. Viral antigen accumulation, as assessed immunohistochemically, was mild and transient in the ordinary smallpox model. In contrast, in the hemorrhagic model antigen distribution was widespread and included tissues and cells not involved in the ordinary model. Hemorrhagic smallpox developed only in the presence of secondary bacterial infections – an observation also commonly noted in historical reports of human smallpox. Together, our results support the macaque model as an excellent surrogate for human smallpox in terms of disease onset, acute disease course, and gross and histopathological lesions

Population Dynamics and Angler Exploitation of the Unique Muskellunge Population in Shoepack Lake, Voyageurs National Park, Minnesota

A unique population of muskellunge Esox masquinongy inhabits Shoepack Lake in Voyageurs National Park, Minnesota. Little is known about its status, dynamics, and angler exploitation, and there is concern for the long-term viability of this population. We used intensive sampling and mark–recapture methods to quantify abundance, survival, growth, condition, age at maturity and fecundity and angler surveys to quantify angler pressure, catch rates, and exploitation. During our study, heavy rain washed out a dam constructed by beavers Castor canadensis which regulates the water level at the lake outlet, resulting in a nearly 50% reduction in surface area. We estimated a population size of 1,120 adult fish at the beginning of the study. No immediate reduction in population size was detected in response to the loss of lake area, although there was a gradual, but significant, decline in population size over the 2-year study. Adults grew less than 50 mm per year, and relative weight (W r) averaged roughly 80. Anglers were successful in catching, on average, two fish during a full day of angling, but harvest was negligible. Shoepack Lake muskellunge exhibit much slower growth rates and lower condition, but much higher densities and angler catch per unit effort (CPUE), than other muskellunge populations. The unique nature, limited distribution, and location of this population in a national park require special consideration for management. The results of this study provide the basis for assessing the long-term viability of the Shoepack Lake muskellunge population through simulations of long-term population dynamics and genetically effective population size

Correlates of protection against symptomatic and asymptomatic SARS-CoV-2 infection

The global supply of COVID-19 vaccines remains limited. An understanding of the immune response that is predictive of protection could facilitate rapid licensure of new vaccines. Data from a randomized efficacy trial of the ChAdOx1 nCoV-19 (AZD1222) vaccine in the United Kingdom was analyzed to determine the antibody levels associated with protection against SARS-CoV-2. Binding and neutralizing antibodies at 28 days after the second dose were measured in infected and noninfected vaccine recipients. Higher levels of all immune markers were correlated with a reduced risk of symptomatic infection. A vaccine efficacy of 80% against symptomatic infection with majority Alpha (B.1.1.7) variant of SARS-CoV-2 was achieved with 264 (95% CI: 108, 806) binding antibody units (BAU)/ml: and 506 (95% CI: 135, not computed (beyond data range) (NC)) BAU/ml for anti-spike and anti-RBD antibodies, and 26 (95% CI: NC, NC) international unit (IU)/ml and 247 (95% CI: 101, NC) normalized neutralization titers (NF50) for pseudovirus and live-virus neutralization, respectively. Immune markers were not correlated with asymptomatic infections at the 5% significance level. These data can be used to bridge to new populations using validated assays, and allow extrapolation of efficacy estimates to new COVID-19 vaccines

Recurrent SARS-CoV-2 mutations in immunodeficient patients

Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COVID-19 Genomics UK (COG-UK) dataset. The spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, T30I was determined to be the second most frequent recurrently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation.There is an apparent selective pressure for mutations that aid cell–cell transmission within the host or persistence which are often different from mutations that aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted