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At least 163 records · Page 9

Immunogenicity and protective efficacy of a rhesus adenoviral vaccine targeting conserved COVID-19 replication transcription complex

The COVID-19 pandemic marks the third coronavirus pandemic this century (SARS-CoV-1, MERS, SARS-CoV-2), emphasizing the need to identify and evaluate conserved immunogens for a pan-sarbecovirus vaccine. Here we investigate the potential utility of a T-cell vaccine strategy targeting conserved regions of the sarbecovirus proteome. We identified the most conserved regions of the sarbecovirus proteome as portions of the RNA-dependent RNA polymerase (RdRp) and Helicase proteins, both of which are part of the coronavirus replication transcription complex (RTC). Fitness constraints suggest that as SARS-CoV-2 continues to evolve these regions may better preserve cross-reactive potential of T-cell responses than Spike, Nucleocapsid, or Membrane proteins. We sought to determine if vaccine-elicited T-cell responses to the highly conserved regions of the RTC would reduce viral loads following challenge with SARS-CoV-2 in mice using a rhesus adenovirus serotype 52 (RhAd52) vector. The RhAd52.CoV.Consv vaccine generated robust cellular immunity in mice and led to significant reductions in viral loads in the nasal turbinates following challenge with a mouse-adapted SARS-CoV-2. These data suggest the potential utility of T-cell targeting of conserved regions for a pan-sarbecovirus vaccine.

60 APPLIED LIFE SCIENCES↗

Accuracy of the explicit energy-conserving particle-in-cell method for under-resolved simulations of capacitively coupled plasma discharges

The traditional explicit electrostatic momentum-conserving particle-in-cell algorithm requires strict resolution of the electron Debye length to deliver numerical stability and accuracy. The explicit electrostatic energy-conserving particle-in-cell algorithm alleviates this constraint with minimal modification to the traditional algorithm, retaining its simplicity, ease of parallelization, and acceleration on modern supercomputing architectures. In this article, we apply the algorithm to model a one-dimensional radio frequency capacitively coupled plasma discharge relevant to industrial applications. The energy-conserving approach closely matches the results from the momentum-conserving algorithm and retains accuracy even for cell sizes up to 8 times the electron Debye length. For even larger cells, the algorithm loses accuracy due to poor resolution of steep gradients within the radio frequency sheath. Accuracy can be recovered by adopting a non-uniform grid, which resolves the sheath and allows for cell sizes up to 32 times the electron Debye length in the quasi-neutral bulk of the discharge. The effect is an up to 8 times reduction in the number of required simulation cells, an improvement that can compound in higher-dimensional simulations. We therefore consider the explicit energy-conserving algorithm as a promising approach to significantly reduce the computational cost of full-scale device simulations and a pathway to delivering kinetic simulation capabilities of use to industry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ON THE CONSERVATION OF CROSS HELICITY AND WAVE ACTION IN SOLAR-WIND MODELS WITH NON-WKB ALFVÉN WAVE REFLECTION

The interaction between Alfvén-wave turbulence and the background solar wind affects the cross helicity (∫d{sup 3}x v⋅B) in two ways. Non-WKB reflection converts outward-propagating Alfvén waves into inward-propagating Alfvén waves and vice versa, and the turbulence transfers momentum to the background flow. When both effects are accounted for, the total cross helicity is conserved. In the special case that the background density and flow speed are independent of time, the equations of cross-helicity conservation and total-energy conservation can be combined to recover a well-known equation derived by Heinemann and Olbert that has been interpreted as a non-WKB generalization of wave-action conservation. This latter equation (in contrast to cross-helicity and energy conservation) does not hold when the background varies in time.

79 ASTRONOMY AND ASTROPHYSICS↗

Energy conserving and well-balanced discontinuous Galerkin methods for the Euler–Poisson equations in spherical symmetry

ABSTRACT This paper presents high-order Runge–Kutta (RK) discontinuous Galerkin methods for the Euler–Poisson equations in spherical symmetry. The scheme can preserve a general polytropic equilibrium state and achieve total energy conservation up to machine precision with carefully designed spatial and temporal discretizations. To achieve the well-balanced property, the numerical solutions are decomposed into equilibrium and fluctuation components that are treated differently in the source term approximation. One non-trivial challenge encountered in the procedure is the complexity of the equilibrium state, which is governed by the Lane–Emden equation. For total energy conservation, we present second- and third-order RK time discretization, where different source term approximations are introduced in each stage of the RK method to ensure the conservation of total energy. A carefully designed slope limiter for spherical symmetry is also introduced to eliminate oscillations near discontinuities while maintaining the well-balanced and total-energy-conserving properties. Extensive numerical examples – including a toy model of stellar core collapse with a phenomenological equation of state that results in core bounce and shock formation – are provided to demonstrate the desired properties of the proposed methods, including the well-balanced property, high-order accuracy, shock-capturing capability, and total energy conservation.

79 ASTRONOMY AND ASTROPHYSICS↗

Conservation law for electromagnetic fields in a space-time-varying medium and its implications

We discuss the propagation of electromagnetic waves in a space-time modulated medium, for which neither energy nor momentum remains conserved. We have found a new conservation law when modulation moves at a constant speed v in a traveling-wave fashion. We use this law to study how light is scattered inside such a medium. We consider both the subluminal (v < c) andsuperluminal (v > c) cases and find that they differ considerably in terms of what remains conserved. We show that the total number of photons is conserved in the subluminal case. In contrast, it is the difference between the forward and backward moving photons that remains conserved in the superluminal case. We also study the reciprocity issue for a space-time modulated medium and found that reciprocity holds in all situations. Here, we develop a quantum formulation of our scattering problem and show that the subluminal case is similar to the action of a beam splitter. In the superluminal case, photon pairs can be generated from vacuum in a fashion analogous to the two-mode frequency down-conversion process.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Charge conservation and higher moments of charge fluctuations

Higher moments of distributions of net charge and baryon number in heavy-ion collisions have been proposed as signals of fundamental QCD phase transitions. In order to better understand background processes for these observables, models are presented which enable one to gauge the effects of local charge conservation, decays of resonances and clusters, Bose symmetrization, and volume fluctuations. Monte Carlo methods for generating samplings of particles consistent with local charge conservation are presented and are followed by a review of simple analytic models involving a single type of charge with a constant experimental efficiency. The main model consists of thermal emission superimposed onto a simple parametrization of collective flow, known as a blast wave, with emission being consistent with individual canonical ensembles. The spatial extent of local charge conservation is parameterized by the size and extent over which charge is conserved. Here, the sensitivity of third- and fourth-order moments, skewness and kurtosis, to these parameters, and to beam energy and baryon density is explored. Comparisons with STAR data show that a significant part of the observed non-Poissonian fluctuations in net-proton fluctuations are explained by charge and baryon-number conservation, but that measurements of the STAR collaboration for fluctuations of net electric charge significantly differ from expectations of the models presented here.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Comparison of Conservation Behavior in Several Variationally Derived Implementations for Simulating Electromagnetic Plasmas

Variational techniques based on Low's Lagrangian formulation have demonstrated significant improvement in conservation properties as compared to traditional particle-in-cell (PIC) algorithms. Previous work showed that equations derived from a discretized Lagrangian preserve a discretized version of the connection between Lagrangian symmetries and conservation laws, i.e., Noether's theorem. Specifically, a thorough analysis of energy conservation within the new system explained the absence of “grid heating” phenomena. In the present work, variationally derived implementations in a gridded periodic domain were compared to analogous implementations using Fourier bases. Since the Fourier basis allows for exact momentum conservation, this approach enables us to compare the relative merits of exact and approximate momentum conservation. Furthermore, to establish a tangible comparison for numerical methods, we investigate two simple physical examples; (1) the coupling of an electrostatic and electromagnetic plasma wave and (2) an equilibrium supporting Weibel instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Phylogenetic and amino acid conservation analyses of bacterial l-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain

Background: All organisms must synthesize the enzymatic cofactor coenzyme A (CoA) from the precursor pantothenate. Most bacteria can synthesize pantothenate de novo by the condensation of pantoate and β-alanine. The synthesis of β-alanine is catalyzed by l-aspartate-α-decarboxylase (PanD), a pyruvoyl enzyme that is initially synthesized as a zymogen (pro-PanD). Active PanD is generated by self-cleavage of pro-PanD at Gly24-Ser25 creating the activesite pyruvoyl moiety. In Salmonella enterica, this cleavage requires PanM, an acetyl-CoA sensor related to the Gcn5-like N-acetyltransferases. PanM does not acetylate pro-PanD, but the recent publication of the three-dimensional crystal structure of the PanM homologue PanZ in complex with the PanD zymogen of Escherichia coli provides validation to our predictions and provides a framework in which to further examine the cleavage mechanism. In contrast, PanD from bacteria lacking PanM efficiently cleaved in the absence of PanM in vivo. Results: Using phylogenetic analyses combined with in vivo phenotypic investigations, we showed that two classes of bacterial l-aspartate-α-decarboxylases exist. This classification is based on their posttranslational activation by self-cleavage of its zymogen. Class I l-aspartate-α-decarboxylase zymogens require the acetyl-CoA sensor PanM to be cleaved into active PanD. This class is found exclusively in the Gammaproteobacteria. Class II l-aspartate-αdecarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla. Several members of the Euryarchaeota and Crenarchaeota also contain Class II l-aspartate-α-decarboxylases. Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583). This conserved region represents a putative domain for interactions with l-aspartate-α-decarboxylase zymogens. This work may inform future biochemical and structural studies of pro-PanD-PanM interactions. Conclusions: Experimental results indicate that S. enterica and C. glutamicum l-aspartate-α-decarboxylases represent two different classes of homologues of these enzymes. Class I homologues require PanM for activation, while Class II self cleave in the absence of PanM. Computer modeling of conserved amino acids using structure coordinates of PanM and l-aspartate-α-decarboxylase available in the protein data bank (RCSB PDB) revealed a putative site of interactions, which may help generate models to help understand the molecular details of the self-cleavage mechanism of l-aspartate-α-decarboxylases.

Aspartate decarboxylase↗

Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery

Arboviruses are a diverse group of insect-transmitted pathogens that pose global public health challenges. Identifying evolutionarily conserved host factors that combat arbovirus replication in disparate eukaryotic hosts is important as they may tip the balance between productive and abortive viral replication, and thus determine virus host range. Here, we exploit naturally abortive arbovirus infections that we identified in lepidopteran cells and use bacterial effector proteins to uncover host factors restricting arbovirus replication. Bacterial effectors are proteins secreted by pathogenic bacteria into eukaryotic hosts cells that can inhibit antimicrobial defenses. Since bacteria and viruses can encounter common host defenses, we hypothesized that some bacterial effectors may inhibit host factors that restrict arbovirus replication in lepidopteran cells. Thus, we used bacterial effectors as molecular tools to identify host factors that restrict four distinct arboviruses in lepidopteran cells. By screening 210 effectors encoded by seven different bacterial pathogens, we identify several effectors that individually rescue the replication of all four arboviruses. We show that these effectors encode diverse enzymatic activities that are required to break arbovirus restriction. We further characterize Shigella flexneri-encoded IpaH4 as an E3 ubiquitin ligase that directly ubiquitinates two evolutionarily conserved proteins, SHOC2 and PSMC1, promoting their degradation in insect and human cells. We show that depletion of either SHOC2 or PSMC1 in insect or human cells promotes arbovirus replication, indicating that these are ancient virus restriction factors conserved across invertebrate and vertebrate hosts. Collectively, our study reveals a novel pathogen-guided approach to identify conserved antimicrobial machinery, new effector functions, and conserved roles for SHOC2 and PSMC1 in virus restriction.

59 BASIC BIOLOGICAL SCIENCES↗

Genome-Wide Identification of Evolutionarily Conserved Alternative Splicing Events in Flowering Plants

Alternative splicing (AS) plays important roles in many plant functions, but its conservation across the plant kingdom is not known. We describe a methodology to identify AS events and identify conserved AS events across large phylogenetic distances using RNASeq datasets. We applied this methodology to transcriptome data from nine angiosperms including Amborella, the single sister species to all other extant flowering plants. AS events within 40–70% of the expressed multi-exonic genes per species were found, 27,120 of which are conserved among two or more of the taxa studied. While many events are species specific, many others are shared across long evolutionary distances suggesting they have functional significance. Conservation of AS event data provides an estimate of the number of ancestral AS events present at each node of the tree representing the nine species studied. Furthermore, the presence or absence of AS isoforms between species with different whole genome duplication (WGD) histories provides the opportunity to examine the impact of WDG on AS potential. Examining AS in gene families identifies those with high rates of AS, and conservation can distinguish ancient events vs. recent or species specific adaptations. The MADS-box and SR protein families are found to represent families with low and high occurrences of AS, respectively, yet their AS events were likely present in the MRCA of angiosperms.

54 ENVIRONMENTAL SCIENCES↗

Fluctuations and Conservation Laws

We report on recent progress concerning effects of global conservation laws on cumulants of conserved quantities. Specifically, we will relate for an arbitrary equation of state cumulants of a conserved charge measured in a subvolume of a thermal system with the corresponding grandcanonical susceptibilities, taking into account exact global conservation of that charge. Applications to actual measurement at the RHIC and LHC as well as extensions to multiple conserved charges will be discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Conservation: Toward firmer ground

The following aspects of energy conservation were reviewed in order to place the problems in proper perspective: history and goals, conservation accounting-criteria, and a method to overcome obstacles. The effect of changing prices and available supplies of energy sources and their causes on consumption levels during the last few decades were described. Some examples of attainable conservation goals were listed and justified. A number of specific criteria applicable to conservation accounting were given. Finally, a discussion was presented to relate together the following aspects of energy conservation: widespread impact, involvement of government, industry, politics, moral and ethical aspects, urgency and time element.

Source record↗

An energy and potential enstrophy conserving scheme for the shallow water equations

A three-dimensional finite difference scheme for the solution of the shallow water momentum equations which accounts for the conservation of potential enstrophy in the flow of a homogeneous incompressible shallow atmosphere over steep topography as well as for total energy conservation is presented. The scheme is derived to be consistent with a reasonable scheme for potential vorticity advection in a long-term integration for a general flow with divergent mass flux. Numerical comparisons of the characteristics of the present potential enstrophy-conserving scheme with those of a scheme that conserves potential enstrophy only for purely horizontal nondivergent flow are presented which demonstrate the reduction of computational noise in the wind field with the enstrophy-conserving scheme and its convergence even in relatively coarse grids.

Arakawa, A.↗

Semi-discrete approximations to nonlinear systems of conservation laws; consistency and L(infinity)-stability imply convergence

A convergence theory for semi-discrete approximations to nonlinear systems of conservation laws is developed. It is shown, by a series of scalar counter-examples, that consistency with the conservation law alone does not guarantee convergence. Instead, a notion of consistency which takes into account both the conservation law and its augmenting entropy condition is introduced. In this context it is concluded that consistency and L(infinity)-stability guarantee for a relevant class of admissible entropy functions, that their entropy production rate belongs to a compact subset of H(loc)sup -1 (x,t). One can now use compensated compactness arguments in order to turn this conclusion into a convergence proof. The current state of the art for these arguments includes the scalar and a wide class of 2 x 2 systems of conservation laws. The general framework of the vanishing viscosity method is studied as an effective way to meet the consistency and L(infinity)-stability requirements. How this method is utilized to enforce consistency and stability for scalar conservation laws is shown. In this context we prove, under the appropriate assumptions, the convergence of finite difference approximations (e.g., the high resolution TVD and UNO methods), finite element approximations (e.g., the Streamline-Diffusion methods) and spectral and pseudospectral approximations (e.g., the Spectral Viscosity methods).

Tadmor, Eitan↗

A new flux conserving Newton's method scheme for the two-dimensional, steady Navier-Stokes equations

A new numerical method is developed for the solution of the two-dimensional, steady Navier-Stokes equations. The method that is presented differs in significant ways from the established numerical methods for solving the Navier-Stokes equations. The major differences are described. First, the focus of the present method is on satisfying flux conservation in an integral formulation, rather than on simulating conservation laws in their differential form. Second, the present approach provides a unified treatment of the dependent variables and their unknown derivatives. All are treated as unknowns together to be solved for through simulating local and global flux conservation. Third, fluxes are balanced at cell interfaces without the use of interpolation or flux limiters. Fourth, flux conservation is achieved through the use of discrete regions known as conservation elements and solution elements. These elements are not the same as the standard control volumes used in the finite volume method. Fifth, the discrete approximation obtained on each solution element is a functional solution of both the integral and differential form of the Navier-Stokes equations. Finally, the method that is presented is a highly localized approach in which the coupling to nearby cells is only in one direction for each spatial coordinate, and involves only the immediately adjacent cells. A general third-order formulation for the steady, compressible Navier-Stokes equations is presented, and then a Newton's method scheme is developed for the solution of incompressible, low Reynolds number channel flow. It is shown that the Jacobian matrix is nearly block diagonal if the nonlinear system of discrete equations is arranged approximately and a proper pivoting strategy is used. Numerical results are presented for Reynolds numbers of 100, 1000, and 2000. Finally, it is shown that the present scheme can resolve the developing channel flow boundary layer using as few as six to ten cells per channel width, depending on the Reynolds number.

Scott, James R.↗

International Conference on Remote Sensing Applications for Archaeological Research and World Heritage Conservation

Contents include the following: Monitoring the Ancient Countryside: Remote Sensing and GIS at the Chora of Chersonesos (Crimea, Ukraine). Integration of Remote Sensing and GIS for Management Decision Support in the Pendjari Biosphere Reserve (Republic of Benin). Monitoring of deforestation invasion in natural reserves of northern Madagascar based on space imagery. Cartography of Kahuzi-Biega National Park. Cartography and Land Use Change of World Heritage Areas and the Benefits of Remote Sensing and GIS for Conservation. Assessing and Monitoring Vegetation in Nabq Protected Area, South Sinai, Egypt, using combine approach of Satellite Imagery and Land Surveys. Evaluation of forage resources in semi-arid savannah environments with satellite imagery: contribution to the management of a protected area (Nakuru National Park) in Kenya. SOGHA, the Surveillance of Gorilla Habitat in World Heritage sites using Space Technologies. Application of Remote Sensing to monitor the Mont-Saint-Michel Bay (France). Application of Remote Sensing & GIS for the Conservation of Natural and Cultural Heritage Sites of the Southern Province of Sri Lanka. Social and Environmental monitoring of a UNESCO Biosphere Reserve: Case Study over the Vosges du Nord and Pfalzerwald Parks using Corona and Spot Imagery. Satellite Remote Sensing as tool to Monitor Indian Reservation in the Brazilian Amazonia. Remote Sensing and GIS Technology for Monitoring UNESCO World Heritage Sites - A Pilot Project. Urban Green Spaces: Modern Heritage. Monitoring of the technical condition of the St. Sophia Cathedral and related monastic buildings in Kiev with Space Applications, geo-positioning systems and GIS tools. The Murghab delta palaeochannel Reconstruction on the Basis of Remote Sensing from Space. Acquisition, Registration and Application of IKONOS Space Imagery for the cultural World Heritage site at Mew, Turkmenistan. Remote Sensing and VR applications for the reconstruction of archaeological landscapes. Archaeology through Space: Experience in Indian Subcontinent. The creation of a GIS Archaeological Site Location Catalogue in Yucatan: A Tool to preserve its Cultural Heritage. Mapping the Ancient Anasazi Roads of Southeast Utah. Remote Sensing and GIS Technology for Identification of Conservation and Heritage sites in Urban Planning. Mapping Angkor: For a new appraisal of the Angkor region. Angkor and radar imaging: seeing a vast pre-industrial low-density, dispersed urban complex. Technical and methodological aspects of archaeological CRM integrating high resolution satellite imagery. The contribution of satellite imagery to archaeological survey: an example from western Syria. The use of satellite images, digital elevation models and ground truth for the monitoring of land degradation in the "Cinque Terre" National park. Remote Sensing and GIS Applications for Protection and Conservation of World Heritage Site on the coast - Case Study of Tamil Nadu Coast, India. Multispectral high resolution satellite imagery in combination with "traditional" remote sensing and ground survey methods to the study of archaeological landscapes. The case study of Tuscany. Use of Remotely-Sensed Imagery in Cultural Landscape. Characterisation at Fort Hood, Texas. Heritage Learning and Data Collection: Biodiversity & Heritage Conservation through Collaborative Monitoring & Research. A collaborative project by UNESCO's WHC (World Heritage Center) & The GLOBE Program (Global Learning and Observations to Benefit the Environment). Practical Remote Sensing Activities in an Interdisciplinary Master-Level Space Course.

Source record↗

Conserved Function of RNA Binding Motif Protein48 (RBM48) and Armadillo Repeat Containing 7 (ARMC7) in Maize and Human U12 Splicing

Splicing of pre-mRNA is fundamental for genes containing introns. Emerging data points to a deeply conserved role of this process in eukaryotic cell differentiation and proliferation. The vast majority of introns termed U2-type introns are spliced by a major spliceosome; however, there also exist rare and more conserved U12-type introns that are spliced by a minor spliceosome. Mutations that disrupt U12 splicing inhibit cell differentiation in both maize endosperm and human blood cells. However, the mechanism underlying this process is not well understood. The maize RNA Binding Motif Protein 48 (RBM48) plays an essential role as a U12 splicing factor and is required for proper maize kernel development. Using human cell lines, CRISPR-Cas9 knockdown of RBM48 demonstrated a conserved function in human U12 intron splicing. RBM48 and Armadillo Repeat Containing 7 (ARMC7) protein interact in both maize and human as part of the activated minor spliceosome. Here we show RBM48 and ARMC7 co-localization in the nucleus of human cell lines. Vertebrate ARMC7 is normally localized in the cytosol, whereas RBM48 is found in the nucleus. Our data suggests that the interaction plays a role in regulating ARMC7 localization or the efficiency of U12 intron splicing. We also performed comprehensive transcriptome profiling and identified a common subset of conserved Minor Intron Containing Genes (MIGs) impacted in both human and maize RBM48 knockout mutants. Of importance, the vast majority of these MIGs are associated with developmental defects in both plants and animals. This suggests that aberrant splicing of these targets has a high likelihood of mediating abnormal cell phenotypes. These data support evolutionarily conserved U12 splicing mechanisms between maize and humans with both RBM48 and ARMC7 having roles in the activated spliceosome.

maize↗

Draft Environmental Impact Statement for Proposed Energy Conservation Standards for Manufactured Housing

This draft environmental impact statement (EIS) analyzes the impacts related to DOE’s proposed energy conservation standards for manufactured homes. DOE’s proposed energy conservation standards are based on the 2021 International Energy Conservation Code (IECC) and relate to the building thermal envelope; air sealing; installation of insulation; duct sealing; heating, ventilation and air conditioning (HVAC); service hot water systems; mechanical ventilation fan efficacy; and heating and cooling equipment sizing. The draft EIS evaluates DOE’s proposed action (energy conservation standards tiered based the manufacturers retail list price), alternatives to the proposed action (including energy conservation standards tiered based on size of the manufactured home and untiered standards), and a no action alternative. The draft EIS presents analysis of impacts related to (1) energy resources; (2) air resources (including greenhouse gases, climate change, ambient air quality and indoor air quality); (3) health and safety; (4) socioeconomics; and (5) environmental justice.

MacDonell, Margaret↗