Fast Differential Emission Measure Inversion of Solar Coronal Data

We present a fast method for reconstructing Differential Emission Measures (DEMs) using solar coronal data. On average, the method computes over 1000 DEMs per second for a sample active region observed by the Atmospheric Imaging Assembly (AIA) on the Solar Dynamics Observatory (SDO), and achieves reduced chi-squared of order unity with no negative emission in all but a few test cases. The high performance of this method is especially relevant in the context of AIA, which images of order one million solar pixels per second. This paper describes the method, analyzes its fidelity, compares its performance and results with other DEM methods, and applies it to an active region and loop observed by AIA and by the Extreme-ultraviolet Imaging Spectrometer (EIS) on Hinode.Comment: 22 Pages, 11 Figures; submitted to The Astrophysical Journal. This version (2) includes clarifications in the text and reflects improvements to the DEM cod

Almost a Teacher: Considering Curriculum Through Reflexion in the Liminal Space

This article examines the liminal space, “the betwixt and between” (V. Turner, 1969), that preservice teachers inhabit after they complete their last practicum and return to campus for final coursework. We look at preservice teachers’ expectations, assumptions, and understandings of questions and content in a senior-level curriculum course as uncovered through their assignment, the commonplace book. In this assignment they examined their understanding and meaning-making, or “truth-telling” (Huebner, 1999), in a personal text, which can allow for continued practice of reflection and reflexivity as they enter into their careers in addition to informing the researchers about how students experience growth in their understanding of issues in curriculum as experienced in the liminal space, grounded in historical, social, cultural, and experiential contexts

Evolution and Conservation of Predicted Inclusion Membrane Proteins in Chlamydiae

Chlamydia spp. are obligate intracellular pathogens that replicate within a vacuole termed the inclusion. Chlamydiae extensively modify the inclusion membrane via the insertion of chlamydial inclusion membrane proteins (Incs) which decorate the cytosolic face of the inclusion. We have assessed the overall relatedness and phylogeny of Incs in order to identify potential evolutionary trends. Despite a high degree of conservation among Incs within C. trachomatis serovars, phylogenetic analysis showed that some Incs cluster according to clinical groupings suggesting that certain Incs may contribute to tissue tropism. Bioinformatic predictions identified Incs in five chlamydial species: 55 in C. trachomatis, 68 in C. felis, 92 in C. pneumoniae, 79 in C. caviae, and 54 in C. muridarum. Inc homologues were compared between chlamydial species and 23 core Incs were identified as shared among all species. Genomic expansion of Incs was identified in C. pneumoniae, C. caviae, and C. felis but not C. trachomatis or C. muridarum

A First Principles Derivation of Energy Conserving Momentum Jumps in Surface Hopping Simulations

The fewest switches surface hopping (FSSH) method proposed by Tully in 1990 [J. C Tully, J. Chem. Phys. 93, 1061 (1990)] -- along with its many later variations -- is basis for most practical simulations of molecular dynamics with electronic transitions in realistic systems. Despite its popularity, a rigorous formal derivation of the algorithm has yet to be achieved. In this paper, we derive the energy conserving momentum jumps characterizing FSSH from the perspective of quantum trajectory surface hopping (QTSH [C. C. Martens, J. Phys. Chem. A 123, 1110 (2019)]. In the limit of localized nonadiabatic transitions, simple mathematical and physical arguments allow the FSSH algorithm to be derived from first principles. For general processes, the quantum forces characterizing the QTSH method provides accurate results for nonadiabatic dynamics with rigorous energy conservation at the ensemble level within the consistency of the underlying stochastic surface hopping without resorting to the artificial momentum rescaling of FSSH.Comment: 11 pages, 4 figure

The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution

BACKGROUND:Giardia lamblia trophozoites colonize the intestines of susceptible mammals and cause diarrhea, which can be prolonged despite an intestinal immune response. The variable expression of the variant-specific surface protein (VSP) genes may contribute to this prolonged infection. Only one is expressed at a time, and switching expression from one gene to another occurs by an epigenetic mechanism.RESULTS:The WB Giardia isolate has been sequenced at 10x coverage and assembled into 306 contigs as large as 870 kb in size. We have used this assembly to evaluate the genomic organization and evolution of the vsp repertoire. We have identified 228 complete and 75 partial vsp gene sequences for an estimated repertoire of 270 to 303, making up about 4% of the genome. The vsp gene diversity includes 30 genes containing tandem repeats, and 14 vsp pairs of identical genes present in either head to head or tail to tail configurations (designated as inverted pairs), where the two genes are separated by 2 to 4 kb of non-coding DNA. Interestingly, over half the total vsp repertoire is present in the form of linear gene arrays that can contain up to 10 vsp gene members. Lastly, evidence for recombination within and across minor clades of vsp genes is provided.CONCLUSIONS:The data we present here is the first comprehensive analysis of the vsp gene family from the Genotype A1 WB isolate with an emphasis on vsp characterization, function, evolution and contributions to pathogenesis of this important pathogen.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]

Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons.

Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is tightly linked to the acquisition of a variant of the energy-yielding ATPases via horizontal transfer. Whereas the ATPase genealogy of neutrophilic Thaumarchaeota is congruent with their organismal genealogy inferred from concatenated conserved proteins, a common clade of V-type ATPases unites phylogenetically distinct clades of acidophilic/acid-tolerant and piezophilic/piezotolerant species. A presumptive function of pumping cytoplasmic protons at low pH is consistent with the experimentally observed increased expression of the V-ATPase in an acid-tolerant thaumarchaeote at low pH. Consistently, heterologous expression of the thaumarchaeotal V-ATPase significantly increased the growth rate of E. coli at low pH. Its adaptive significance to growth in ocean trenches may relate to pressure-related changes in membrane structure in which this complex molecular machine must function. Together, our findings reveal that the habitat expansion of Thaumarchaeota is tightly correlated with extensive horizontal transfer of atp operons

A guide to the Proteomics Identifications Database proteomics data repository

The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across-domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy-to-use, platform-independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium

Surface Hopping without Momentum Jumps: A Quantum-Trajectory-Based Approach to Nonadiabatic Dynamics.

We describe a new method for simulating nonadiabatic dynamics using stochastic trajectories. The method, which we call quantum trajectory surface hopping (QTSH), is a variant of the popular fewest-switches surface-hopping (FSSH) approach, but with important differences. We briefly review and significantly extend our recently described consensus surface-hopping (CSH) formalism, which captures quantum effects such as coherence and decoherence via a collective representation of the quantum dynamics at the ensemble level. Using well-controlled further approximations, we derive an independent trajectory limit of CSH that recovers the FSSH stochastic algorithm but rejects the ad hoc momentum rescaling of FSSH in favor of quantum forces that couple classical and quantum degrees of freedom and lead to nonclassical trajectory dynamics. The approach is well-defined in both the diabatic and adiabatic representations. In the adiabatic representation, the classical dynamics are modified by a quantum-state-dependent vector potential, introducing geometric phase effects into the dynamics of multidimensional systems. Unlike FSSH, our method obeys energy conservation without any artificial momentum rescaling, eliminating undesirable features of the former such as forbidden hops and breakdown of the internal consistency of quantum and ensemble-based state probabilities. Corrections emerge naturally in the formalism that allow approximate incorporation of decoherence without the computational expense of the full CSH approach. The method is tested on several model systems. QTSH provides a surface-hopping methodology that has a rigorous foundation and broader applicability than FSSH while retaining the low computational cost of an independent trajectory framework