Canonical Structure Research Articles

Complex structures on jet spaces and bosonic Fock space dynamics for causal variational principles

Based on conservation laws for surface layer integrals for critical points of causal variational principles, it is shown how jet spaces can be endowed with an almost-complex structure. We analyze under which conditions the almost-complex structure can be integrated to a canonical complex structure. Combined with the scalar product expressed by a surface layer integral, we obtain a complex Hilbert space $\mathfrak{h}$. The Euler-Lagrange equations of the causal variational principle describe a nonlinear time evolution on $\mathfrak{h}$. Rewriting multilinear operators on $\mathfrak{h}$ as linear operators on corresponding tensor products and using a conservation law for a nonlinear surface layer integral, we obtain a linear norm-preserving time evolution on bosonic Fock spaces. The so-called holomorphic approximation is introduced, in which the dynamics is described by a unitary time evolution on the bosonic Fock space. The error of this approximation is quantified. Our constructions explain why and under which assumptions critical points of causal variational principles give rise to a second-quantized, unitary dynamics on Fock spaces.

Generalized chain surgeries and applications

We describe the Stein handlebody diagrams of Milnor fibers of Brieskorn singularities $x^p + y^q + z^r = 0$. We also study the natural symplectic operation by exchanging two Stein fillings of the canonical contact structure on the links in the case $p = q = r$, where one of the fillings comes from the minimal resolution and the other is the Milnor fiber. We give two different interpretations of this operation, one as a symplectic sum and the other as a monodromy substitution in a Lefschetz fibration.

Seasonality in the Vertical Structure of Long-Term Temperature Trends Over North America

ABSTRACT The surface warming of northern continents during the twentieth century is not uniform across seasons. Surface warming is particularly pronounced over northwestern Canada, where winter trends are much larger than summer ones. The upper-air temperature trends over the region are analyzed in three radiosonde datasets from 1958 to 2012 to assess their seasonal structure. The seasonal variation of upper-air trends can provide insights into the dynamical and thermodynamical processes generating these trends, including warming at the surface. The focus is not on the canonical structure of secular (i.e., long-term) trends—tropospheric warming and stratospheric cooling—but its seasonal variation. We find the boreal winter-minus-summer difference in trends over northwestern Canada to be positive and large in the lower troposphere (p ≳ 500 hPa) and lower stratosphere (50 hPa ≲ p ≲ 150 hPa); it is largest at the surface and smallest at the tropopause. The decreasing seasonality of the tropospheric trend with height supports the attribution of the notable seasonality of surface warming in this region to both land–surface–hydroclimate interactions and changes in winter circulation. In the lower stratosphere, a cooling trend is evident in all seasons, not unexpectedly, but a pronounced seasonality is again apparent, with the strongest cooling in summer. The near-zero trend tropopause region is a rare point of confluence for seasonal trends.

Heterogeneous Non-Canonical Nucleosomes Predominate in Yeast Cells <i>In Situ</i>

Nuclear processes depend heavily on the organization of chromatin, whose subunits are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ resemble the canonical structure determined in vitro 24 years ago. The structure of nucleosomes in situ is otherwise poorly understood. Here we use cryo-ET and 3-D classification analysis to study the structure of yeast nucleosomes both in vitro and in situ. We show that the class averages of GFP-tagged yeast nucleosomes in vitro resemble canonical nucleosomes, with additional GFP densities. In contrast, none of the class averages of nucleosome-like particles in situ (inside cells) resemble canonical nucleosomes. The heterogeneous nature of the in situ class averages suggests that the intranuclear environment favors multiple conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average yeast nucleosome's DNA is partially detached in situ.

Complex s-Plane Modeling and 2D Characterization of the Stochastic Scattering Loss in Symmetric Dielectric Slab Waveguides Exhibiting Ergodic Surface-Roughness With an Exponential Autocorrelation Function

The symmetric dielectric slab waveguide serves as an important canonical structure for the high-speed high-bandwidth optical and opto-electronic silicon-on-insulator interconnects. A stochastic model of propagation loss, due to electromagnetic wave scattering with surface-roughness of the nano-scale waveguide excited at frequencies in the 100s of THz, provides useful insights for analysis and design optimization of optical interconnects. In this work, we propose an analytic solution for the stochastic scattering integral based on contour integration of the exponential autocorrelation function in the complex s-plane that improves performance at larger autocorrelation length values, compared to previous works. An expression is proposed for computing the upper-bound value of scattering loss. Results show that the proposed 2D formulation offers reasonable correlation against data from experimental measurements of loss by previous investigators, while several discrepancies are noted compared to previous 2D models. An expression is proposed for the transverse magnetic (TM) modal field amplitude, and several discrepancies in the transverse electric (TE) modal amplitudes are noted compared to previous works. A method is proposed for computation of the effective index (and propagation constant) for arbitrary cladding that improves convergence of the Newton search method, and it is compared to two other methods. Background discussions include the stochastic theory and assumptions that lead to the stationary and ergodic treatment of the surface-roughness, extension of the ensemble-average and time-average to the spatial domain, and effective thickness due to the Goos-Hänchen shift.

Au service de la Paix entre les Armes: L’Aumônerie Militaire Catholique en République Démocratique du Congo by Yves Kingata and Robert Lusilu Bipa

Reviewed by: Au service de la Paix entre les Armes: L’Aumônerie Militaire Catholique en République Démocratique du Congo by Yves Kingata and Robert Lusilu Bipa Siobhan M. Verbeek Au service de la Paix entre les Armes: L’Aumônerie Militaire Catholique en République Démocratique du Congo, by Yves Kingata and Robert Lusilu Bipa. Kononistische Reihe 28. Sankt Ottilien: EOS Verlag, 2017. Pp. 5–199. When Pope Francis addressed the bishops of the Democratic Republic of Congo during their ad limina visit in September 2014, he reminded them: “[Y]ou are called to offer direction and solutions for the promotion of a society founded on respect for the dignity of the human person.” It is in this spirit that the experienced and knowledgeable authors of this comprehensive study construct a compelling argument for the erection of a military ordinariate to provide for the pastoral care of military personnel and their families of that country. The study is comprised of four parts. Part one provides historical and socio-political context for the discussion. Its concise treatment (17–27) contains general geographical and demographic information about the Democratic Republic of Congo. In addition, it establishes an historical timeline marking the colonization of the territory by King Léopold II of Belgium (1885), the country’s eventual independence (1960), and its ongoing struggles to establish a stable form of democracy amidst great turmoil. A brief history of the Congolese Catholic Church is also provided, highlighting its existence as a missionary territory and the subsequent establishment of a stable ecclesiastical hierarchy. Part two (29–55) will likely interest canonists the most. It begins by providing definitions of the terms “chaplain” and “chaplaincy.” Taking the 1917 Code of Canon Law as a starting point, the authors next present an overview of key universal Church documents addressing military chaplains. The presentation understandably focuses on the April 23, 1951 instruction of the Sacred Consistorial Congregation Sollemne semper, and the April 21, 1986 apostolic constitution Spirituali militum curae of St. John [End Page 225] Paul II. Acknowledging the latter as the ius vigens, the part details the erection of military ordinariates by the Holy See, including the approval of an ordinariate’s statutes. It details the appointment of the ordinary and his power of jurisdiction and identifies the clergy and faithful of these personal jurisdictions. Cross-references to the 1983 Code of Canon Law are distributed throughout the discussion as a benefit to the reader. A presentation on the notion of cumulative jurisdiction and a brief excursus on the similarities and differences between ordinariates and particular churches are instructive. Part three (57–72) explores the subject from the perspective of the state through an examination of evolving secular regulations governing the nation’s Catholic military chaplaincy. Only three religious groups within the country are provided an official chaplaincy, the other two being Protestants and the Kimbanguiste. The authors’ extensive research from the state’s archives provides evidence of a long-observed protection of religious liberty and an accommodation of religious interests despite repeated periods of upheaval. Explanations of the qualifications needed for the appointment of chaplains, their rights and responsibilities, and their cessation from service are detailed. The book culminates in part four (73–126), developing the main thesis for the study, i.e., the authors’ cogent argument for the erection of a military ordinariate for the Democratic Republic of Congo. Conjuring the scriptural adage of placing “new wine in fresh wineskins” (Mk 2:22), the writers contend that a stable canonical structure is critical to ensure the effective pastoral care of military personnel and their families because of their condition and circumstance in life (Christus Dominus 43). Effective evangelization will further contribute to the moral fiber of the nation’s armed forces. A digression on the treatment of the military chaplaincy in statements emanating from the Conférence Épiscopale Nationale du Congo is insightful. Finally, the study’s general conclusions identify various topics to be addressed in a canonical framework. In the authors’ own words, this study is intended for multiple audiences. Primarily, it hopes to persuade ecclesiastical authorities to establish a stable canonical structure for the Catholic military chaplaincy in the...

Equivariant Hodge theory and noncommutative geometry

We develop a version of Hodge theory for a large class of smooth formally proper quotient stacks $X/G$ analogous to Hodge theory for smooth projective schemes. We show that the noncommutative Hodge-de Rham sequence for the category of equivariant coherent sheaves degenerates. This spectral sequence converges to the periodic cyclic homology, which we canonically identify with the topological equivariant K-theory of $X$ with respect to a maximal compact subgroup of $G$, equipping the latter with a canonical pure Hodge structure. We also establish Hodge-de Rham degeneration for categories of matrix factorizations for a large class of equivariant Landau-Ginzburg models.

Quarterly Projection Model for the National Bank of Rwanda

National Bank of Rwanda (BNR) modernized monetary policy and transited to the price-based policy framework in January 2019. The Forecasting and Policy Analysis System (FPAS) is the cornerstone for the new forward-looking framework, which mobilizes and organizes resources and sets processes for regular forecasting rounds. The core of this system is a structural macroeconomic model for macroeconomic analysis and projections to support the BNR staff’s policy recommendations to the monetary policy committee. This paper documents the quarterly projection model (QPM) at the core of the FPAS at the BNR. The model is an extension of the canonical structure in Berg et al (2006) to reflect specifics of the interest-rate-based policy framework with a managed exchange rate, the effect of agricultural sector and harvests on prices, and the role of fiscal policies and aid flows.

Quarterly Projection Model for the National Bank of Rwanda

National Bank of Rwanda (BNR) modernized monetary policy and transited to the price-based policy framework in January 2019. The Forecasting and Policy Analysis System (FPAS) is the cornerstone for the new forward-looking framework, which mobilizes and organizes resources and sets processes for regular forecasting rounds. The core of this system is a structural macroeconomic model for macroeconomic analysis and projections to support the BNR staff’s policy recommendations to the monetary policy committee. This paper documents the quarterly projection model (QPM) at the core of the FPAS at the BNR. The model is an extension of the canonical structure in Berg et al (2006) to reflect specifics of the interest-rate-based policy framework with a managed exchange rate, the effect of agricultural sector and harvests on prices, and the role of fiscal policies and aid flows.

A Learning Framework for Personalized Random Utility Maximization (RUM) Modeling of User Behavior.

Understanding user behavior is crucial for the success of many emerging applications that aim to provide personalized services for target users, such as many patient-centered health apps and transportation apps. Models based on the random utility maximization (RUM) theory are widely used in learning and understanding behavioral preferences on the population level but find difficult to estimate individuals' preferences, particularly when individuals' data are limited and fragmented. To address this problem, our framework builds on the concepts such as canonical structure and membership vectors invented in recent works on collaborative learning and is suitable for modeling heterogeneous population with insufficient data from each individual. We further propose an extension of the collaborative learning framework using pairwise-fusion regularization as a knowledge discovery tool for real-world applications where the canonical structure is uneven, e.g., some canonical models may only represent minor subpopulations. Computationally competent algorithms are developed to solve the corresponding optimization challenges. Extensive simulation studies and a real-world application in smart transportation demand management (TDM) show the effectiveness of our proposed methods.

Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing

BackgroundThe presence of nuclear mitochondrial DNA (numtDNA) has been reported within several nuclear genomes. Next to mitochondrial protein-coding genes, numtDNA sequences also encode for mitochondrial tRNA genes. However, the biological roles of numtDNA remain elusive.ResultsEmploying in silico analysis, we identify 281 mitochondrial tRNA homologs in the human genome, which we term nimtRNAs (nuclear intronic mitochondrial-derived tRNAs), being contained within introns of 76 nuclear host genes. Despite base changes in nimtRNAs when compared to their mtRNA homologs, a canonical tRNA cloverleaf structure is maintained. To address potential functions of intronic nimtRNAs, we insert them into introns of constitutive and alternative splicing reporters and demonstrate that nimtRNAs promote pre-mRNA splicing, dependent on the number and positioning of nimtRNA genes and splice site recognition efficiency. A mutational analysis reveals that the nimtRNA cloverleaf structure is required for the observed splicing increase. Utilizing a CRISPR/Cas9 approach, we show that a partial deletion of a single endogenous nimtRNALys within intron 28 of the PPFIBP1 gene decreases inclusion of the downstream-located exon 29 of the PPFIBP1 mRNA. By employing a pull-down approach followed by mass spectrometry, a 3′-splice site-associated protein network is identified, including KHDRBS1, which we show directly interacts with nimtRNATyr by an electrophoretic mobility shift assay.ConclusionsWe propose that nimtRNAs, along with associated protein factors, can act as a novel class of intronic splicing regulatory elements in the human genome by participating in the regulation of splicing.

Experiencia perceptiva y falsos planos subjetivos en El eclipse (Michelangelo Antonioni, 1962) y Muerte en Venecia (Luchino Visconti, 1971)

Los planos subjetivos son un recurso poderoso cuando aparecen en su estructura canónica, pero también presentan un gran potencial estético cuando esta se altera para romper las expectativas del espectador. Por ejemplo, en los casos de “falso plano subjetivo” en los que el espectador se enfrenta a la necesidad de reevaluar la condición subjetiva del plano que observa al aparecer en el mismo el personaje con el que creía estar compartiendo la mirada. Todos los falsos planos subjetivos producen experiencias que comparten ciertas cualidades fenomenológicas por el modo en que actúan sobre las expectativas y la percepción del espectador. Este artículo reflexiona en torno a cuatro de estos efectos, describiendo su alcance general y profundizando en sus posibilidades expresivas a partir del análisis de sendas escenas de El eclipse (Michelangelo Antonioni, 1962) y Muerte en Venecia (Luchino Visconti, 1971).

IRMPD Spectroscopic and Theoretical Structural Investigations of Zinc and Cadmium Dications Bound to Histidine Dimers

Metallated gas-phase structures consisting of a deprotonated and an intact histidine (His) ligand, yielding M(His-H)(His)+, where M = Zn and Cd, were examined with infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light from a free-electron laser (FEL). In parallel, quantum chemical calculations identified several low-energy isomers for each complex. Experimental action spectra were compared to linear spectra calculated at the B3LYP level of theory using the 6-311+G(d,p) and def2-TZVP basis sets for the zinc and cadmium complexes, respectively. For both Zn and Cd species, the definitive assignment is complicated by conflicting relative energetics, which were calculated at B3LYP, B3LYP-GD3BJ, B3P86, and MP2(full) levels. Spectral comparison for both species indicates that the dominant conformation, [Nα,Nπ,CO-][CO2-](NπH+), has the deprotonated His chelating the metal at the amine nitrogen, π nitrogen of the imidazole ring, and the deprotonated carbonyl oxygen and that the intact His ligand adopts a salt-bridge bidentate binding motif, coordinating the metal with both carboxylate oxygens. There is also evidence for a conformation where the deprotonated His coordination is maintained, but the intact His ligand adopts a more canonical structure, coordinating with the metal atom at the amine nitrogen and π nitrogen, [Nα,Nπ,CO-][Nα,Nπ]gtgg. For both metallated species, B3LYP, B3P86, and B3LYP-GD3BJ levels of theory appear to describe the relative stability of the dominant zwitterionic species more accurately than the MP2(full) level.

Phenotypic characterization of Raya cattle in northern Ethiopia.

Thirteen qualitative and six morphometric variables on a total of 651 adult cattle (76 oxen and 575 cows) from four purposively selected districts were recorded to characterize the cattle populations in and around the breeding tract of Raya cattle. General linear model, frequency, and multivariate analysis procedures of Statistical Analysis Software (SAS 9.0) were used to analyze the data by splitting and merging the sexes. Higher measurement values for oxen were recorded over the cows. Location affects the studied traits significantly. The cattle population from Habru district was significantly differentiated from Raya cattle. Among the districts of Raya cattle, lowest values for most of the linear measurements were observed in Kobo district. Majority of the Raya cattle possess upright, lyre-shaped horn, small, and erected hump placed at the cervical thoracic position, large dewlap, naval flap, and perpetual sheath sizes and dominantly dark red body color with uniform body color pattern. Stepwise discriminant function analysis reveals horn length, ear length, and height at wither were the first three most important morphometric variables used in discriminating the cattle populations. Canonical discrimination analysis showed that the first canonical structure explains majority (94.13%) of the total variation with eigenvalue of 2.07 and canonical correlation of 82.14%. Discriminant function analysis showed the classification of an average 61% of the studied animals into their respective districts. Pairwise Mahalanobis distances between populations from different districts were found to be highly significant. Habru cattle population relates distantly from Raya cattle except its short distance with Kobo district. The shortest distance was observed between Raya cattle of Alamata and Raya Azebo districts. In conclusion, cattle from Alamata, Raya Azebo, and Kobo districts can be categorized as Raya cattle, while strong similarities between the first two districts in showing the real characteristics and morphology of Raya cattle were also revealed.

Integrability via Geometry: Dispersionless Differential Equations in Three and Four Dimensions

We prove that the existence of a dispersionless Lax pair with spectral parameter for a nondegenerate hyperbolic second order partial differential equation (PDE) is equivalent to the canonical conformal structure defined by the symbol being Einstein–Weyl on any solution in 3D, and self-dual on any solution in 4D. The first main ingredient in the proof is a characteristic property for dispersionless Lax pairs. The second is the projective behaviour of the Lax pair with respect to the spectral parameter. Both are established for nondegenerate determined systems of PDEs of any order. Thus our main result applies more generally to any such PDE system whose characteristic variety is a quadric hypersurface.

Structure of English Locative Inversion

A sentence structure involves the packaging of meaning. Words and their order decide the meaning of a sentence conveyed. This study discussed two points of problems. The first one is locative inversion structure in sentences taken from Corpus of Contemporary American English. The other problem is the constraints of locative inversion in the English grammar. The problems are discussed based on the theory of inversion by Hewings (2005). Method used to collect the data was documentation method. The analysis was conducted using descriptive qualitative method. The result of the analysis is shown using informal method. As results, this study shows that locative inversion structure is different from canonical structures. It has a distinct feature contrasting it with canonical structure. It also has several constraints regarding subject, predicate, and salient information affecting its formation. 

Comparative analysis of the complete mitochondrial genomes in two limpets from Lottiidae (Gastropoda: Patellogastropoda): rare irregular gene rearrangement within Gastropoda

To improve the systematics and taxonomy of Patellogastropoda within the evolution of gastropods, we determined the complete mitochondrial genome sequences of Lottia goshimai and Nipponacmea fuscoviridis in the family Lottiidae, which presented sizes of 18,192 bp and 18,720 bp, respectively. In addition to 37 common genes among metazoa, we observed duplication of the trnM gene in L. goshimai and the trnM and trnW genes in N. fuscoviridis. The highest A + T contents of the two species were found within protein-coding genes (59.95% and 54.55%), followed by rRNAs (56.50% and 52.44%) and tRNAs (56.42% and 52.41%). trnS1 and trnS2 could not form the canonical cloverleaf secondary structure due to the lack of a dihydrouracil arm in both species. The gene arrangements in all Patellogastropoda compared with those of ancestral gastropods showed different levels of gene rearrangement, including the shuffling, translocation and inversion of single genes or gene fragments. This kind of irregular rearrangement is particularly obvious in the Lottiidae family. The results of phylogenetic and gene rearrangement analyses showed that L. goshimai and Lottia digitalis clustered into one group, which in turn clustered with N. fuscoviridis in Patellogastropoda. This study demonstrates the significance of complete mitogenomes for phylogenetic analysis and enhances our understanding of the evolution of Patellogastropoda.

Expression of four new ferritins from grooved carpet shell clam Ruditapes decussatus challenged with Perkinsus olseni and metals (Cd, Cu and Zn)

Iron has a fundamental role in life and in its biochemical reactions but, when in excess, it can promote the formation of free radicals which can lead to cell death. Therefore, managing the levels of iron is essential to regulate the production of oxidative stress related to iron, and ferritins are one of the main protein families involved in this process. Ferritins are ≈480 kDa multimeric proteins composed by 24 subunits, each with 19−26 kDa, which can accumulate up to 4500 iron atoms. Besides their role in managing iron bioavailability, they have also developed a role in organism immunity and defence present throughout evolution. In this work, we identified and characterized, for the first time, four different ferritin subunits in the clam Ruditapes decussatus, a bivalve commercially and ecologically important along the south Atlantic coast and in the Mediterranean basin, which is a major target of the parasitic protozoa Perkinsus olseni, considered one of the main causes of high levels of clam mortality. Following phylogenetic annotation, the four ferritins subunits identified were subdivided into two cytosolic and two secreted forms. All four subunits maintain the canonical ferritin structure with four main helices α (A–D) and a small helix (E), but the secreted ferritins present an additional helix in their N-terminal region (F), located after the signal peptide and with possible antimicrobial properties. Additionally, we identified in ferritin 4 an extra helix α (G) located between helices B and C. These alpha helix domains revealed high degree of similarity with antimicrobial peptides associated with antibacterial and antifungal activities. Analysis of the expression of these subunits showed that ferritins 1 and 2 are ubiquitously expressed while ferritins 3 and 4 are present mainly in visceral mass. Ferritin 1 lacked a putative functional iron response element (IRE) and appeared to be under a tight regulation. Ferritins 2 and 3 showed a strong response to infection by parasite Perkinsus olseni in contrast to ferritin 4, whose main response was related to exposure to a combination of metals. The synergistic effect between metals and infection promoted a general upregulation of the four ferritins. In conclusion, our results suggest that ferritins, besides their function in iron and metals detoxification, may play a determinant role in clam immune response.

Geometric Aspects of the Isentropic Liquid Dynamics and Vorticity Invariants.

We review a modern differential geometric description of fluid isentropic motion and features of it including diffeomorphism group structure, modelling the related dynamics, as well as its compatibility with the quasi-stationary thermodynamical constraints. We analyze the adiabatic liquid dynamics, within which, following the general approach, the nature of the related Poissonian structure on the fluid motion phase space as a semidirect Banach groups product, and a natural reduction of the canonical symplectic structure on its cotangent space to the classical Lie-Poisson bracket on the adjoint space to the corresponding semidirect Lie algebras product are explained in detail. We also present a modification of the Hamiltonian analysis in case of a flow governed by isothermal liquid dynamics. We study the differential-geometric structure of isentropic magneto-hydrodynamic superfluid phase space and its related motion within the Hamiltonian analysis and related invariant theory. In particular, we construct an infinite hierarchy of different kinds of integral magneto-hydrodynamic invariants, generalizing those previously constructed in the literature, and analyzing their differential-geometric origins. A charged liquid dynamics on the phase space invariant with respect to an abelian gauge group transformation is also investigated, and some generalizations of the canonical Lie-Poisson type bracket is presented.

Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis.

Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes.