Complete Space Research Articles

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

Genotyping methods and genome sequencing are indispensable to reveal genomic structure of bacterial species displaying high level of genome plasticity. However, reconstruction of genome or assembly is not straightforward due to data complexity, including repeats, mobile and accessory genetic elements of bacterial genomes. Moreover, since the solution to this problem is strongly influenced by sequencing technology, bioinformatics pipelines, and selection criteria to assess assemblers, there is no systematic way to select a priori the optimal assembler and parameter settings. To assembly the genome of Pseudomonas aeruginosa strain AG1 (PaeAG1), short reads (Illumina) and long reads (Oxford Nanopore) sequencing data were used in 13 different non-hybrid and hybrid approaches. PaeAG1 is a multiresistant high-risk sequence type 111 (ST-111) clone that was isolated from a Costa Rican hospital and it was the first report of an isolate of P. aeruginosa carrying both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes. To assess the assemblies, multiple metrics regard to contiguity, correctness and completeness (3C criterion, as we define here) were used for benchmarking the 13 approaches and select a definitive assembly. In addition, annotation was done to identify genes (coding and RNA regions) and to describe the genomic content of PaeAG1. Whereas long reads and hybrid approaches showed better performances in terms of contiguity, higher correctness and completeness metrics were obtained for short read only and hybrid approaches. A manually curated and polished hybrid assembly gave rise to a single circular sequence with 100% of core genes and known regions identified, >98% of reads mapped back, no gaps, and uniform coverage. The strategy followed to obtain this high-quality 3C assembly is detailed in the manuscript and we provide readers with an all-in-one script to replicate our results or to apply it to other troublesome cases. The final 3C assembly revealed that the PaeAG1 genome has 7,190,208 bp, a 65.7% GC content and 6,709 genes (6,620 coding sequences), many of which are included in multiple mobile genomic elements, such as 57 genomic islands, six prophages, and two complete integrons with blaVIM-2 and blaIMP-18 MBL genes. Up to 250 and 60 of the predicted genes are anticipated to play a role in virulence (adherence, quorum sensing and secretion) or antibiotic resistance (β-lactamases, efflux pumps, etc). Altogether, the assembly and annotation of the PaeAG1 genome provide new perspectives to continue studying the genomic diversity and gene content of this important human pathogen.

Selective hybridization between the main band and the superstructure band in the Bi2Sr2CaCu2O8+δ superconductor

High-resolution laser-based angle-resolved photoemission measurements have been carried out on Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ (Bi2212) and Bi$_2$Sr$_{2-x}$La$_x$CuO$_{6+\delta}$ (Bi2201) superconductors. Unexpected hybridization between the main band and the superstructure band in Bi2212 is clearly revealed. In the momentum space where one main Fermi surface intersects with one superstructure Fermi surface, four bands are observed instead of two. The hybridization exists in both superconducting state and normal state, and in Bi2212 samples with different doping levels. Such a hybridization is not observed in Bi2201. This phenomenon can be understood by considering the bilayer splitting in Bi2212, the selective hybridization of two bands with peculiar combinations, and the altered matrix element effects of the hybridized bands. These observations provide strong evidence on the origin of the superstructure band which is intrinsic to the CuO$_2$ planes. Therefore, understanding physical properties and superconductivity mechanism in Bi2212 should consider the complete Fermi surface topology which involves the main bands, the superstructure bands and their interactions.

Theoretical Aspects of Iterative Coupling for Linear Oligomers and Polymers

AbstractA conceptual study of iterative coupling (IC) is performed, providing a unified description and new research directions. IC chain growth rates and functional group choice are analyzed, guiding construction of efficient schemes. The concept of cycle efficiency is defined as a more complete metric of experimental implementations of IC, and then applied to the main linear and exponential IC processes. The mathematical relations between individual reactions, cycles, and the iterative process as a whole are studied. Finally, macromolecule IC is proposed as a strikingly complementary process to standard IC, with potential to reduce the dispersity of non‐uniform samples. Due to its connection with the central limit theorem of statistics, it provides an unusually robust, powerful, and general method for scalable production of polymer samples with narrow distribution. In all, this contribution assists development of improved IC processes targeting low dispersity linear oligomers and polymers.

RR Lyrae Star Candidates from SDSS Databases by Cost-sensitive Random Forests

Abstract With the increase of known RR Lyrae stars, it is reliable to create classifiers of RR Lyrae stars based on their photometric data or combined photometric and spectroscopic data. Nevertheless the total number of known RR Lyrae stars is still too small compared with the large survey databases. So classification of RR Lyrae stars and other sources belongs to imbalanced learning. Based on Sloan Digital Sky Survey (SDSS) photometric and spectroscopic data, we apply cost-sensitive Random Forests fit for imbalanced learning to preselect RR Lyrae star candidates. Only with photometric data, is the best input pattern. While also considering physical parameters (T eff, [Fe/H], log(g)), the optimal input pattern is T eff, [Fe/H], log(g), , at this moment for cost-sensitive Random Forests, the performance metrics of completeness, contamination, and Matthews correlation coefficient are 0.975, 0.019, and 0.975, respectively. It indicates that adding stellar physical parameters is helpful for identifying RR Lyrae stars from other stars. We apply the best classifiers on the SDSS photometric data and combined photometric data with physical parameters to select RR Lyrae star candidates. Finally 11,041 photometric candidates with spectral type A and F are obtained, and then 304 candidates with physical parameters are selected out. Among the 304 candidates, a small part are HB stars, BS stars, RGB stars, and peculiar stars, and the rest are unknown in the Simbad database. These candidates may be used as the input catalog for time-series follow-up observations.

CRIC: Computing Resource Information Catalogue as a unified topology system for a large scale, heterogeneous and dynamic computing infrastructure

CRIC is a high-level information system which provides flexible, reliable and complete topology and configuration description for a large scale distributed heterogeneous computing infrastructure. CRIC aims to facilitate distributed computing operations for the LHC experiments and consolidate WLCG topology information. It aggregates information coming from various low-level information sources and complements topology description with experimentspecific data structures and settings required by the LHC VOs in order to exploit computing resources. Being an experiment-oriented but still experiment-independent information middleware, CRIC offers a generic solution, in the form of a suitable framework with appropriate interfaces implemented, which can be successfully applied on the global WLCG level or at the level of a particular LHC experiment. For example there are CRIC instances for CMS[11] and ATLAS[10]. CRIC can even be used for a special task. For example, a dedicated CRIC instance has been built to support transfer tests performed by DOMA Third Party Copy working group. Moreover, extensibility and flexibility of the system allow CRIC to follow technology evolution and easily implement concepts required to describe new types of computing and storage resources. The contribution describes the overall CRIC architecture, the plug-in based implementation of the CRIC components as well as recent developments and future plans.

Гибридное моделирование распределенной генерации в электроэнергетических системах

As many countries seek to use distributed energy more and move away from conventional centralized electricity delivery, the functioning of grids carrying distributed generation facilities becomes a relevant matter. Adoption of distributed generation fundamentally alters the properties of distribution grids, transforming them from passive transports and distributors into active distribution systems that have novel properties and dynamic characteristics, which inevitably causes the processes at major generation nodes and remote load nodes to affect each other in the context of reverse, rapidly changing power flows. Analysis presented herein shows that the mutual influence of distributed generation facilities and in-grid processes are ambiguous, and each case calls for analysis of its own, since, while being an advantage for the grid, distributed generation has negative impact, too, which pertains to the operating parameters of various DG types and units. How DG facilities and the grid affect each other can only be found by mathematical modeling; to maximize the accuracy, such modeling has to reproduce the most complete and detailed topology of grids carrying DG facilities; however, there are known limitations of software and hardware that prevent such modeling from returning accurate results. The authors hereof propose an alternative, hybrid approach to modeling electric systems (grid) that combines digital, analog, and physical-level modeling; the approach has been implemented as the All-Mode Real-Time Grid Simulation Complex. A specialized hybrid wind-farm processor has been designed and tested as a distributed generation unit of Tomsk Electric Grids.

Network Topology Inference Based on Subset Structure Fusion

Network topology measurement is an important component in network research. Network tomography is able to accurately infer network topology by using end-to-end measurement without cooperation of internal routers. Unfortunately, traditional network tomography methods can not accurately estimate topology in the non-stationary network due to the variability of traffic distribution. In this paper, we present a novel network topology inference method based on subset structure fusion for accurate topology inference in the non-stationary network. First, we propose an end-to-end measurement method named three-packet to accurately probe the three-leaf-nodes subset structures of the network without the assumption that the packet delay or loss follows a stable distribution. Second, we propose a metric for the shared path length based on the structural characteristics of the subset structures to fuse these subset structures into a correct complete topology. The analytical and simulation results show that our method is more applicable for topology inference in the non-stationary network compared with the existing methods.

Calabi–Yau structures and special Lagrangian submanifolds of complexified symmetric spaces

It is known that there exist Calabi–Yau structures on the complexifications of symmetric spaces of compact type. In this paper, we first construct explicit complete Ricci-flat Kaehler metrics (which give Calabi–Yau structures) for complexified symmetric spaces of arbitrary rank in terms of the Schwarz’s theorem. We consider the case where the Calabi–Yau structure arises from the generalized Stenzel metric. In the complexified symmetric spaces equipped with such a Calabi–Yau structure, we give constructions of special Lagrangian submanifolds of any given phase which are invariant under the actions of symmetric subgroups of the isometry group of the original symmetric space of compact type.

Canonical Kähler metrics on classes of Lorentzian 4-manifolds

Conditions for the existence of Kahler–Einstein metrics and central Kahler metrics (Maschler in Trans Am Math Soc 355:2161–2182, 2003) along with examples, both old and new, are given on classes of Lorentzian 4-manifolds with two distinguished vector fields. The results utilize the general construction (Aazami and Maschler in Kahler metrics via Lorentzian geometry in dimension four, Complex Manifolds 7:36–61 (2020) of Kahler metrics on such manifolds. The examples include both complete and incomplete metrics, and some reside on Lie groups associated with four types of Lie algebras. An appendix includes a similar construction for scalar-flat Kahler metrics.

A Topological Approach to Indices of Geometric Operators on Manifolds with Fibered Boundaries

In this paper, we investigate topological aspects of indices of twisted geometric operators on manifolds equipped with fibered boundaries. We define K-groups relative to the pushforward for boundary fibration, and show that indices of twisted geometric operators, defined by complete Phi or edge metrics, can be regarded as the index pairing over these K-groups. We also prove various properties of these indices using groupoid deformation techniques. Using these properties, we give an application to the localization problem of signature operators for singular fiber bundles.

Context-aware Modeling for Spatio-temporal Data Transmitted from a Wireless Body Sensor Network

Context-aware systems must be interoperable and work across different platforms at any time and in any place. Context data collected from wireless body area networks (WBAN) may be heterogeneous and imperfect, which makes their design and implementation difficult. In this research, we introduce a model which takes the dynamic nature of a context-aware system into consideration. This model is constructed according to the four-dimensional objects approach and three-dimensional events for the data collected from a WBAN. In order to support mobility and reasoning on temporal data transmitted from WBAN, a hierarchical model based on ontology is presented. It supports the relationship between heterogeneous environments and reasoning on the context data for extracting higher-level knowledge. Location is considered a temporal attribute. To support temporal entity, reification method and Allen’s algebra relations are used. Using reification, new classes Time_slice and Time_Interval and new attributes ts_time_slice and ts_time_Interval are defined in context-aware ontology. Then the thirteen logic relations of Allen such as Equal, After, Before is added by OWL-Time ontology to the properties. Integration and consistency of context-aware ontology are checked by the Pellet reasoner. This hybrid context-aware ontology is evaluated by three experts using the FOCA method based on the Goal-Question-Metrics (GQM) approach. This evaluation methodology diagnoses the ontology numerically and decreases the subjectivity and dependency on the evaluator’s experience. The overall performance quality according to completeness, adaptability, conciseness, consistency, computational efficiency and clarity metrics is 0.9137.

Engagement With a Digital Platform for Multimodal Cognitive Assessment and Multidomain Intervention in a Japanese Population: Pilot, Quasi-Experimental, Longitudinal Study.

BackgroundAs the global prevalence of dementia continues to rise, multidomain lifestyle interventions that address modifiable risk factors associated with pathological cognitive decline are increasing. Although some digital options have been developed to increase the reach and scalability of these programs, because of cultural differences, the efficacy of the programs in one population cannot easily be generalized to populations in other countries.ObjectiveThis investigation aimed to examine the usability and engagement of a digitally delivered multidomain cognitive lifestyle intervention developed in the United States for a Japanese population.MethodsThis feasibility investigation utilized a quasi-experimental, single-arm, nonrandomized, longitudinal design where participants engaged in the behavioral intervention on a smartphone. Of the 559 participants that initially enrolled (age: mean 51 years, SD 7.5 years; 51.7% female [289/559]), 242 completed the final testing trial. Participants enrolled in a multidomain lifestyle program that consisted of (1) psychoeducational material, (2) physical activity tracker, (3) nutrition tracker, (4) audio-based meditations, and (5) health coaching. Engagement with the program was assessed through the total number of app sessions and the use of the exercise, diet, and meditation tracking features within the app. The total number of minutes exercised was collected through subjective user inputs, and nutrition was quantified by the Mediterranean-DASH Intervention for Neurodegenerative Delay diet adherence score.ResultsSignificant relationships existed between overall nutrition score and frequency of nutrition tracking (r=0.18), frequency of physical activity tracking (r=0.19), and the total number of minutes exercised (r=0.22). Total minutes exercised was significantly correlated with total app sessions (r=0.57), frequency of physical activity tracking (r=0.85), frequency of nutrition tracking (r=0.64), number of times participants meditated (r=0.46), and total lessons read (r=0.36). The number of completed lessons was significantly related to frequency of physical activity tracking (r=0.40), frequency of nutrition tracking (r=0.43), the total number of times participants meditated (r=0.35), and total minutes exercised (r=0.33). Dividing the cohort into two groups based on lesson completion (<10 lessons completed vs ≥10 lessons completed), significant differences were observed between the total minutes exercised, frequency of physical activity tracking, frequency of nutrition tracking, and total number of times participants meditated (all P values <.01).ConclusionsOverall, this cross-cultural feasibility study in Japanese users demonstrated that the various engagement metrics were significantly correlated, and greater engagement was related to improved nutrition scores and increased time exercising. In addition, the relationships between lesson completion and other engagement metrics suggest that there may be value in exploring mechanisms that enhance lesson completion. Future research should examine the program in randomized control trials to more rigorously evaluate program efficacy.

Convergence of metric two-level measure spaces

We extend the notion of metric measure spaces to so-called metric two-level measure spaces (m2m spaces): An m2m space (X,r,ν) is a Polish metric space (X,r) equipped with a two-level measure ν∈Mf(Mf(X)), i.e. a finite measure on the set of finite measures on X. We introduce a topology on the set of (equivalence classes of) m2m spaces induced by certain test functions (i.e. the initial topology with respect to these test functions) and show that this topology is Polish by providing a complete metric. The framework introduced in this article is motivated by possible applications in biology. It is well suited for modeling the random evolution of the genealogy of a population in a hierarchical system with two levels, for example, host–parasite systems or populations which are divided into colonies. As an example we apply our theory to construct a random m2m space modeling the genealogy of a nested Kingman coalescent.

Does the innovative 4R Care Delivery Model improve timing and sequencing of guideline recommended breast cancer care in safety net and non-safety net centers?

36 Background: Under the NCI ASCO Teams Project, we proposed a 4R Model which enables patient (pt) and care team to manage timing and sequencing of interdependent care with a novel multimodality 4R Care Project Plan (Trosman JOP ’16). 4R (Right Info/Care/Patient/Time) was previously piloted at 3 Chicago centers (Weldon ASCO ‘18). Methods: A new study tested impact of 4R on timing and sequencing of guideline recommended care at 4 safety net and 3 non safety net US centers. 4R Plans were provided to stage 0-III breast cancer pts Jan - Nov’18, 4R cohort. Clinical and pt reported data analyses compared 4R cohort (N = 105) to a historical control cohort of pts who received care pre-4R, Jan - Dec ’17 (N = 190). Results: We significantly improved 3 referral metrics and 4 referral completion metrics - receipt of care by pts who were referred (Table). After referrals, safety net pts had a significant increase in 4R vs control cohort in receiving genetic consult (72%, 21/29 vs. 42%, 18/43, p = .02) and dental visit (100%, 6/6 vs. 20%, 1/5, p = .02). They had lower increases in flu shot referrals (41%, 24/58, vs 36%, 37/104, NS) and dental referrals (10%, 6/58, vs 5%, 5/104, NS) than non safety net pts who had significant increases. Other metrics improved at a similar rate for safety net and non safety net pts. Conclusions: 4R markedly improved referral and receipt of interdependent guideline recommended breast cancer care. For most metrics safety net pts benefited from 4R at a similar or higher rate than non safety net pts, indicating that 4R may reduce care disparities. Low increases in referrals for safety net pts and in trial referral/enrollment for all pts must be addressed. An expansion of 4R across the US continues this work. [Table: see text]

Prescribed Schouten Tensor in Locally Conformally Flat Manifolds

We consider the pseudo-Euclidean space ({mathbb {R}}^n,g), with n ge 3 and g_{ij} = delta _{ij} varepsilon _{i}, where varepsilon _{i} = pm 1, with at least one positive varepsilon _{i} and non-diagonal symmetric tensors T = sum nolimits _{i,j}f_{ij}(x) dx_i otimes dx_{j} . Assuming that the solutions are invariant by the action of a translation (n-1)- dimensional group, we find the necessary and sufficient conditions for the existence of a metric bar{g} conformal to g, such that the Schouten tensor bar{g}, is equal to T. From the obtained results, we show that for certain functions h, defined in mathbb {R}^{n}, there exist complete metrics bar{g}, conformal to the Euclidean metric g, whose curvature sigma _{2}(bar{g}) = h.

Ideal polyhedral surfaces in Fuchsian manifolds

Let S_{g,n} be a surface of genus g > 1 with n>0 punctures equipped with a complete hyperbolic cusp metric. Then it can be uniquely realized as the boundary metric of an ideal Fuchsian polyhedron. In the present paper we give a new variational proof of this result. We also give an alternative proof of the existence and uniqueness of a hyperbolic polyhedral metric with prescribed curvature in a given conformal class.

Pinpointing Morphology and Projection of Excitatory Neurons in Mouse Visual Cortex.

The excitatory neurons in the visual cortex are of great significance for us in understanding brain functions. However, the diverse neuron types and their morphological properties have not been fully deciphered. In this paper, we applied the brain-wide positioning system (BPS) to image the entire brain of two Thy1-eYFP H-line male mice at 0.2 μm × 0.2 μm × 1 μm voxel resolution. A total of 103 neurons were reconstructed in layers 5 and 6 of the visual cortex with single-axon-level resolution. Based on the complete topology of neurons and the inherent positioning function of the imaging method, we classified the observed neurons into six types according to their apical dendrites and somata location: star pyramidal cells in layer 5 (L5-sp), slender-tufted pyramidal cells in layer 5 (L5-st), tufted pyramidal cells in layer 5 (L5-tt), spiny stellate-like cells in layer 6 (L6-ss), star pyramidal cells in layer 6 (L6-sp), and slender-tufted pyramidal cells in layer 6 (L6-st). By examining the axonal projection patterns of individual neurons, they can be categorized into three modes: ipsilateral circuit connection neurons, callosal projection neurons and corticofugal projection neurons. Correlating the two types of classifications, we have found that there are at least two projection modes comprised in the former defined neuron types except for L5-tt. On the other hand, each projection mode may consist of four dendritic types defined in this study. The axon projection mode only partially correlates with the apical dendrite feature. This work has demonstrated a paradigm for resolving the visual cortex through single-neuron-level quantification and has shown potential to be extended to reveal the connectome of other defined sensory and motor systems.

Johnson’s Theorem on Banach–Jordan Systems

The goal of this paper consists of proving the inclusion of separating subspace of epimorphisms onto a Banach–Jordan system (pair or algebra) in its Jacobson radical. This yields Johnson’s Theorem for epimorphisms onto Banach–Jordan systems, and consequently the uniqueness of their complete norm topology.

Metrics on sets of interval partitions with diversity

We first consider interval partitions whose complements are Lebesgue-null and introduce a complete metric that induces the same topology as the Hausdorff distance (between complements). This is done using correspondences between intervals. Further restricting to interval partitions with $\alpha $-diversity, we then adjust the metric to incorporate diversities. We show that this second metric space is Lusin. An important feature of this topology is that path-continuity in this topology implies the continuous evolution of diversities. This is important in related work on tree-valued stochastic processes where diversities are branch lengths.

Invariant Ricci-flat metrics of cohomogeneity one with Wallach spaces as principal orbits

We construct a continuous 1-parameter family of smooth complete Ricci-flat metrics of cohomogeneity one on vector bundles over $\mathbb{CP}^2$, $\mathbb{HP}^2$ and $\mathbb{OP}^2$ with respective principal orbits $G/K$ the Wallach spaces $SU(3)/T^2$, $Sp(3)/(Sp(1)Sp(1)Sp(1))$ and $F_4/\mathrm{spin}(8)$. Almost all the Ricci-flat metrics constructed have generic holonomy. The only exception is the complete $G_2$ metric discovered in [BS89][GPP90]. It lies in the interior of the 1-parameter family on $\bigwedge_-^2\mathbb{CP}^2$. All the Ricci-flat metrics constructed have asymptotically conical limits given by the metric cone over a suitable multiple of the normal Einstein metric on $G/K$.