Stein's method of exchangeable pairs in multivariate functional approximations

In this paper we develop a framework for multivariate functional approximation by a suitable Gaussian process via an exchangeable pairs coupling that satisfies a suitable approximate linear regression property, thereby building on work by Barbour (1990) and Kasprzak (2020). We demonstrate the applicability of our results by applying it to joint subgraph counts in an Erd\H{o}s-Renyi random graph model on the one hand and to vectors of weighted, degenerate $U$-processes on the other hand. As a concrete instance of the latter class of examples, we provide a bound for the functional approximation of a vector of success runs of different lengths by a suitable Gaussian process which, even in the situation of just a single run, would be outside the scope of the existing theory

A quantitative central limit theorem for linear statistics of random matrix eigenvalues

It is known that the fluctuations of suitable linear statistics of Haar distributed elements of the compact classical groups satisfy a central limit theorem. We show that if the corresponding test functions are sufficiently smooth, a rate of convergence of order almost $1/n$ can be obtained using a quantitative multivariate CLT for traces of powers that was recently proven using Stein's method of exchangeable pairs.Comment: Title modified; main result stated under slightly weaker conditions; accepted for publication in the Journal of Theoretical Probabilit

Fatal affairs - conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales

The roseobacter group of marine bacteria is characterized by a mosaic distribution of ecologically important phenotypes. These are often encoded on mobile extrachromosomal replicons. So far, conjugation had only been experimentally proven between the two model organisms Phaeobacter inhibens and Dinoroseobacter shibae. Here, we show that two large natural RepABC-type plasmids from D. shibae can be transferred into representatives of all known major Rhodobacterales lineages. Complete genome sequencing of the newly established Phaeobacter inhibens transconjugants confirmed their genomic integrity. The conjugated plasmids were stably maintained as single copy number replicons in the genuine as well as the new host. Co-cultivation of Phaeobacter inhibens and the transconjugants with the dinoflagellate Prorocentrum minimum demonstrated that Phaeobacter inhibens is a probiotic strain that improves the yield and stability of the dinoflagellate culture. The transconjugant carrying the 191 kb plasmid, but not the 126 kb sister plasmid, killed the dinoflagellate in co-culture

Analysis of silica-supported vanadia by X-ray absorption spectroscopy: Combined theoretical and experimental studies

In this study we combine density-functional theory (DFT) calculations on oxygen core excitations in vanadia-silica model clusters with in situ X-ray absorption fine structure (NEXAFS) measurements near the oxygen K-edge of vanadia model catalysts supported by silica SBA-15 in order to analyze structural details of the vanadia species. The silica support is found to contribute to the NEXAFS spectrum in an energy range well above that of the vanadium oxide units allowing a clear separation between the corresponding contributions. Further, differently coordinated oxygen which is characteristic for particular vanadia species, monomeric or non-monomeric, can be identified in the theoretical spectra consistent with the oxygen K-edge NEXAFS measurements. The comparison of the theoretical and experimental NEXAFS spectra provides clear evidence that under in situ conditions different molecular vanadia species, in particular non-monomeric VxOy, exist at the catalyst surface and the exclusive presence of monomeric vanadia groups can be ruled out. The present analysis goes beyond earlier work applying vibrational spectroscopy to the present systems where, as a result of extended vibrational coupling, a separation between vanadia, silica, and interface contributions was less successful

An evaluation of Bradfordizing effects

The purpose of this paper is to apply and evaluate the bibliometric method Bradfordizing for information retrieval (IR) experiments. Bradfordizing is used for generating core document sets for subject-specific questions and to reorder result sets from distributed searches. The method will be applied and tested in a controlled scenario of scientific literature databases from social and political sciences, economics, psychology and medical science (SOLIS, SoLit, USB Köln Opac, CSA Sociological Abstracts, World Affairs Online, Psyndex and Medline) and 164 standardized topics. An evaluation of the method and its effects is carried out in two laboratory-based information retrieval experiments (CLEF and KoMoHe) using a controlled document corpus and human relevance assessments. The results show that Bradfordizing is a very robust method for re-ranking the main document types (journal articles and monographs) in today’s digital libraries (DL). The IR tests show that relevance distributions after re-ranking improve at a significant level if articles in the core are compared with articles in the succeeding zones. The items in the core are significantly more often assessed as relevant, than items in zone 2 (z2) or zone 3 (z3). The improvements between the zones are statistically significant based on the Wilcoxon signed-rank test and the paired T-Test

Reconstruction and subsurface lattice distortions in the (2 × 1)O-Ni(110) structure: A LEED analysis

LEED analysis of the reconstructed (2 × 1)O-Ni(110) system clearly favors the “missing row” structure over the “saw-tooth” and “buckled row” models. By using a novel computational procedure 8 structural parameters could be refined simultaneously, leading to excellent R-factors (RZJ = 0.09, RP = 0.18). The adsorbed O atoms are located 0.2 Å above the long bridge sites in [001] direction, presumably with a slight displacement ( 0.1 Å) in [1 0] direction to an asymmetric adsorption site. The nearest-neighbor Ni---O bond lengths (1.77 Å) are rather short. The separation between the topmost two Ni layers is expanded to 1.30 Å (bulk value 1.25 Å), while that between the second and third layer is slightly contracted to 1.23 Å. The third layer is, in addition, slightly buckled (±0.05 Å). The results are discussed on the basis of our present general knowledge about the structure of adsorbate covered metallic surfaces

Author disambiguation using multi-aspect similarity indicators

Key to accurate bibliometric analyses is the ability to correctly link individuals to their corpus of work, with an optimal balance between precision and recall. We have developed an algorithm that does this disambiguation task with a very high recall and precision. The method addresses the issues of discarded records due to null data fields and their resultant effect on recall, precision and F-measure results. We have implemented a dynamic approach to similarity calculations based on all available data fields. We have also included differences in author contribution and age difference between publications, both of which have meaningful effects on overall similarity measurements, resulting in significantly higher recall and precision of returned records. The results are presented from a test dataset of heterogeneous catalysis publications. Results demonstrate significantly high average F-measure scores and substantial improvements on previous and stand-alone techniques

Gain and Loss of Phototrophic Genes Revealed by Comparison of Two Citromicrobium Bacterial Genomes

Proteobacteria are thought to have diverged from a phototrophic ancestor, according to the scattered distribution of phototrophy throughout the proteobacterial clade, and so the occurrence of numerous closely related phototrophic and chemotrophic microorganisms may be the result of the loss of genes for phototrophy. A widespread form of bacterial phototrophy is based on the photochemical reaction center, encoded by puf and puh operons that typically are in a ‘photosynthesis gene cluster’ (abbreviated as the PGC) with pigment biosynthesis genes. Comparison of two closely related Citromicrobial genomes (98.1% sequence identity of complete 16S rRNA genes), Citromicrobium sp. JL354, which contains two copies of reaction center genes, and Citromicrobium strain JLT1363, which is chemotrophic, revealed evidence for the loss of phototrophic genes. However, evidence of horizontal gene transfer was found in these two bacterial genomes. An incomplete PGC (pufLMC-puhCBA) in strain JL354 was located within an integrating conjugative element, which indicates a potential mechanism for the horizontal transfer of genes for phototrophy

Diverse Arrangement of Photosynthetic Gene Clusters in Aerobic Anoxygenic Phototrophic Bacteria

BACKGROUND: Aerobic anoxygenic photototrophic (AAP) bacteria represent an important group of marine microorganisms inhabiting the euphotic zone of the ocean. They harvest light using bacteriochlorophyll (BChl) a and are thought to be important players in carbon cycling in the ocean. METHODOLOGY/PRINCIPAL FINDINGS: Aerobic anoxygenic phototrophic (AAP) bacteria represent an important part of marine microbial communities. Their photosynthetic apparatus is encoded by a number of genes organized in a so-called photosynthetic gene cluster (PGC). In this study, the organization of PGCs was analyzed in ten AAP species belonging to the orders Rhodobacterales, Sphingomonadales and the NOR5/OM60 clade. Sphingomonadales contained comparatively smaller PGCs with an approximately size of 39 kb whereas the average size of PGCs in Rhodobacterales and NOR5/OM60 clade was about 45 kb. The distribution of four arrangements, based on the permutation and combination of the two conserved regions bchFNBHLM-LhaA-puhABC and crtF-bchCXYZ, does not correspond to the phylogenetic affiliation of individual AAP bacterial species. While PGCs of all analyzed species contained the same set of genes for bacteriochlorophyll synthesis and assembly of photosynthetic centers, they differed largely in the carotenoid biosynthetic genes. Spheroidenone, spirilloxanthin, and zeaxanthin biosynthetic pathways were found in each clade respectively. All of the carotenoid biosynthetic genes were found in the PGCs of Rhodobacterales, however Sphingomonadales and NOR5/OM60 strains contained some of the carotenoid biosynthetic pathway genes outside of the PGC. CONCLUSIONS/SIGNIFICANCE: Our investigations shed light on the evolution and functional implications in PGCs of marine aerobic anoxygenic phototrophs, and support the notion that AAP are a heterogenous physiological group phylogenetically scattered among Proteobacteria