Defining bacterial species in the genomic era : insights from the genus Acinetobacter

Background: Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data. Results: In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species. Conclusion: We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin’s vision of classification becoming, as far as is possible, genealogical

Spin Lefschetz fibrations are abundant

We prove that any finitely presented group can be realized as the fundamental group of a spin Lefschetz fibration over the 2-sphere. We moreover show that any admissible lattice point in the symplectic geography plane below the Noether line can be realized by a simply-connected spin Lefschetz fibration.Comment: 15 pages, several figures in color, corrected typo

Impact of self-heating on the statistical variability in bulk and SOI FinFETs

In this paper for the first time we study the impact of self-heating on the statistical variability of bulk and SOI FinFETs designed to meet the requirements of the 14/16nm technology node. The simulations are performed using the GSS ‘atomistic’ simulator GARAND using an enhanced electro-thermal model that takes into account the impact of the fin geometry on the thermal conductivity. In the simulations we have compared the statistical variability obtained from full-scale electro-thermal simulations with the variability at uniform room temperature and at the maximum or average temperatures obtained in the electro-thermal simulations. The combined effects of line edge roughness and metal gate granularity are taken into account. The distributions and the correlations between key figures of merit including the threshold voltage, on-current, subthreshold slope and leakage current are presented and analysed

Comment on Phys. Rev. B 83, 054515 (2011) by V. G. Kogan and J. Schmalian and comment on their reply Phys. Rev. B 86, 016502 (2012)

The recent paper by V. G. Kogan and J. Schmalian Phys. Rev. B 83, 054515 (2011) argues that the widely used two-component Ginzburg-Landau (GL) models are not correct, and further concludes that in the regime which is described by a GL theory there could be no disparity in the coherence lengths of two superconducting components. This would in particular imply that (in contrast to $U(1)\times U(1)$ superconductors), there could be no "type-1.5" superconducting regime in U(1) multiband systems for any finite interband coupling strength. We point out that these claims are incorrect and based on an erroneous scheme of reduction of a two-component GL theory. We also attach a separate rejoinder on reply by Kogan and Schmalian. In their reply Phys. Rev. B 86, 016502 (2012) to our comment Phys. Rev. B 86, 016501 (2012) Kogan and Schmalian did not refute or, indeed, discuss the main points of criticism in the comment. Unfortunately they instead advance new incorrect claims regarding two-band and type-1.5 superconductivity. The main purpose of the attached rejoinder is to discuss these new incorrect claims.Comment: v3: a comment on reply by Kogan and Schmalian is include

On the connectivity of graph Lipscomb's space

A central role in topological dimension theory is played by Lipscomb's space $J_{A}$ since it is a universal space for metric spaces of weight $|A|\geq \aleph _{0}$. On the one hand, Lipscomb's space is the attractor of a possibly infinite iterated function system, i.e. it is a generalized Hutchinson-Barnsley fractal. As, on the other hand, some classical fractal sets are universal spaces, one can conclude that there exists a strong connection between topological dimension theory and fractal set theory. A generalization of Lipscomb's space, using graphs, has been recently introduced (see R. Miculescu, A. Mihail, Graph Lipscomb's space is a generalized Hutchinson-Barnsley fractal, Aequat. Math., \textbf{96} (2022), 1141-1157). It is denoted by J_{A}^{\G} and it is called graph Lipscomb's space associated with the graph \G on the set $A$. It turns out that it is a topological copy of a generalized Hutchinson-Barnsley fractal. This paper provides a characterization of those graphs \G for which J_{A}^{\G} is connected. In the particular case when $A$ is finite, some supplementary characterizations are presented.Comment: 13 page

Asymptotic behavior of the number of Eulerian orientations of graphs

We consider the class of simple graphs with large algebraic connectivity (the second-smallest eigenvalue of the Laplacian matrix). For this class of graphs we determine the asymptotic behavior of the number of Eulerian orientations. In addition, we establish some new properties of the Laplacian matrix, as well as an estimate of a conditionality of matrices with the asymptotic diagonal predominanceComment: arXiv admin note: text overlap with arXiv:1104.304

Quantum wire junctions breaking time reversal invariance

We explore the possibility to break time reversal invariance at the junction of quantum wires. The universal features in the bulk of the wires are described by the anyon Luttinger liquid. A simple necessary and sufficient condition for the breaking of time reversal invariance is formulated in terms of the scattering matrix at the junction. The phase diagram of a junction with generic number of wires is investigated in this framework. We give an explicit classification of those critical points which can be reached by bosonization and study the interplay between their stability and symmetry content.Comment: Extended version (Appendices C and D and some references added, typos corrected) to appear in Phys. Rev.

A Microfluidic Platform for Precision Small-volume Sample Processing and Its Use to Size Separate Biological Particles with an Acoustic Microdevice.

A major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. However, to achieve robust sample manipulation it is necessary to address device integration with the macroscale environment. To realize repeatable, sensitive particle separation with microfluidic devices, this protocol presents a complete automated and integrated microfluidic platform that enables precise processing of 0.15-1.5 ml samples using microfluidic devices. Important aspects of this system include modular device layout and robust fixtures resulting in reliable and flexible world to chip connections, and fully-automated fluid handling which accomplishes closed-loop sample collection, system cleaning and priming steps to ensure repeatable operation. Different microfluidic devices can be used interchangeably with this architecture. Here we incorporate an acoustofluidic device, detail its characterization, performance optimization, and demonstrate its use for size-separation of biological samples. By using real-time feedback during separation experiments, sample collection is optimized to conserve and concentrate sample. Although requiring the integration of multiple pieces of equipment, advantages of this architecture include the ability to process unknown samples with no additional system optimization, ease of device replacement, and precise, robust sample processing

ARMC 5 Variants and Risk of Hypertension in Blacks: MH- GRID Study.

Background We recently found that ARMC 5 variants may be associated with primary aldosteronism in blacks. We investigated a cohort from the MH - GRID (Minority Health Genomics and Translational Research Bio-Repository Database) and tested the association between ARMC 5 variants and blood pressure in black s. Methods and Results Whole exome sequencing data of 1377 black s were analyzed. Target single-variant and gene-based association analyses of hypertension were performed for ARMC 5, and replicated in a subset of 3015 individuals of African descent from the UK Biobank cohort. Sixteen rare variants were significantly associated with hypertension ( P=0.0402) in the gene-based (optimized sequenced kernel association test) analysis; the 16 and one other, rs116201073, together, showed a strong association ( P=0.0003) with blood pressure in this data set. The presence of the rs116201073 variant was associated with lower blood pressure. We then used human embryonic kidney 293 and adrenocortical H295R cells transfected with an ARMC 5 construct containing rs116201073 (c.*920T>C). The latter was common in both the discovery ( MH - GRID ) and replication ( UK Biobank) data and reached statistical significance ( P=0.044 [odds ratio, 0.7] and P=0.007 [odds ratio, 0.76], respectively). The allele carrying rs116201073 increased levels of ARMC5 mRNA , consistent with its protective effect in the epidemiological data. Conclusions ARMC 5 shows an association with hypertension in black s when rare variants within the gene are considered. We also identified a protective variant of the ARMC 5 gene with an effect on ARMC 5 expression confirmed in vitro. These results extend our previous report of ARMC 5's possible involvement in the determination of blood pressure in blacks

Lattice fence and hedge barriers around an apiary increase honey bee flight height and decrease stings to people nearby

Urban beekeeping is becoming more popular in the UK. One of the challenges faced by urban beekeepers is finding a suitable apiary location. Honey bees are often perceived as a nuisance, mainly due to their stinging behaviour. Here, we experimentally test the assumption that barriers around an apiary such as walls or fences, force the bees to fly above human height, thereby reducing collisions with people and, consequently, stinging. The experiment was conducted in two apiaries using two common types of barrier: a lattice fence (trellis) and hedge. Barriers were 2 m high, which is taller than > 99% of humans and is also the maximum height allowed by UK planning regulations for garden fences or walls. We found that barriers were effective at both raising the mean honey bee flight height and reducing stinging. However, the effects were only seen when the barrier had been in place for a few days, not immediately after the barrier was put in place. Although this raises interesting questions regarding honey bee navigation and memory, it is not a problem for beekeepers, as any barrier placed around an apiary will be permanent. The effect of the barriers on raising bee flight height to a mean of c. 2.2-2.5 m was somewhat weak and inconsistent, probably because the bees flew high, mean of c. 1.6-2.0 m, even in the absence of a barrier. As barriers can also reduce wind exposure, improve security and are inexpensive, we recommend their use around urban apiaries in places such as private gardens or allotments, where nuisance to humans is likely to be a problem