Search results for "c space"

2016

AbstractThe different factors involved in the growth process of complex networks imprint valuable information in their observable topologies. How to exploit this information to accurately predict structural network changes is the subject of active research. A recent model of network growth sustains that the emergence of properties common to most complex systems is the result of certain trade-offs between node birth-time and similarity. This model has a geometric interpretation in hyperbolic space, where distances between nodes abstract this optimisation process. Current methods for network hyperbolic embedding search for node coordinates that maximise the likelihood that the network was pro…

The latent geometry of the human protein interaction network

2017

Abstract Motivation A series of recently introduced algorithms and models advocates for the existence of a hyperbolic geometry underlying the network representation of complex systems. Since the human protein interaction network (hPIN) has a complex architecture, we hypothesized that uncovering its latent geometry could ease challenging problems in systems biology, translating them into measuring distances between proteins. Results We embedded the hPIN to hyperbolic space and found that the inferred coordinates of nodes capture biologically relevant features, like protein age, function and cellular localization. This means that the representation of the hPIN in the two-dimensional hyperboli…

Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family

2017

AbstractWe introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the …

2,4-D impact on bacterial communities, and the activity and genetic potential of 2,4-D degrading communities in soil

2006

The key role of telluric microorganisms in pesticide degradation is well recognized but the possible relationships between the biodiversity of soil microbial communities and their functions still remain poorly documented. If microorganisms influence the fate of pesticides, pesticide application may reciprocally affect soil microorganisms. The objective of our work was to estimate the impact of 2,4-D application on the genetic structure of bacterial communities and the 2,4-D-degrading genetic potential in relation to 2,4-D mineralization. Experiments combined isotope measurements with molecular analyses. The impact of 2,4-D on soil bacterial populations was followed with ribosomal intergenic…

Effect of ferritin overexpression in tobacco on the structure of bacterial and pseudomonad communities associated with the roots

2006

The genetic structures of total bacterial and pseudomonad communities were characterized in rhizosphere soil and rhizoplane+root tissues of tobacco wild type and a ferritin overexpressor transgenic line (P6) by a cultivation-independent method using directly extracted DNA at the end of three consecutive plant cultures. The structure of total bacterial communities was characterized by automated ribosomal intergenic spacer analysis (A-RISA), and that of pseudomonad communities was characterized by PCR-restriction fragment length polymorphism (PCR-RFLP) from DNA amplified with specific primers. The structure of total bacterial communities was significantly modified in the rhizosphere soil by t…

Field and microcosm experiments to evaluate the effects of agricultural Cu treatment on the density and genetic structure of microbial communities in…

2006

The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO(4), Ca(OH)(2)] at the standard rate used in viticulture (B1=16 kg Cu kg(-1) soil) and at a higher level of contamination (B3=48 kg Cu ha(-1) soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modi…

Space-filling vs. Luzin's condition (N)

2013

Let us assume that we are given two metric spaces, where the Hausdorff dimension of the first space is strictly smaller than the one of the second space. Suppose further that the first space has sigma-finite measure with respect to the Hausdorff measure of the corresponding dimension. We show for quite general metric spaces that for any measurable surjection from the first onto the second space, there is a set of measure zero that is mapped to a set of positive measure (both measures are the Hausdorff measures corresponding to the Hausdorff dimension of the first space). We also study more general situations where the measures on the two metric spaces are not necessarily the same and not ne…

Isometric embeddings of snowflakes into finite-dimensional Banach spaces

2016

We consider a general notion of snowflake of a metric space by composing the distance by a nontrivial concave function. We prove that a snowflake of a metric space $X$ isometrically embeds into some finite-dimensional normed space if and only if $X$ is finite. In the case of power functions we give a uniform bound on the cardinality of $X$ depending only on the power exponent and the dimension of the vector space.

Duality of moduli in regular toroidal metric spaces

2020

We generalize a result of Freedman and He [4, Theorem 2.5], concerning the duality of moduli and capacities in solid tori, to sufficiently regular metric spaces. This is a continuation of the work of the author and Rajala [12] on the corresponding duality in condensers. peerReviewed

Sharp capacity estimates for annuli in weighted R^n and in metric spaces

2017

We obtain estimates for the nonlinear variational capacity of annuli in weighted R^n and in metric spaces. We introduce four different (pointwise) exponent sets, show that they all play fundamental roles for capacity estimates, and also demonstrate that whether an end point of an exponent set is attained or not is important. As a consequence of our estimates we obtain, for instance, criteria for points to have zero (resp. positive) capacity. Our discussion holds in rather general metric spaces, including Carnot groups and many manifolds, but it is just as relevant on weighted R^n. Indeed, to illustrate the sharpness of our estimates, we give several examples of radially weighted R^n, which …