A Fast and Efficient Incremental Approach toward Dynamic Community Detection

Community detection is a discovery tool used by network scientists to analyze the structure of real-world networks. It seeks to identify natural divisions that may exist in the input networks that partition the vertices into coherent modules (or communities). While this problem space is rich with efficient algorithms and software, most of this literature caters to the static use-case where the underlying network does not change. However, many emerging real-world use-cases give rise to a need to incorporate dynamic graphs as inputs. In this paper, we present a fast and efficient incremental approach toward dynamic community detection. The key contribution is a generic technique called $\Delta-screening$, which examines the most recent batch of changes made to an input graph and selects a subset of vertices to reevaluate for potential community (re)assignment. This technique can be incorporated into any of the community detection methods that use modularity as its objective function for clustering. For demonstration purposes, we incorporated the technique into two well-known community detection tools. Our experiments demonstrate that our new incremental approach is able to generate performance speedups without compromising on the output quality (despite its heuristic nature). For instance, on a real-world network with 63M temporal edges (over 12 time steps), our approach was able to complete in 1056 seconds, yielding a 3x speedup over a baseline implementation. In addition to demonstrating the performance benefits, we also show how to use our approach to delineate appropriate intervals of temporal resolutions at which to analyze an input network

How to Deal with Weak Interactions in Noncovalent Complexes Analyzed by Electrospray Mass Spectrometry: Cyclopeptidic Inhibitors of the Nuclear Receptor Coactivator 1-STAT6

Mass spectrometry, and especially electrospray ionization, is now an efficient tool to study noncovalent interactions between proteins and inhibitors. It is used here to study the interaction of some weak inhibitors with the NCoA-1/STAT6 protein with KD values in the μM range. High signal intensities corresponding to some nonspecific electrostatic interactions between NCoA-1 and the oppositely charged inhibitors were observed by nanoelectrospray mass spectrometry, due to the use of high ligand concentrations. Diverse strategies have already been developed to deal with nonspecific interactions, such as controlled dissociation in the gas phase, mathematical modeling, or the use of a reference protein to monitor the appearance of nonspecific complexes. We demonstrate here that this last methodology, validated only in the case of neutral sugar–protein interactions, i.e., where dipole–dipole interactions are crucial, is not relevant in the case of strong electrostatic interactions. Thus, we developed a novel strategy based on half-maximal inhibitory concentration (IC50) measurements in a competitive assay with readout by nanoelectrospray mass spectrometry. IC50 values determined by MS were finally converted into dissociation constants that showed very good agreement with values determined in the liquid phase using a fluorescence polarization assay

Understanding the risk of emerging bacterial resistance to over the counter antibiotics in topical sore throat medicines

Aims The aims of this study were to explore the development of bacterial resistance and cross‐resistance in four common human pathogens following realistic exposure to antibiotics found in over‐the‐counter (OTC) sore throat medicines: gramicidin, neomycin, bacitracin and tyrothricin. Methods and Results Bacterial exposure to in‐use (concentration in the product before use) and diluted concentration (i.e. during use ) of antibiotic where conducted in broth for 24 h or until growth was visible. The changes in bacterial susceptibility profile before and after exposure was determined using standardized ISO microdilution broth. Antibiotic testing was performed according to EUCAST guidelines. We demonstrated that test bacteria were able to survive exposure to the in‐use concentrations of some antibiotics used in OTC medicines. Exposure to during use concentrations of bacitracin resulted in stable increase in minimal inhibitory concentration (MIC) (>8‐fold) in Staphylococcus aureus and Acinetobacter baumannii . Exposure to tyrothricin resulted in a stable increase in MIC (2·4‐fold) in Klebsiella pneumoniae , and exposure to neomycin resulted in a stable increase MIC (5000‐fold higher than the baseline) in Streptococcus pyogenes . Clinical cross‐resistance to other antibiotics (ciprofloxacin, fusidic acid, gentamicin, cefpodoxime, amoxicillin/clavulanic acid and cefotaxime) was also demonstrated following exposure to bacitracin or tyrothricin. Bacitracin exposure lead to a stable bacterial resistance after 10 passages. Conclusions Our results indicate that OTC antibiotic medicines have the potential to drive resistance and cross‐resistance in vitro . Significance and Impact of the Study Tackling antibiotic resistance is a high worldwide priority. It is widely accepted that the overuse and misuse of antibiotics increase the risk of the development and spread of antibiotic resistance within communities. A number of OTC sore throat products, widely available across the world for topical use in respiratory indications, contain locally delivered antibiotics. Our findings showed that these antibiotics in OTC medicines present a risk for emerging cross‐resistance in a number of bacterial respiratory pathogens

The mutual interplay of gut microbiota, diet and human disease

The intestinal milieu harbours the gut microbiota, consisting of a complex community of bacteria, archaea, fungi, viruses, and protozoans that bring to the host organism an endowment of cells and genes more numerous than its own. In the last ten years, mounting evidence has highlighted the prominent influence of the gut mutualistic bacterial communities on human health. Microbial colonization occurs alongside with immune system development and plays a role in intestinal physiology. The community of the gut microbiota does not undergo significant fluctuations throughout adult life. However, bacterial infections, antibiotic treatment, lifestyle, surgery, and diet might profoundly affect it. Gut microbiota dysbiosis, defined as marked alterations in the amount and function of the intestinal microorganisms, is correlated with the aetiology of chronic non-communicable diseases, ranging from cardiovascular, neurologic, respiratory, and metabolic illnesses to cancer. In this review, we focus on the interplay among gut microbiota, diet, and host to provide a perspective on the role of microbiota and their unique metabolites in the pathogenesis and/or progression of various human disorders. We discuss interventions based on microbiome studies, i.e. faecal microbiota transplantation, probiotics, and prebiotics, to introduce the concept that correcting gut dysbiosis can ameliorate disease symptoms, thus offering a new approach toward disease treatment

Holonomic functions of several complex variables and singularities of anisotropic Ising n-fold integrals

Lattice statistical mechanics, often provides a natural (holonomic) framework to perform singularity analysis with several complex variables that would, in a general mathematical framework, be too complex, or could not be defined. Considering several Picard-Fuchs systems of two-variables "above" Calabi-Yau ODEs, associated with double hypergeometric series, we show that holonomic functions are actually a good framework for actually finding the singular manifolds. We, then, analyse the singular algebraic varieties of the n-fold integrals $\chi^{(n)}$, corresponding to the decomposition of the magnetic susceptibility of the anisotropic square Ising model. We revisit a set of Nickelian singularities that turns out to be a two-parameter family of elliptic curves. We then find a first set of non-Nickelian singularities for $\chi^{(3)}$ and $\chi^{(4)}$, that also turns out to be rational or ellipic curves. We underline the fact that these singular curves depend on the anisotropy of the Ising model. We address, from a birational viewpoint, the emergence of families of elliptic curves, and of Calabi-Yau manifolds on such problems. We discuss the accumulation of these singular curves for the non-holonomic anisotropic full susceptibility.Comment: 36 page

Near-forward Raman scattering by bulk and surface phonon-polaritons in the model percolation-type ZnBeSe alloy

We study the bulk and surface phonon-polaritons of the Zn0.67Be0.33Se zincblende alloy by near-forward Raman scattering. The short (Be-Se) bond exhibits a distinct percolation doublet in the conventional backscattering Raman spectra, corresponding to a three-mode behavior in total [1(Zn-Se),2(Be-Se)] for Zn0.67Be0.33Se. This offers an opportunity to achieve a refined understanding of the phonon-polariton modes of a zincblende alloy beyond the current two-mode approximation, corresponding to a [1(Zn-Se),1(Be-Se)] description in the present case. The discussion is supported by contour modeling of the Raman signals of the multi-mode bulk and surface phonon-polaritons within the formalism of the linear dielectric response

On the Symmetries of Integrability

We show that the Yang-Baxter equations for two dimensional models admit as a group of symmetry the infinite discrete group $A_2^{(1)}$. The existence of this symmetry explains the presence of a spectral parameter in the solutions of the equations. We show that similarly, for three-dimensional vertex models and the associated tetrahedron equations, there also exists an infinite discrete group of symmetry. Although generalizing naturally the previous one, it is a much bigger hyperbolic Coxeter group. We indicate how this symmetry can help to resolve the Yang-Baxter equations and their higher-dimensional generalizations and initiate the study of three-dimensional vertex models. These symmetries are naturally represented as birational projective transformations. They may preserve non trivial algebraic varieties, and lead to proper parametrizations of the models, be they integrable or not. We mention the relation existing between spin models and the Bose-Messner algebras of algebraic combinatorics. Our results also yield the generalization of the condition $q^n=1$ so often mentioned in the theory of quantum groups, when no $q$ parameter is available.Comment: 23 page

The diagonal Ising susceptibility

We use the recently derived form factor expansions of the diagonal two-point correlation function of the square Ising model to study the susceptibility for a magnetic field applied only to one diagonal of the lattice, for the isotropic Ising model. We exactly evaluate the one and two particle contributions $\chi_{d}^{(1)}$ and $\chi_{d}^{(2)}$ of the corresponding susceptibility, and obtain linear differential equations for the three and four particle contributions, as well as the five particle contribution ${\chi}^{(5)}_d(t)$, but only modulo a given prime. We use these exact linear differential equations to show that, not only the russian-doll structure, but also the direct sum structure on the linear differential operators for the $n$-particle contributions $\chi_{d}^{(n)}$ are quite directly inherited from the direct sum structure on the form factors $f^{(n)}$. We show that the $n^{th}$ particle contributions $\chi_{d}^{(n)}$ have their singularities at roots of unity. These singularities become dense on the unit circle $|\sinh2E_v/kT \sinh 2E_h/kT|=1$ as $n\to \infty$.Comment: 18 page

Critical manifold of the kagome-lattice Potts model

Any two-dimensional infinite regular lattice G can be produced by tiling the plane with a finite subgraph B of G; we call B a basis of G. We introduce a two-parameter graph polynomial P_B(q,v) that depends on B and its embedding in G. The algebraic curve P_B(q,v) = 0 is shown to provide an approximation to the critical manifold of the q-state Potts model, with coupling v = exp(K)-1, defined on G. This curve predicts the phase diagram both in the ferromagnetic (v>0) and antiferromagnetic (v<0) regions. For larger bases B the approximations become increasingly accurate, and we conjecture that P_B(q,v) = 0 provides the exact critical manifold in the limit of infinite B. Furthermore, for some lattices G, or for the Ising model (q=2) on any G, P_B(q,v) factorises for any choice of B: the zero set of the recurrent factor then provides the exact critical manifold. In this sense, the computation of P_B(q,v) can be used to detect exact solvability of the Potts model on G. We illustrate the method for the square lattice, where the Potts model has been exactly solved, and the kagome lattice, where it has not. For the square lattice we correctly reproduce the known phase diagram, including the antiferromagnetic transition and the singularities in the Berker-Kadanoff phase. For the kagome lattice, taking the smallest basis with six edges we recover a well-known (but now refuted) conjecture of F.Y. Wu. Larger bases provide successive improvements on this formula, giving a natural extension of Wu's approach. The polynomial predictions are in excellent agreement with numerical computations. For v>0 the accuracy of the predicted critical coupling v_c is of the order 10^{-4} or 10^{-5} for the 6-edge basis, and improves to 10^{-6} or 10^{-7} for the largest basis studied (with 36 edges).Comment: 31 pages, 12 figure