Motifs in Temporal Networks

Networks are a fundamental tool for modeling complex systems in a variety of domains including social and communication networks as well as biology and neuroscience. Small subgraph patterns in networks, called network motifs, are crucial to understanding the structure and function of these systems. However, the role of network motifs in temporal networks, which contain many timestamped links between the nodes, is not yet well understood. Here we develop a notion of a temporal network motif as an elementary unit of temporal networks and provide a general methodology for counting such motifs. We define temporal network motifs as induced subgraphs on sequences of temporal edges, design fast algorithms for counting temporal motifs, and prove their runtime complexity. Our fast algorithms achieve up to 56.5x speedup compared to a baseline method. Furthermore, we use our algorithms to count temporal motifs in a variety of networks. Results show that networks from different domains have significantly different motif counts, whereas networks from the same domain tend to have similar motif counts. We also find that different motifs occur at different time scales, which provides further insights into structure and function of temporal networks

Investigating the transcriptional regulation by OxyR in Porphyromonas gingivalis.

Periodontal diseases are bacterially induced, inflammatory diseases which are responsible for loss of alveolar bone and connective tissue supporting the teeth which results in loss of teeth. Gram negative anaerobic bacteria are highly associated with these diseases. One of them is Porphyromonas gingivalis belonging to the phylum Bacteroidetes. Infection by P. gingivalis is recurrent after physical removal of the bacteria from the oral cavity and even after antibiotic treatment as development of resistance is not rare. Hence complete understanding the biology of this bacterium is of significance. This gram negative obligate anaerobe, being aerotolerant, manages to survive inside the oral cavity, where oxidative stress is ubiquitous. Genome sequence of P. gingivalis shows the presence of a transcriptional regulator OxyR which is a homologue of OxyR present in E. coli. P. gingivalis OxyR induces the expression of antioxidant defense genes like sod, ahpC-F, dps to protect the bacteria from oxidative stress. Expression of P. gingivalis OxyR regulon is not very well understood. Microarray studies carried out in our lab using P. gingivalis W83 to study gene regulation by OxyR, indicated that several genes in P. gingivalis are co-regulated by iron-and OxyR. Literature also supports that in iron deplete conditions genes involved in oxidative stress are down-regulated. These studies formed the basis of our hypothesis that OxyR might regulate the genes in P. gingivalis in an iron dependent manner. To study the mechanism of regulation by P. gingivalis OxyR and to determine whether OxyR regulation is iron dependent, two approaches were applied - in vitro characterization of binding and in vivo characterization. First step of in vitro characterization was to perform CHIP-chip assay to determine OxyR-binding sites present on the genomic DNA of P. gingivalis. As this assay was performed under completely anaerobic conditions, the target fragments to which OxyR was found to bind during this assay were not same as reported in literature. These and the fragments reported in literature were used for EMSA. EMSAs carried out using crude cell lysates and in vitro OxyR protein preparations showed expected results but the results were not reproducible. In vivo expressed and purified P. gingivalis OxyR never bound to the target fragments used. Preparation of a stable protein preparation and improvement in the parameters of EMSA is very important to further investigate the binding in vitro. The second approach is based on in vivo characterization of binding. This requires tagging the P. gingivalis OxyR at its C-terminus with fluorescent protein to observe its binding to the target DNA sequences. Fluorescently tagged OxyR, is expected to emit fluorescence from a highly localized area to produce sharp fluorescent spots when it is bound to its target sequences. Unbound OxyR is expected to emit a fluorescent signal which is spread over the entire area of the cell. This technique will help to determine the conditions under which OxyR binds to its target DNA sequences. This provides a means to confirm the results obtained from in vitro characterization instead of just extrapolating them

Soft Bootstrap and Supersymmetry

The soft bootstrap is an on-shell method to constrain the landscape of effective field theories (EFTs) of massless particles via the consistency of the low-energy S-matrix. Given assumptions on the on-shell data (particle spectra, linear symmetries, and low-energy theorems), the soft bootstrap is an efficient algorithm for determining the possible consistency of an EFT with those properties. The implementation of the soft bootstrap uses the recently discovered method of soft subtracted recursion. We derive a precise criterion for the validity of these recursion relations and show that they fail exactly when the assumed symmetries can be trivially realized by independent operators in the effective action. We use this to show that the possible pure (real and complex) scalar, fermion, and vector exceptional EFTs are highly constrained. Next, we prove how the soft behavior of states in a supermultiplet must be related and illustrate the results in extended supergravity. We demonstrate the power of the soft bootstrap in two applications. First, for the N= 1 and N=2 CP^1 nonlinear sigma models, we show that on-shell constructibility establishes the emergence of accidental IR symmetries. This includes a new on-shell perspective on the interplay between N=2 supersymmetry, low-energy theorems, and electromagnetic duality. We also show that N=2 supersymmetry requires 3-point interactions with the photon that make the soft behavior of the scalar O(1) instead of vanishing, despite the underlying symmetric coset. Second, we study Galileon theories, including aspects of supersymmetrization, the possibility of a vector-scalar Galileon EFT, and the existence of higher-derivative corrections preserving the enhanced special Galileon symmetry. This is addressed by soft bootstrap and by application of double-copy/KLT relations applied to higher-derivative corrections of chiral perturbation theory.Comment: 71 pages, no figures. v2: significant new material about the N=2 CP^1 NLSM; typos correcte

Spontaneous Symmetry Breaking and the Renormalization of the Chern-Simons Term

We calculate the one-loop perturbative correction to the coefficient of the \cs term in non-abelian gauge theory in the presence of Higgs fields, with a variety of symmetry-breaking structures. In the case of a residual $U(1)$ symmetry, radiative corrections do not change the coefficient of the \cs term. In the case of an unbroken non-abelian subgroup, the coefficient of the relevant \cs term (suitably normalized) attains an integral correction, as required for consistency of the quantum theory. Interestingly, this coefficient arises purely from the unbroken non-abelian sector in question; the orthogonal sector makes no contribution. This implies that the coefficient of the \cs term is a discontinuous function over the phase diagram of the theory.Comment: Version to be published in Phys Lett B., minor additional change

Detection of Circulating Filarial Antigen

Affinity binding to specific solid phase antibody, immune complex binding to Raji cells or PEG precipitation of immune complexes was used in conjunction with Western blotting to detect circulating filarial antigen in filarial sera. A high molecular weight antigen was present in free as well as complex form. PEG precipitation method revealed specific filarial antigens in the low molecular weight region also

Phase transitions in a gas of anyons

We continue our numerical Monte Carlo simulation of a gas of closed loops on a 3 dimensional lattice, however now in the presence of a topological term added to the action corresponding to the total linking number between the loops. We compute the linking number using certain notions from knot theory. Adding the topological term converts the particles into anyons. Using the correspondence that the model is an effective theory that describes the 2+1-dimensional Abelian Higgs model in the asymptotic strong coupling regime, the topological linking number simply corresponds to the addition to the action of the Chern-Simons term. We find the following new results. The system continues to exhibit a phase transition as a function of the anyon mass as it becomes small \cite{mnp}, although the phases do not change the manifestation of the symmetry. The Chern-Simons term has no effect on the Wilson loop, but it does affect the {\rm '}t Hooft loop. For a given configuration it adds the linking number of the 't Hooft loop with all of the dynamical vortex loops to the action. We find that both the Wilson loop and the 't Hooft loop exhibit a perimeter law even though there are no massless particles in the theory, which is unexpected.Comment: 6 pages, 5 figure

Increased serum levels of anti-filarial (IgA) antibodies in patients with tropical pulmonary eosinophilia

Tropical Pulmonary Eosinophilia (TPE) is diagnosed on the basis of high peripheral eosinophilia associated with clinical symptoms and signs. Elevated levels of total and antifilarial immunoglobulins is one of the characteristic features of TPE. Ten clinically diagnosed TPE patients and ten controls were compared for their anti-filarial and anti-ascaris antibody levels of classes IgG, IgM and IgA. While, IgG antibodies exhibited considerable cross reactivity between Ascaris and Filarial antigens, IgM antibodies showed nonspecific binding to filarial antigens. However, IgA antibodies were found to discriminate between TPE and control sera better than IgG and IgM antibodies

On the Coleman-Hill theorem

The Coleman-Hill theorem prohibits the appearance of radiative corrections to the topological mass (more precisely, to the parity-odd part of the vacuum polarization tensor at zero mementum) in a wide class of abelian gauge theories in 2+ 1 dimensions. We re-express the theorem in terms of the effective action rather than in terms of the vacuum polarization tensor. The theorem so restated becomes somewhat stronger: a known exception to the theorem, spontaneously broken scalar Chern-Simons electro-dynamics, obeys the new non-renormalization theorem. Whereas the vacuum polarization does receive a one-loop, parity--odd correction, this does not translate to a radiative contribution to the Chern-Simons term in the effective action. We also point out a new situation, involving scalar fields and parity-odd couplings, which was overlooked in the orginal analysis, where the conditions of the theorem are satisfied and where the topological mass does, in fact, get a radiative correction