Different approaches to community detection

A precise definition of what constitutes a community in networks has remained elusive. Consequently, network scientists have compared community detection algorithms on benchmark networks with a particular form of community structure and classified them based on the mathematical techniques they employ. However, this comparison can be misleading because apparent similarities in their mathematical machinery can disguise different reasons for why we would want to employ community detection in the first place. Here we provide a focused review of these different motivations that underpin community detection. This problem-driven classification is useful in applied network science, where it is important to select an appropriate algorithm for the given purpose. Moreover, highlighting the different approaches to community detection also delineates the many lines of research and points out open directions and avenues for future research.Comment: 14 pages, 2 figures. Written as a chapter for forthcoming Advances in network clustering and blockmodeling, and based on an extended version of The many facets of community detection in complex networks, Appl. Netw. Sci. 2: 4 (2017) by the same author

The structure of algebraic covariant derivative curvature tensors

We use the Nash embedding theorem to construct generators for the space of algebraic covariant derivative curvature tensors

Generalized modularity matrices

Various modularity matrices appeared in the recent literature on network analysis and algebraic graph theory. Their purpose is to allow writing as quadratic forms certain combinatorial functions appearing in the framework of graph clustering problems. In this paper we put in evidence certain common traits of various modularity matrices and shed light on their spectral properties that are at the basis of various theoretical results and practical spectral-type algorithms for community detection

Preparation of a Semiquinonate-Bridged Diiron(II) Complex and Elucidation of its Geometric and Electronic Structures

The synthesis and crystal structure of a diiron(II) complex containing a bridging semiquinonate radical are presented. The unique electronic structure of this S = 7/2 complex is examined with spectroscopic (absorption, EPR, resonance Raman) and computational methods

Synthesis and Spectroscopic Characterization of High-Spin Mononuclear Iron(II) \u3cem\u3ep\u3c/em\u3e-Semiquinonate Complexes

Two mononuclear iron(II) p-semiquinonate (pSQ) complexes have been generated via one-electron reduction of precursor complexes containing a substituted 1,4-naphthoquinone ligand. Detailed spectroscopic and computational analysis confirmed the presence of a coordinated pSQ radical ferromagnetically coupled to the high-spin FeII center. The complexes are intended to model electronic interactions between (semi)quinone and iron cofactors in biology

Structural, Spectroscopic, and Electrochemical Properties of Nonheme Fe(II)-Hydroquinonate Complexes: Synthetic Models of Hydroquinone Dioxygenases

Using the tris(3,5-diphenylpyrazol-1-yl)borate (Ph2Tp) supporting ligand, a series of mono- and dinuclear ferrous complexes containing hydroquinonate (HQate) ligands have been prepared and structurally characterized with X-ray crystallography. The monoiron(II) complexes serve as faithful mimics of the substrate-bound form of hydroquinone dioxygenases (HQDOs) – a family of nonheme Fe enzymes that catalyze the oxidative cleavage of 1,4-dihydroxybenzene units. Reflecting the variety of HQDO substrates, the synthetic complexes feature both mono- and bidentate HQate ligands. The bidentate HQates cleanly provide five-coordinate, high-spin Fe(II) complexes with the general formula [Fe(Ph2Tp)(HLX)] (1X), where HLX is a HQate(1-) ligand substituted at the 2-position with a benzimidazolyl (1A), acetyl (1B and 1C), or methoxy (1D) group. In contrast, the monodentate ligand 2,6-dimethylhydroquinone (H2LF) exhibited a greater tendency to bridge between two Fe(II) centers, resulting in formation of [Fe2(Ph2Tp)2(μ-LF)(MeCN)]·[2F(MeCN)]. However, addition of one equivalent of “free” pyrazole (Ph2pz) ligand provided the mononuclear complex, [Fe(Ph2Tp)(HLF)(Ph2pz)]·[1F(Ph2pz)], which is stabilized by an intramolecular hydrogen bond between the HLF and Ph2pz donors. Complex 1F(Ph2pz) represents the first crystallographically-characterized example of a monoiron complex bound to an untethered HQate ligand. The geometric and electronic structures of the Fe/HQate complexes were further probed with spectroscopic (UV-vis absorption, 1H NMR) and electrochemical methods. Cyclic voltammograms of complexes in the 1X series revealed an Fe-based oxidation between 0 and −300 mV (vs. Fc+/0), in addition to irreversible oxidation(s) of the HQate ligand at higher potentials. The one-electron oxidized species (1Xoxox) were examined with UV-vis absorption and electron paramagnetic resonance (EPR) spectroscopies

Encoding dynamics for multiscale community detection: Markov time sweeping for the Map equation

The detection of community structure in networks is intimately related to finding a concise description of the network in terms of its modules. This notion has been recently exploited by the Map equation formalism (M. Rosvall and C.T. Bergstrom, PNAS, 105(4), pp.1118--1123, 2008) through an information-theoretic description of the process of coding inter- and intra-community transitions of a random walker in the network at stationarity. However, a thorough study of the relationship between the full Markov dynamics and the coding mechanism is still lacking. We show here that the original Map coding scheme, which is both block-averaged and one-step, neglects the internal structure of the communities and introduces an upper scale, the `field-of-view' limit, in the communities it can detect. As a consequence, Map is well tuned to detect clique-like communities but can lead to undesirable overpartitioning when communities are far from clique-like. We show that a signature of this behavior is a large compression gap: the Map description length is far from its ideal limit. To address this issue, we propose a simple dynamic approach that introduces time explicitly into the Map coding through the analysis of the weighted adjacency matrix of the time-dependent multistep transition matrix of the Markov process. The resulting Markov time sweeping induces a dynamical zooming across scales that can reveal (potentially multiscale) community structure above the field-of-view limit, with the relevant partitions indicated by a small compression gap.Comment: 10 pages, 6 figure

Chronic Stress Triggers Expression of Immediate Early Genes and Differentially Affects the Expression of AMPA and NMDA Subunits in Dorsal and Ventral Hippocampus of Rats

Indexación: Web of Science; Scopus.Previous studies in rats have demonstrated that chronic restraint stress triggers anhedonia, depressive-like behaviors, anxiety and a reduction in dendritic spine density in hippocampal neurons. In this study, we compared the effect of repeated stress on the expression of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and N-methyl-D-aspartate (NMDA) receptor subunits in dorsal and ventral hippocampus (VH). Adult male Sprague-Dawley rats were randomly divided into control and stressed groups, and were daily restrained in their motion (2.5 h/day) during 14 days. We found that chronic stress promotes an increase in c-Fos mRNA levels in both hippocampal areas, although it was observed a reduction in the immunoreactivity at pyramidal cell layer. Furthermore, Arc mRNAs levels were increased in both dorsal and VH, accompanied by an increase in Arc immunoreactivity in dendritic hippocampal layers. Furthermore, stress triggered a reduction in PSD-95 and NR1 protein levels in whole extract of dorsal and VH. Moreover, a reduction in NR2A/NR2B ratio was observed only in dorsal pole. In synaptosomal fractions, we detected a rise in NR1 in dorsal hippocampus (DH). By indirect immunofluorescence we found that NR1 subunits rise, especially in neuropil areas of dorsal, but not VH. In relation to AMPA receptor (AMPAR) subunits, chronic stress did not trigger any change, either in dorsal or ventral hippocampal areas. These data suggest that DH is more sensitive than VH to chronic stress exposure, mainly altering the expression of NMDA receptor (NMDAR) subunits, and probably favors changes in the configuration of this receptor that may influence the function of this area.https://www.frontiersin.org/articles/10.3389/fnmol.2017.00244/ful

The ROCK inhibitor Fasudil prevents chronic restraint stress-induced depressive-like behaviors and dendritic spine loss in rat hippocampus

Indexación: Web of Science; Scopus.Background: Dendritic arbor simplification and dendritic spine loss in the hippocampus, a limbic structure implicated in mood disorders, are assumed to contribute to symptoms of depression. These morphological changes imply modifications in dendritic cytoskeleton. Rho GTPases are regulators of actin dynamics through their effector Rho kinase. We have reported that chronic stress promotes depressive-like behaviors in rats along with dendritic spine loss in apical dendrites of hippocampal pyramidal neurons, changes associated with Rho kinase activation. The present study proposes that the Rho kinase inhibitor Fasudil may prevent the stress-induced behavior and dendritic spine loss. Methods: Adult male Sprague-Dawley rats were injected with saline or Fasudil (i.p., 10 mg/kg) starting 4 days prior to and maintained during the restraint stress procedure (2.5 h/d for 14 days). Nonstressed control animals were injected with saline or Fasudil for 18 days. At 24 hours after treatment, forced swimming test, Golgi-staining, and immuno-western blot were performed. Results: Fasudil prevented stress-induced immobility observed in the forced swimming test. On the other hand, Fasudiltreated control animals showed behavioral patterns similar to those of saline-treated controls. Furthermore, we observed that stress induced an increase in the phosphorylation of MYPT1 in the hippocampus, an exclusive target of Rho kinase. This change was accompanied by dendritic spine loss of apical dendrites of pyramidal hippocampal neurons. Interestingly, increased pMYPT1 levels and spine loss were both prevented by Fasudil administration. Conclusion: Our findings suggest that Fasudil may prevent the development of abnormal behavior and spine loss induced by chronic stress by blocking Rho kinase activity.https://academic.oup.com/ijnp/article/20/4/336/263217