Browsing by Subject "networks"
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Item Gene Bionetworks Involved in the Epigenetic Transgenerational Inheritance of Altered Mate Preference: Environmental Epigenetics and Evolutionary Biology(2014-05) Skinner, Michael K.; Savenkova, Marina I.; Zhang, Bin; Gore, Andrea C.; Crews, David; Gore, Andrea C.Mate preference behavior is an essential first step in sexual selection and is a critical determinant in evolutionary biology. Previously an environmental compound (the fungicide vinclozolin) was found to promote the epigenetic transgenerational inheritance of an altered sperm epigenome and modified mate preference characteristics for three generations after exposure of a gestating female. Results: The current study investigated gene networks involved in various regions of the brain that correlated with the altered mate preference behavior in the male and female. Statistically significant correlations of gene clusters and modules were identified to associate with specific mate preference behaviors. This novel systems biology approach identified gene networks (bionetworks) involved in sex-specific mate preference behavior. Observations demonstrate the ability of environmental factors to promote the epigenetic transgenerational inheritance of this altered evolutionary biology determinant. Conclusions: Combined observations elucidate the potential molecular control of mate preference behavior and suggests environmental epigenetics can have a role in evolutionary biology.Item In-Person Contact Begets Calling and Texting: Interpersonal Motives for Cell Phone Use, Face-to-Face interaction, and Loneliness(2010-12) Jin, Borae; Park, Namkee; Jin, BoraeThis study examined how cell-phone use is related to interpersonal motives for using cell phones, face-to-face communication, and loneliness. A survey of 232 college students who owned a cell phone revealed that affection and inclusion were relatively strong motivations for using voice calls and text messaging, and that interpersonal motives were positively related to the amount of cell-phone use, including calling and texting. The amount of face-to-face interaction was positively associated with the participants' cell-phone use and their interpersonal motives for using cell phones: the more the participants engaged in face-to-face interaction with other people, the higher their motives were and the more frequent cell-phone use was. Loneliness did not have a direct relation to cell-phone use. Instead, the participants with higher levels of loneliness were less likely to engage in face-to-face social interaction, which led them to use cell phones less and to be less motivated to use cell phones for interpersonal purposes.Item Multi Component Self-Assembly: Supramolecular Organic Frameworks Containing Metal-Rotaxane Subunits (RSOFs)(2011-11) Gong, Han-Yuan; Rambo, Brett M.; Nelson, Cory A.; Cho, Won; Lynch, Vincent M.; Zhu, Xiaoyang Y.; Oh, Moonhyun; Sessler, Jonathan L.; Gong, Han-Yuan; Rambo, Brett M.; Nelson, Cory A.; Cho, Won; Lynch, Vincent M.; Zhu, Xiaoyang Y.A facile, one-pot synthesis of rotaxanated supramolecular organic frameworks (RSOFs) is reported. These systems consist of bis-carboxylate anions threaded through the core of tetraimidazolium macrocycles. Trivalent metal cations, yttrium(III) and smaller lanthanides, are used to "lock" the threaded strut in place. This results in the formation of three-dimensional RSOFs.Item Opinion dynamics of random-walking agents on a lattice(2011-05) Ree, Suhan; Ree, SuhanThe opinion dynamics of random-walking agents on finite two-dimensional lattices is studied. In the model, the opinion is continuous, and both the lattice and the opinion can be either periodic or nonperiodic. At each time step, all agents move randomly on the lattice, and update their opinions based on those of neighbors with whom the differences of opinion are not greater than a given threshold. Due to the effect of repeated averaging, opinions first converge locally, and eventually reach steady states. As in other models with bounded confidence, steady states in general are those with one or more opinion groups in which all agents have the same opinion. When both the lattice and the opinion are periodic, however, metastable states can emerge, in which the whole spectrum of location-dependent opinions can coexist. This result shows that, when a set of continuous opinions forms a structure like a circle, unlike the typically used linear opinions, rich dynamic behavior can arise. When there are geographical restrictions in real situations, a complete consensus is rarely reached, and metastable states here might be one of the explanations for these situations, especially when opinions are not linear.Item Percolation, statistical topography, and transport in random-media(1992-10) Isichenko, Michael B.; Isichenko, Michael B.A review of classical percolation theory is presented, with an emphasis on novel applications to statistical topography, turbulent diffusion, and heterogeneous media. Statistical topography involves the geometrical properties of the isosets (contour lines or surfaces) of a random potential psi(x). For rapidly decaying correlations of psi, the isopotentials fall into the same universality class as the perimeters of percolation clusters. The topography of long-range correlated potentials involves many length scales and is associated either with the correlated percolation problem or with Mandelbrot's fractional Brownian reliefs. In all cases, the concept of fractal dimension is particularly fruitful in characterizing the geometry of random fields. The physical applications of statistical topography include diffusion in random velocity fields, heat and particle transport in turbulent plasmas, quantum Hall effect, magnetoresistance in inhomogeneous conductors with the classical Hall effect, and many others where random isopotentials are relevant. A geometrical approach to studying transport in random media, which captures essential qualitative features of the described phenomena, is advocated.Item Supervised Community Detection in Protein-interaction Networks(2019) Palukuri, Meghana; Marcotte, EdwardCommunity detection problems arise in several fields with networks, from biology and medicine to social studies and cybersecurity. Networks in these fields tend to be massive - for instance hu.MAP, the human protein interaction network assembled by our lab has 17 million edges. The problem of community detection here translates to finding protein complexes, which will help advance our understanding of several cellular functions and disease mechanisms. To solve this computationally challenging big data problem, we developed Super.Complex (short for Supervised Complex), a computational pipeline employing auto-ML and subgraph sampling techniques. While most state-of-the-art algorithms employ unsupervised graph clustering methods, a supervised approach holds more promise towards finding accurate communities mimicking the real world. With data on known communities becoming increasingly available in many applications, supervised methods become more relevant. Super.Complex implements a streamlined algorithm which samples subgraphs from the weighted network and classifies them as communities or non-communities via a supervised ML model. The steps involved are (i) sampling non-community data as random walks on the graph (ii) feature extraction and selection for known communities and generated non-communities, (iii) autoML pipeline for identification and training of thebest supervised machine learning model for binary classification of subgraphs (iv) intelligent sampling of candidate subgraphs for classification via 3 search techniques – greedy, iterative simulated annealing and metropolis. The last step is in fact a solution to the NP hard problem of identifying maximally scoring subgraphs in a network. The algorithm is applied to real data of different human and yeast protein interaction networks, yielding F1 scores ranging from 0.96 to 0.99 and identifying previously unknown biological complexes. Further, Super.Complex outperforms many state-of-the-art algorithms both in terms of accuracy and performance, with scalability to huge networks through its distributed framework.Item Syntheses, Structures, and Photoluminescence of 1-D Lanthanide Coordination Polymers(2009-10) Yang, Xiaoping; Jones, Richard A.; Rivers, Joseph H.; Wong, Wai-Kwok; Yang, Xiaoping; Jones, Richard A.; Rivers, Joseph H.Five new lanthanide 1-D coordination polymers are reported which are formed from flexible salen type Schiff-base ligands H(2)L and H(2)L' (H(2)L = N, N(1)-ethylene bis(salicylideneimine); H(2)L' = N,N(1)-bis(3-methoxysalicylidene) ethylene-1,2-diamine). The polymeric structures are formed by bridging neutral H(2)L units in the case of {[Ln(2)L(2)(CF(3)SO(3))(H(2)L)(4)(MeOH)]center dot CF(3)SO(3)}(n) (Ln = Eu (1), Nd (2) and Er (3)), and by acetate (OAc(-)) groups in [Yb(2)(L)(2)(OAc)(2)(MeOH)(2)](n) (4) and {[Tb(3)(L')(2)(OAc)(5)]center dot Et(2)O center dot(MeOH)(0.5)}(n) (5). The structures of 1-5 were determined by single crystal X-ray crystallographic studies and the luminescence properties of 1 and 5 in MeOH solution were determined.Item Voice Flows To And Around Leaders: Understanding When Units Are Helped Or Hurt By Employee Voice(2013-12) Detert, J. R.; Burris, E. R.; Harrison, D. A.; Martin, S. R.; Burris, Ethan R.; Harrison, David AIn two studies, we develop and test theory about the relationship between speaking up, one type of organizational citizenship behavior, and unit performance by accounting for where employee voice is flowing. Results from a qualitative study of managers and professionals across a variety of industries suggest that voice to targets at different formal power levels (peers or superiors) and locations in the organization (inside or outside a focal unit) differs systematically in terms of its usefulness in generating actions to a unit's benefit on the issues raised and in the likely information value of the ideas expressed. We then theorize how distinct voice flows should be differentially related to unit performance based on these core characteristics and test our hypotheses using time-lagged field data from 801 employees and their managers in 93 units across nine North American credit unions. Results demonstrate that voice flows are positively related to a unit's effectiveness when they are targeted at the focal leader of that unitwho should be able to take actionwhether from that leader's own subordinates or those in other units, and negatively related to a unit's effectiveness when they are targeted at coworkers who have little power to effect change. Together, these studies provide a structural framework for studying the nature and impact of multiple voice flows, some along formal reporting lines and others that reflect the informal communication structure within organizations. This research demonstrates that understanding the potential performance benefits and costs of voice for leaders and their units requires attention to the structure and complexity of multiple voice flows rather than to an undifferentiated amount of voice.