Symmetry in Critical Random Boolean Network Dynamics

Using Boolean networks as prototypical examples, the role of symmetry in the dynamics of heterogeneous complex systems is explored. We show that symmetry of the dynamics, especially in critical states, is a controlling feature that can be used both to greatly simplify analysis and to characterize different types of dynamics. Symmetry in Boolean networks is found by determining the frequency at which the various Boolean output functions occur. There are classes of functions that consist of Boolean functions that behave similarly. These classes are orbits of the controlling symmetry group. We find that the symmetry that controls the critical random Boolean networks is expressed through the frequency by which output functions are utilized by nodes that remain active on dynamical attractors. This symmetry preserves canalization, a form of network robustness. We compare it to a different symmetry known to control the dynamics of an evolutionary process that allows Boolean networks to organize into a critical state. Our results demonstrate the usefulness and power of using the symmetry of the behavior of the nodes to characterize complex network dynamics, and introduce a novel approach to the analysis of heterogeneous complex systems

Microbial diversity in the thermal springs within Hot Springs National Park

The thermal water systems of Hot Springs National Park (HSNP) in Hot Springs, Arkansas exist in relative isolation from other North American thermal systems. The HSNP waters could therefore serve as a unique center of thermophilic microbial biodiversity. However, these springs remain largely unexplored using culture-independent next generation sequencing techniques to classify species of thermophilic organisms. Additionally, HSNP has been the focus of anthropogenic development, capping and diverting the springs for use in recreational bathhouse facilities. Human modification of these springs may have impacted the structure of these bacterial communities compared to springs left in a relative natural state. The goal of this study was to compare the community structure in two capped springs and two uncapped springs in HSNP, as well as broadly survey the microbial diversity of the springs. We used Illumina 16S rRNA sequencing of water samples from each spring, the QIIME workflow for sequence analysis, and generated measures of genera and phyla richness, diversity, and evenness. In total, over 700 genera were detected and most individual samples had more than 100 genera. There were also several uncharacterized sequences that could not be placed in known taxa, indicating the sampled springs contain undescribed bacteria. There was great variation both between sites and within samples, so no significant differences were detected in community structure between sites. Our results suggest that these springs, regardless of their human modification, contain a considerable amount of biodiversity, some of it potentially unique to the study site

Evolving relativistic fluid spacetimes using pseudospectral methods and finite differencing

We present a new code for solving the coupled Einstein-hydrodynamics equations to evolve relativistic, self-gravitating fluids. The Einstein field equations are solved on one grid using pseudospectral methods, while the fluids are evolved on another grid by finite differencing. We discuss implementation details, such as the communication between the grids and the treatment of stellar surfaces, and present code tests.Comment: To appear in the Proceedings of the Eleventh Marcel Grossmann Meetin

Solid phase chemistry to covalently and reversibly capture thiolated RNA.

Here, we describe an approach to enrich newly transcribed RNAs from primary mouse neurons using 4-thiouridine (s4U) metabolic labeling and solid phase chemistry. This one-step enrichment procedure captures s4U-RNA by using highly efficient methane thiosulfonate (MTS) chemistry in an immobilized format. Like solution-based methods, this solid-phase enrichment can distinguish mature RNAs (mRNA) with differential stability, and can be used to reveal transient RNAs such as enhancer RNAs (eRNAs) and primary microRNAs (pri-miRNAs) from short metabolic labeling. Most importantly, the efficiency of this solid-phase chemistry made possible the first large scale measurements of RNA polymerase II (RNAPII) elongation rates in mouse cortical neurons. Thus, our approach provides the means to study regulation of RNA metabolism in specific tissue contexts as a means to better understand gene expression in vivo

Averting Robot Eyes

Home robots will cause privacy harms. At the same time, they can provide beneficial services—as long as consumers trust them. This Essay evaluates potential technological solutions that could help home robots keep their promises, avert their eyes, and otherwise mitigate privacy harms. Our goals are to inform regulators of robot-related privacy harms and the available technological tools for mitigating them, and to spur technologists to employ existing tools and develop new ones by articulating principles for avoiding privacy harms. We posit that home robots will raise privacy problems of three basic types: (1) data privacy problems; (2) boundary management problems; and (3) social/relational problems. Technological design can ward off, if not fully prevent, a number of these harms. We propose five principles for home robots and privacy design: data minimization, purpose specifications, use limitations, honest anthropomorphism, and dynamic feedback and participation. We review current research into privacy-sensitive robotics, evaluating what technological solutions are feasible and where the harder problems lie. We close by contemplating legal frameworks that might encourage the implementation of such design, while also recognizing the potential costs of regulation at these early stages of the technology

Endogenous Dopamine and Endocannabinoid Signaling Mediate Cocaine-Induced Reversal of AMPAR Synaptic Potentiation in the Nucleus Accumbens Shell

Repeated exposure to drugs of abuse alters the structure and function of neural circuits mediating reward, generating maladaptive plasticity in circuits critical for motivated behavior. Within meso-corticolimbic dopamine circuitry, repeated exposure to cocaine induces progressive alterations in AMPAR-mediated glutamatergic synaptic transmission. During a 10–14 day period of abstinence from cocaine, AMPAR signaling is potentiated at synapses on nucleus accumbens (NAc) medium spiny neurons (MSNs), promoting a state of heightened synaptic excitability. Re-exposure to cocaine during abstinence, however, rapidly reverses and depotentiates enhanced AMPAR signaling. To understand how re-exposure to cocaine alters AMPAR synaptic transmission, we investigated the roles of dopamine and endocannabinoid (eCB) signaling in modifying synaptic strength in the NAc shell. Using patch-clamp recordings from NAc slices prepared after 10–14 days of abstinence from repeated cocaine, we found that AMPAR-mediated depotentiation is rapidly induced in the NAc shell within 20 min of cocaine re-exposure ex vivo, and persists for up to five days before synapses return to levels of potentiation observed during abstinence. In cocaine-treated animals, global dopamine receptor activation was both necessary and sufficient for the cocaine-evoked depotentiation of AMPAR synaptic function. Additionally, we identified that CB1 receptors are engaged by endogenous endocannabinoids (eCBs) during re-exposure to cocaine ex vivo. Overall, these results indicate the central role that dopamine and eCB signaling mechanisms play in modulating cocaine-induced AMPAR plasticity in the NAc shell