The CHR site: definition and genome-wide identification of a cell cycle transcriptional element

The cell cycle genes homology region (CHR) has been identified as a DNA element with an important role in transcriptional regulation of late cell cycle genes. It has been shown that such genes are controlled by DREAM, MMB and FOXM1-MuvB and that these protein complexes can contact DNA via CHR sites. However, it has not been elucidated which sequence variations of the canonical CHR are functional and how frequent CHR-based regulation is utilized in mammalian genomes. Here, we define the spectrum of functional CHR elements. As the basis for a computational meta-analysis, we identify new CHR sequences and compile phylogenetic motif conservation as well as genome-wide protein-DNA binding and gene expression data. We identify CHR elements in most late cell cycle genes binding DREAM, MMB, or FOXM1-MuvB. In contrast, Myb- and forkhead-binding sites are underrepresented in both early and late cell cycle genes. Our findings support a general mechanism: sequential binding of DREAM, MMB and FOXM1-MuvB complexes to late cell cycle genes requires CHR elements. Taken together, we define the group of CHR-regulated genes in mammalian genomes and provide evidence that the CHR is the central promoter element in transcriptional regulation of late cell cycle genes by DREAM, MMB and FOXM1-MuvB

Pure dephasing in flux qubits due to flux noise with spectral density scaling as 1/fα1/ f^\alpha

For many types of superconducting qubits, magnetic flux noise is a source of pure dephasing. Measurements on a representative dc superconducting quantum interference device (SQUID) over a range of temperatures show that $S_\Phi(f) = A^2/(f/1 \hbox{Hz})^\alpha$, where $S_\Phi$ is the flux noise spectral density, $A$ is of the order of 1 $\mu\Phi_0 \, \hbox{Hz}^{-1/2}$ and $0.61 \leq \alpha \leq 0.95$; $\Phi_{0}$ is the flux quantum. For a qubit with an energy level splitting linearly coupled to the applied flux, calculations of the dependence of the pure dephasing time $\tau_\phi$ of Ramsey and echo pulse sequences on $\alpha$ for fixed $A$ show that $\tau_\phi$ decreases rapidly as $\alpha$ is reduced. We find that $\tau_\phi$ is relatively insensitive to the noise bandwidth, $f_1 \leq f \leq f_2$, for all $\alpha$ provided the ultraviolet cutoff frequency $f_2 > 1/\tau_\phi$. We calculate the ratio $\tau_{\phi,E} / \tau_{\phi,R}$ of the echo ($E$) and Ramsey ($R$) sequences, and the dependence of the decay function on $\alpha$ and $f_2$. We investigate the case in which $S_\Phi(f_0)$ is fixed at the "pivot frequency" $f_0 \neq 1$ Hz while $\alpha$ is varied, and find that the choice of $f_0$ can greatly influence the sensitivity of $\tau_{\phi,E}$ and $\tau_{\phi,R}$ to the value of $\alpha$. Finally, we present calculated values of $\tau_\phi$ in a qubit corresponding to the values of $A$ and $\alpha$ measured in our SQUID.Comment: 7 pages, 8 figures, 1 tabl

Demonstrating Advantages of Neuromorphic Computation: A Pilot Study

Neuromorphic devices represent an attempt to mimic aspects of the brain's architecture and dynamics with the aim of replicating its hallmark functional capabilities in terms of computational power, robust learning and energy efficiency. We employ a single-chip prototype of the BrainScaleS 2 neuromorphic system to implement a proof-of-concept demonstration of reward-modulated spike-timing-dependent plasticity in a spiking network that learns to play the Pong video game by smooth pursuit. This system combines an electronic mixed-signal substrate for emulating neuron and synapse dynamics with an embedded digital processor for on-chip learning, which in this work also serves to simulate the virtual environment and learning agent. The analog emulation of neuronal membrane dynamics enables a 1000-fold acceleration with respect to biological real-time, with the entire chip operating on a power budget of 57mW. Compared to an equivalent simulation using state-of-the-art software, the on-chip emulation is at least one order of magnitude faster and three orders of magnitude more energy-efficient. We demonstrate how on-chip learning can mitigate the effects of fixed-pattern noise, which is unavoidable in analog substrates, while making use of temporal variability for action exploration. Learning compensates imperfections of the physical substrate, as manifested in neuronal parameter variability, by adapting synaptic weights to match respective excitability of individual neurons.Comment: Added measurements with noise in NEST simulation, add notice about journal publication. Frontiers in Neuromorphic Engineering (2019

How to orchestrate a soccer team: Generalized synchronization promoted by rhythmic acoustic stimuli

Interpersonal coordination requires precise actions concerted in space and time in a self-organized manner. We found, using soccer teams as a testing ground, that a common timeframe provided by adequate acoustic stimuli improves the interplay between teammates. We provide quantitative evidence that the connectivity between teammates and the scoring rate of male soccer teams improve significantly when playing under the influence of an appropriate acoustic environment. Unexpectedly, female teams do not show any improvement under the same experimental conditions. We show by follow-up experiments that the acoustic rhythm modulates the attention level of the participants with a pronounced tempo preference and a marked gender difference in the preferred tempo. These results lead to a consistent explanation in terms of the dynamical system theory, nonlinear resonances, and dynamic attention theory, which may illuminate generic mechanisms of the brain dynamics and may have an impact on the design of novel training strategies in team sports

Mixing and Circulation in the Tropical Atlantic Cruise No. M98

July 01 – July 28, 2013 Fortaleza (Brazil) – Walvis Bay (Namibia

Versatile emulation of spiking neural networks on an accelerated neuromorphic substrate

We present first experimental results on the novel BrainScaleS-2 neuromorphic architecture based on an analog neuro-synaptic core and augmented by embedded microprocessors for complex plasticity and experiment control. The high acceleration factor of 1000 compared to biological dynamics enables the execution of computationally expensive tasks, by allowing the fast emulation of long-duration experiments or rapid iteration over many consecutive trials. The flexibility of our architecture is demonstrated in a suite of five distinct experiments, which emphasize different aspects of the BrainScaleS-2 system

Cadherin-9 Is a Novel Cell Surface Marker for the Heterogeneous Pool of Renal Fibroblasts

BACKGROUND: Interstitial fibroblasts are a minor, but nevertheless very important, component of the kidney. They secrete and remodel extracellular matrix and they produce active compounds such as erythropoietin. However, studying human renal fibroblasts has been hampered by the lack of appropriate surface markers. METHODS AND FINDINGS: The expression of cadherin-9 in various human renal cell lines and tissues was studied on the mRNA level by RT-PCR and on the protein level with the help of newly generated cadherin-9 antibodies. The classical type II cadherin-9, so far only described in the neural system, was identified as a reliable surface marker for renal fibroblasts. Compared to FSP1, a widely-used cytosolic renal fibroblast marker, cadherin-9 showed a more restricted expression pattern in human kidney. Under pathological conditions, cadherin-9 was expressed in the stroma of renal cell carcinoma, but not in the tumor cells themselves, and in renal fibrosis the percentage of cadherin-9-positive cells was clearly elevated 3 to 5 times compared to healthy kidney tissue. Induction of epithelial mesenchymal transition in renal epithelial cells with cyclosporin-A, which causes renal fibrosis as a side effect, induced cadherin-9 expression. Functional studies following siRNA-mediated knockdown of cadherin-9 revealed that it acts in the kidney like a typical classical cadherin. It was found to be associated with catenins and to mediate homophilic but not heterophilic cell interactions. CONCLUSIONS: Cadherin-9 represents a novel and reliable cell surface marker for fibroblasts in healthy and diseased kidneys. Together with the established marker molecules FSP1, CD45 and alpha smooth muscle actin, cadherin-9 can now be used to differentiate the heterogenic pool of renal fibroblasts into resident and activated fibroblasts, immigrated bone marrow derived fibroblast precursors and cells in different stages of epithelial mesenchymal transition