@article{1804, abstract = {It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control.}, author = {Altmeyer, Sebastian and Do, Younghae and Lai, Ying}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Transition to turbulence in Taylor-Couette ferrofluidic flow}}, doi = {10.1038/srep10781}, volume = {5}, year = {2015}, } @article{1803, abstract = {Repeated stress has been suggested to underlie learning and memory deficits via the basolateral amygdala (BLA) and the hippocampus; however, the functional contribution of BLA inputs to the hippocampus and their molecular repercussions are not well understood. Here we show that repeated stress is accompanied by generation of the Cdk5 (cyclin-dependent kinase 5)-activator p25, up-regulation and phosphorylation of glucocorticoid receptors, increased HDAC2 expression, and reduced expression of memoryrelated genes in the hippocampus. A combination of optogenetic and pharmacosynthetic approaches shows that BLA activation is both necessary and sufficient for stress-associated molecular changes and memory impairments. Furthermore, we show that this effect relies on direct glutamatergic projections from the BLA to the dorsal hippocampus. Finally, we show that p25 generation is necessary for the stress-induced memory dysfunction. Taken together, our data provide a neural circuit model for stress-induced hippocampal memory deficits through BLA activity-dependent p25 generation.}, author = {Rei, Damien and Mason, Xenos and Seo, Jinsoo and Gräff, Johannes and Rudenko, Andrii and Wang, Jùn and Rueda, Richard and Sandra Siegert and Cho, Sukhee and Canter, Rebecca G and Mungenast, Alison E and Deisseroth, Karl A and Tsai, Lihuei}, journal = {PNAS}, number = {23}, pages = {7291 -- 7296}, publisher = {National Academy of Sciences}, title = {{Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway}}, doi = {10.1073/pnas.1415845112}, volume = {112}, year = {2015}, } @article{1807, abstract = {We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential.}, author = {Goldman, Michael and Royo-Letelier, Jimena}, journal = {ESAIM - Control, Optimisation and Calculus of Variations}, number = {3}, pages = {603 -- 624}, publisher = {EDP Sciences}, title = {{Sharp interface limit for two components Bose-Einstein condensates}}, doi = {10.1051/cocv/2014040}, volume = {21}, year = {2015}, } @article{1802, abstract = {Noncoding variants in the human MIR137 gene locus increase schizophrenia risk with genome-wide significance. However, the functional consequence of these risk alleles is unknown. Here we examined induced human neurons harboring the minor alleles of four disease-associated single nucleotide polymorphisms in MIR137. We observed increased MIR137 levels compared to those in major allele–carrying cells. microRNA-137 gain of function caused downregulation of the presynaptic target genes complexin-1 (Cplx1), Nsf and synaptotagmin-1 (Syt1), leading to impaired vesicle release. In vivo, miR-137 gain of function resulted in changes in synaptic vesicle pool distribution, impaired induction of mossy fiber long-term potentiation and deficits in hippocampus-dependent learning and memory. By sequestering endogenous miR-137, we were able to ameliorate the synaptic phenotypes. Moreover, reinstatement of Syt1 expression partially restored synaptic plasticity, demonstrating the importance of Syt1 as a miR-137 target. Our data provide new insight into the mechanism by which miR-137 dysregulation can impair synaptic plasticity in the hippocampus.}, author = {Sandra Siegert and Seo, Jinsoo and Kwon, Ester J and Rudenko, Andrii and Cho, Sukhee and Wang, Wenyuan and Flood, Zachary C and Martorell, Anthony J and Ericsson, Maria and Mungenast, Alison E and Tsai, Lihuei}, journal = {Nature Neuroscience}, pages = {1008 -- 1016}, publisher = {Nature Publishing Group}, title = {{The schizophrenia risk gene product miR-137 alters presynaptic plasticity}}, doi = {10.1038/nn.4023}, volume = {18}, year = {2015}, } @article{1810, abstract = {Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.}, author = {Bollenbach, Mark Tobias}, journal = {Current Opinion in Microbiology}, pages = {1 -- 9}, publisher = {Elsevier}, title = {{Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution}}, doi = {10.1016/j.mib.2015.05.008}, volume = {27}, year = {2015}, } @article{1812, abstract = {We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules. }, author = {Lahrz, Martin and Lemeshko, Mikhail and Mathey, Ludwig}, journal = {New Journal of Physics}, number = {4}, publisher = {IOP Publishing Ltd.}, title = {{Exotic roton excitations in quadrupolar Bose–Einstein condensates }}, doi = {10.1088/1367-2630/17/4/045005}, volume = {17}, year = {2015}, } @article{1811, abstract = {Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.}, author = {Safari, Laleh and Santos, José and Amaro, Pedro and Jänkälä, Kari and Fratini, Filippo}, journal = {Journal of Mathematical Physics}, number = {5}, publisher = {American Institute of Physics}, title = {{Analytical evaluation of atomic form factors: Application to Rayleigh scattering}}, doi = {10.1063/1.4921227}, volume = {56}, year = {2015}, } @article{1813, abstract = {We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.}, author = {Schmidt, Richard and Lemeshko, Mikhail}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{Rotation of quantum impurities in the presence of a many-body environment}}, doi = {10.1103/PhysRevLett.114.203001}, volume = {114}, year = {2015}, } @article{1808, author = {Gupta, Ashutosh and Henzinger, Thomas A}, journal = {ACM Transactions on Modeling and Computer Simulation}, number = {2}, publisher = {ACM}, title = {{Guest editors' introduction to special issue on computational methods in systems biology}}, doi = {10.1145/2745799}, volume = {25}, year = {2015}, } @article{1817, abstract = {Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. }, author = {Porazinski, Sean and Wang, Huijia and Asaoka, Yoichi and Behrndt, Martin and Miyamoto, Tatsuo and Morita, Hitoshi and Hata, Shoji and Sasaki, Takashi and Krens, Gabriel and Osada, Yumi and Asaka, Satoshi and Momoi, Akihiro and Linton, Sarah and Miesfeld, Joel and Link, Brian and Senga, Takeshi and Castillo Morales, Atahualpa and Urrutia, Araxi and Shimizu, Nobuyoshi and Nagase, Hideaki and Matsuura, Shinya and Bagby, Stefan and Kondoh, Hisato and Nishina, Hiroshi and Heisenberg, Carl-Philipp J and Furutani Seiki, Makoto}, journal = {Nature}, number = {7551}, pages = {217 -- 221}, publisher = {Nature Publishing Group}, title = {{YAP is essential for tissue tension to ensure vertebrate 3D body shape}}, doi = {10.1038/nature14215}, volume = {521}, year = {2015}, }