@phdthesis{6947,
  abstract     = {Lymph nodes  are es s ential organs  of the immune  s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular  cells (FRCs) are  the  main  stromal  cells and  form  a sponge-like extracellular matrix network,   called  conduits ,  which  they   thems elves   enwrap   and  contract.  Lymph,  containing  s oluble  antigens ,  arrive in  lymph  nodes  via afferent lymphatic  vessels that  connect  to  the  s ubcaps ular  s inus   and  conduit  network.  According  to  the  current  paradigm,  the  conduit  network   dis tributes   afferent  lymph  through   lymph  nodes   and  thus   provides   acces s   for  immune  cells to lymph-borne  antigens. An  elas tic  caps ule  s urrounds   the  organ  and  confines   the immune  cells and  FRC  network.   Lymph   nodes   are  completely  packed  with  lymphocytes   and  lymphocyte  numbers  directly  dictates  the size  of  the  organ.  Although  lymphocytes   cons tantly  enter  and  leave  the  lymph  node,  its   s ize  remains   remarkedly   s table  under  homeostatic conditions. It is only partly known  how the cellularity and s ize of the lymph node is regulated and  how  the  lymph  node  is able to swell in inflammation.  The role of the FRC network   in  lymph  node   s welling  and  trans fer  of  fluids   are  inves tigated in  this   thes is.  Furthermore,   we  s tudied  what  trafficking  routes   are  us ed  by  cancer  cells   in  lymph  nodes   to  form  distal metastases.We examined the role of a mechanical feedback in regulation of lymph  node swelling. Using parallel plate compression  and UV-las er  cutting  experiments   we  dis s ected  the  mechanical  force dynamics  of the whole lymph  node, and individually for FRCs  and the  caps ule. Physical forces   generated  by  packed  lymphocytes   directly  affect  the  tens ion  on  the  FRC  network  and  capsule,  which  increases  its  resistance  to   swelling.  This  implies  a  feedback  mechanism  between   tis s ue   pres s ure   and   ability   of   lymphocytes    to   enter   the   organ.   Following   inflammation,  the  lymph  node  swells ∼10 fold in two weeks . Yet, what  is  the role  for tens ion on  the  FRC  network   and  caps ule,  and  how  are  lymphocytes   able  to  enter  in  conditions  that resist swelling remain open ques tions . We s how that tens ion on the FRC network is  important to  limit  the  swelling  rate  of  the  organ  so  that  the  FRC  network  can  grow  in  a  coordinated  fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates  and a dis organized FRC network  in the inflamed lymph  node. Growth  of the FRC network  in  turn  is   expected  to  releas e  tens ion  on  thes e  s tructures   and  lowers   the  res is tance  to  swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of  swelling coincides   with  a  thickening  of  the  caps ule,  which  forms   a  thick  res is tant  band  around  the organ and lowers  tens ion on the FRC network  to form a new force equilibrium.The  FRC  and  conduit   network   are  further   believed  to  be  a  privileged  s ite  of  s oluble  information  within  the  lymph  node,  although  many  details   remain  uns olved.  We  s how  by  3D  ultra-recons truction   that  FRCs   and  antigen  pres enting  cells   cover  the  s urface  of  conduit  s ys tem for more  than 99% and we dis cus s  the implications  for s oluble information  exchangeat the conduit level.Finally, there  is an ongoing debate in the cancer field whether and how cancer cells  in lymph nodes   s eed  dis tal  metas tas es .  We  s how  that  cancer  cells   infus ed  into  the  lymph  node  can  utilize trafficking routes of immune  cells and  rapidly  migrate  to  blood  vessels. Once  in  the  blood circulation,  these cells are able to form  metastases in distal tissues.},
  author       = {Assen, Frank P},
  issn         = {2663-337X},
  pages        = {142},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking}},
  doi          = {10.15479/AT:ISTA:6947},
  year         = {2019},
}

@article{6955,
  abstract     = {We study few-body bound states of charged particles subject to attractive zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic length scales of the system at zero energy are set by the Coulomb length scale D and the Coulomb-modified effective range r eff. We study shallow bound states of charged particles with D >> r eff and show that these systems obey universal scaling laws different from neutral particles. An accurate description of these states requires both the Coulomb-modified scattering length and the effective range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant for bound states whose spatial extent is significantly larger than the range of the attractive potential. These states enjoy universality – their character is independent of the shape of the short-range potential.},
  author       = {Schmickler, C.H. and Hammer, H.-W. and Volosniev, Artem},
  issn         = {0370-2693},
  journal      = {Physics Letters B},
  publisher    = {Elsevier},
  title        = {{Universal physics of bound states of a few charged particles}},
  doi          = {10.1016/j.physletb.2019.135016},
  volume       = {798},
  year         = {2019},
}

@phdthesis{6957,
  abstract     = {In many shear flows like pipe flow, plane Couette flow, plane Poiseuille flow,  etc. turbulence emerges subcritically. Here, when subjected to strong enough perturbations, the flow becomes turbulent in spite of the laminar base flow being linearly stable.  The nature of this instability has puzzled the scientific community for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally intermittent.  In pipe flow the localized turbulent structures are referred to as puffs and in planar flows like plane Couette and channel flow, patches arise in the form of localized oblique bands. In this thesis, we study the onset of turbulence in channel flow in direct numerical simulations from a dynamical system theory perspective, as well as by performing experiments in a large aspect ratio channel.

The aim of the experimental work is to determine the critical Reynolds number where turbulence first becomes sustained. Recently, the onset of turbulence has been described in analogy to absorbing state phase transition (i.e. directed percolation). In particular, it has been shown that the critical point can be estimated from the competition between spreading and decay processes. Here, by performing experiments, we identify the mechanisms underlying turbulence proliferation in channel flow and find the critical Reynolds number, above which turbulence becomes sustained. Above the critical point, the continuous growth at the tip of the stripes outweighs the stochastic shedding of turbulent patches at the tail and the stripes expand. For growing stripes, the probability to decay decreases while the probability of stripe splitting increases. Consequently, and unlike for the puffs in pipe flow, neither of these two processes is time-independent i.e. memoryless. Coupling between stripe expansion and creation of new stripes via splitting leads to a significantly lower critical point ($Re_c=670+/-10$) than most earlier studies suggest.  

While the above approach sheds light on how turbulence first becomes sustained, it provides no insight into the origin of the stripes themselves. In the numerical part of the thesis we investigate how turbulent stripes form from invariant solutions of the Navier-Stokes equations. The origin of these turbulent stripes can be identified by applying concepts from the dynamical system theory. In doing so, we identify the exact coherent structures underlying stripes and their bifurcations and how they give rise to the turbulent attractor in phase space. We first report a family of localized nonlinear traveling wave solutions of the Navier-Stokes equations in channel flow. These solutions show structural similarities with turbulent stripes in experiments like obliqueness, quasi-streamwise streaks and vortices, etc. A parametric study of these traveling wave solution is performed, with parameters like Reynolds number, stripe tilt angle and domain size, including the stability of the solutions. These solutions emerge through saddle-node bifurcations and form a phase space skeleton for the turbulent stripes observed in the experiments. The lower branches of these TW solutions at different tilt angles undergo Hopf bifurcation and new solutions branches of relative periodic orbits emerge. These RPO solutions do not belong to the same family and therefore the routes to chaos for different angles are different.  

In shear flows, turbulence at onset is transient in nature.  Consequently,turbulence can not be tracked to lower Reynolds numbers, where the dynamics may simplify. Before this happens, turbulence becomes short-lived and laminarizes. In the last part of the thesis, we show that using numerical simulations we can continue turbulent stripes in channel flow past the 'relaminarization barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies and the fluctuations are no longer stochastic and the stripe settles down to a relative periodic orbit. This relative periodic orbit originates from the aforementioned traveling wave solutions. Starting from the relative periodic orbit, a small increase in speed i.e. Reynolds number gives rise to chaos and the attractor dimension sharply increases in contrast to the classical transition scenario where the instabilities affect the flow globally and give rise to much more gradual route to turbulence.},
  author       = {Paranjape, Chaitanya S},
  issn         = {2663-337X},
  keywords     = {Instabilities, Turbulence, Nonlinear dynamics},
  pages        = {138},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Onset of turbulence in plane Poiseuille flow}},
  doi          = {10.15479/AT:ISTA:6957},
  year         = {2019},
}

@article{6972,
  abstract     = {We give fault-tolerant algorithms for establishing synchrony in distributed systems in which each of thennodes has its own clock. Our algorithms operate in a very strong fault model: we require self-stabilisation, i.e.,the initial state of the system may be arbitrary, and there can be up to f<n/3 ongoing Byzantine faults, i.e.,nodes that deviate from the protocol in an arbitrary manner. Furthermore, we assume that the local clocks ofthe nodes may progress at different speeds (clock drift) and communication has bounded delay. In this model,we study the pulse synchronisation problem, where the task is to guarantee that eventually all correct nodesgenerate well-separated local pulse events (i.e., unlabelled logical clock ticks) in a synchronised manner.Compared to prior work, we achieveexponentialimprovements in stabilisation time and the number ofcommunicated bits, and give the first sublinear-time algorithm for the problem:•In the deterministic setting, the state-of-the-art solutions stabilise in timeΘ(f)and have each nodebroadcastΘ(flogf)bits per time unit. We exponentially reduce the number of bits broadcasted pertime unit toΘ(logf)while retaining the same stabilisation time.•In the randomised setting, the state-of-the-art solutions stabilise in timeΘ(f)and have each nodebroadcastO(1)bits per time unit. We exponentially reduce the stabilisation time to polylogfwhileeach node broadcasts polylogfbits per time unit.These results are obtained by means of a recursive approach reducing the above task ofself-stabilisingpulse synchronisation in thebounded-delaymodel tonon-self-stabilisingbinary consensus in thesynchro-nousmodel. In general, our approach introduces at most logarithmic overheads in terms of stabilisation timeand broadcasted bits over the underlying consensus routine.},
  author       = {Lenzen, Christoph and Rybicki, Joel},
  issn         = {0004-5411},
  journal      = {Journal of the ACM},
  number       = {5},
  publisher    = {ACM},
  title        = {{Self-stabilising Byzantine clock synchronisation is almost as easy as consensus}},
  doi          = {10.1145/3339471},
  volume       = {66},
  year         = {2019},
}

@article{6978,
  abstract     = {In  pipes  and  channels,  the  onset  of  turbulence  is  initially  dominated  by  localizedtransients,  which  lead  to  sustained  turbulence  through  their  collective  dynamics.  In  thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating  laminar  and  turbulent  flow,  we  identify  transverse  homoclinic  orbits,  thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence.},
  author       = {Budanur, Nazmi B and Dogra, Akshunna and Hof, Björn},
  journal      = {Physical Review Fluids},
  number       = {10},
  pages        = {102401},
  publisher    = {American Physical Society},
  title        = {{Geometry of transient chaos in streamwise-localized pipe flow turbulence}},
  doi          = {10.1103/PhysRevFluids.4.102401},
  volume       = {4},
  year         = {2019},
}

@article{6979,
  author       = {Kopf, Aglaja and Sixt, Michael K},
  issn         = {1879-0445},
  journal      = {Current Biology},
  number       = {20},
  pages        = {R1091--R1093},
  publisher    = {Cell Press},
  title        = {{Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal}},
  doi          = {10.1016/j.cub.2019.08.068},
  volume       = {29},
  year         = {2019},
}

@article{6980,
  abstract     = {Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development.},
  author       = {Petridou, Nicoletta and Heisenberg, Carl-Philipp J},
  issn         = {1460-2075},
  journal      = {The EMBO Journal},
  number       = {20},
  publisher    = {EMBO},
  title        = {{Tissue rheology in embryonic organization}},
  doi          = {10.15252/embj.2019102497},
  volume       = {38},
  year         = {2019},
}

@article{6982,
  abstract     = {We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to the same point or overlapping arcs due to data compression or low resolution. This raises the computational problem of deciding whether a given map ϕ : G → M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖ is the unform norm.
A polynomial-time algorithm for recognizing weak embeddings has recently been found by Fulek and Kynčl. It reduces the problem to solving a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler: We perform a sequence of local operations that gradually “untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak embedding. It combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.
},
  author       = {Akitaya, Hugo and Fulek, Radoslav and Tóth, Csaba},
  journal      = {ACM Transactions on Algorithms},
  number       = {4},
  publisher    = {ACM},
  title        = {{Recognizing weak embeddings of graphs}},
  doi          = {10.1145/3344549},
  volume       = {15},
  year         = {2019},
}

@article{6983,
  abstract     = {Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver.},
  author       = {Kelemen, Réka K and Rajakaruna, H and Cockburn, IA and Ganusov, VV},
  issn         = {1664-3224},
  journal      = {Frontiers in Immunology},
  publisher    = {Frontiers},
  title        = {{Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells}},
  doi          = {10.3389/fimmu.2019.02153},
  volume       = {10},
  year         = {2019},
}

@inproceedings{6985,
  abstract     = {In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets.},
  author       = {Hasani, Ramin and Amini, Alexander and Lechner, Mathias and Naser, Felix and Grosu, Radu and Rus, Daniela},
  booktitle    = {Proceedings of the International Joint Conference on Neural Networks},
  isbn         = {9781728119854},
  location     = {Budapest, Hungary},
  publisher    = {IEEE},
  title        = {{Response characterization for auditing cell dynamics in long short-term memory networks}},
  doi          = {10.1109/ijcnn.2019.8851954},
  year         = {2019},
}

@article{6986,
  abstract     = {Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory. },
  author       = {Li, Penghui},
  issn         = {1088-6826},
  journal      = {Proceedings of the American Mathematical Society},
  number       = {11},
  pages        = {4597--4604},
  publisher    = {AMS},
  title        = {{A colimit of traces of reflection groups}},
  doi          = {10.1090/proc/14586},
  volume       = {147},
  year         = {2019},
}

@inbook{6987,
  abstract     = {Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern.},
  author       = {McDougall, Alex and Chenevert, Janet and Godard, Benoit G and Dumollard, Remi},
  booktitle    = {Evo-Devo: Non-model species in cell and developmental biology},
  editor       = {Tworzydlo, Waclaw and Bilinski, Szczepan M.},
  isbn         = {9783030234584},
  issn         = {1861-0412},
  pages        = {127--154},
  publisher    = {Springer Nature},
  title        = {{Emergence of embryo shape during cleavage divisions}},
  doi          = {10.1007/978-3-030-23459-1_6},
  volume       = {68},
  year         = {2019},
}

@article{6988,
  abstract     = {Platelets are central players in thrombosis and hemostasis but are increasingly recognized as key components of the immune system. They shape ensuing immune responses by recruiting leukocytes, and support the development of adaptive immunity. Recent data shed new light on the complex role of platelets in immunity. Here, we summarize experimental and clinical data on the role of platelets in host defense against bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet proinflammatory effector functions and cross-talk with the coagulation system, can also result in damage to the host (e.g., acute lung injury and sepsis). Novel clinical insights support this dichotomy: platelet inhibition/thrombocytopenia can be either harmful or protective, depending on pathophysiological context. Clinical studies are currently addressing this aspect in greater depth.},
  author       = {Nicolai, Leo and Gärtner, Florian R and Massberg, Steffen},
  issn         = {1471-4906},
  journal      = {Trends in Immunology},
  number       = {10},
  pages        = {922--938},
  publisher    = {Cell Press},
  title        = {{Platelets in host defense: Experimental and clinical insights}},
  doi          = {10.1016/j.it.2019.08.004},
  volume       = {40},
  year         = {2019},
}

@inproceedings{6989,
  abstract     = {When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. },
  author       = {Aichholzer, Oswin and Akitaya, Hugo A and Cheung, Kenneth C and Demaine, Erik D and Demaine, Martin L and Fekete, Sandor P and Kleist, Linda and Kostitsyna, Irina and Löffler, Maarten and Masárová, Zuzana and Mundilova, Klara and Schmidt, Christiane},
  booktitle    = {Proceedings of the 31st Canadian Conference on Computational Geometry},
  location     = {Edmonton, Canada},
  pages        = {164--170},
  publisher    = {Canadian Conference on Computational Geometry},
  title        = {{Folding polyominoes with holes into a cube}},
  year         = {2019},
}

@article{6999,
  abstract     = {Plasmodesmata (PD) are plant-specific membrane-lined channels that create cytoplasmic and membrane continuities between adjacent cells, thereby facilitating cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms to regulate PD plasticity in response to numerous environmental stimuli. In particular, during defense against plant pathogens, the defense hormone, salicylic acid (SA), plays a crucial role in the regulation of PD permeability in a callose-dependent manner. Here, we uncover a mechanism by which plants restrict the spreading of virus and PD cargoes using SA signaling by increasing lipid order and closure of PD. We showed that exogenous SA application triggered the compartmentalization of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein, Remorin (REM). Genetic studies, superresolution imaging, and transmission electron microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3 are crucial for plasma membrane nanodomain assembly to control PD aperture and functionality. In addition, we also found that a 14-3-3 epsilon protein modulates REM clustering and membrane nanodomain compartmentalization through its direct interaction with REM proteins. This study unveils a molecular mechanism by which the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization, thereby regulating PD closure to impede virus spreading.},
  author       = {Huang, D and Sun, Y and Ma, Z and Ke, M and Cui, Y and Chen, Z and Chen, C and Ji, C and Tran, TM and Yang, L and Lam, SM and Han, Y and Shu, G and Friml, Jiří and Miao, Y and Jiang, L and Chen, X},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {42},
  pages        = {21274--21284},
  publisher    = {Proceedings of the National Academy of Sciences},
  title        = {{Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization}},
  doi          = {10.1073/pnas.1911892116},
  volume       = {116},
  year         = {2019},
}

@article{7000,
  abstract     = {The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps.},
  author       = {Shehu, Yekini and Iyiola, Olaniyi S. and Li, Xiao-Huan and Dong, Qiao-Li},
  issn         = {1807-0302},
  journal      = {Computational and Applied Mathematics},
  number       = {4},
  publisher    = {Springer Nature},
  title        = {{Convergence analysis of projection method for variational inequalities}},
  doi          = {10.1007/s40314-019-0955-9},
  volume       = {38},
  year         = {2019},
}

@article{7001,
  author       = {Schwayer, Cornelia and Shamipour, Shayan and Pranjic-Ferscha, Kornelija and Schauer, Alexandra and Balda, M and Tada, M and Matter, K and Heisenberg, Carl-Philipp J},
  issn         = {1097-4172},
  journal      = {Cell},
  number       = {4},
  pages        = {937--952.e18},
  publisher    = {Cell Press},
  title        = {{Mechanosensation of tight junctions depends on ZO-1 phase separation and flow}},
  doi          = {10.1016/j.cell.2019.10.006},
  volume       = {179},
  year         = {2019},
}

@article{7002,
  abstract     = {Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem.},
  author       = {Kondapaneni, Ivo and Vevoda, Petr and Grittmann, Pascal and Skrivan, Tomas and Slusallek, Philipp and Křivánek, Jaroslav},
  issn         = {0730-0301},
  journal      = {ACM Transactions on Graphics},
  number       = {4},
  publisher    = {ACM},
  title        = {{Optimal multiple importance sampling}},
  doi          = {10.1145/3306346.3323009},
  volume       = {38},
  year         = {2019},
}

@article{7005,
  abstract     = {Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes.},
  author       = {Cheung, Giselle T and Cousin, Michael A.},
  issn         = {1471-4159},
  journal      = {Journal of Neurochemistry},
  number       = {5},
  pages        = {570--583},
  publisher    = {Wiley},
  title        = {{Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction}},
  doi          = {10.1111/jnc.14862},
  volume       = {151},
  year         = {2019},
}

@article{7007,
  abstract     = {We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds.},
  author       = {Mondelli, Marco and Hassani, S. Hamed and Urbanke, Rüdiger},
  issn         = {1999-4893},
  journal      = {Algorithms},
  number       = {10},
  publisher    = {MDPI},
  title        = {{A new coding paradigm for the primitive relay channel}},
  doi          = {10.3390/a12100218},
  volume       = {12},
  year         = {2019},
}

