TY - DATA
AB - Small synthetic discrete tomography problems.
Sizes are 32x32, 64z64 and 256x256.
Projection angles are 2, 4, and 6.
Number of labels are 3 and 5.
AU - Swoboda, Paul
ID - 5557
KW - discrete tomography
TI - Synthetic discrete tomography problems
ER -
TY - DATA
AB - PhD thesis LaTeX source code
AU - Bojsen-Hansen, Morten
ID - 5558
TI - Tracking, Correcting and Absorbing Water Surface Waves
ER -
TY - JOUR
AB - Retroviruses such as HIV-1 assemble and bud from infected cells in an immature, non-infectious form. Subsequently, a series of proteolytic cleavages catalysed by the viral protease leads to a spectacular structural rearrangement of the viral particle into a mature form that is competent to fuse with and infect a new cell. Maturation involves changes in the structures of protein domains, in the interactions between protein domains, and in the architecture of the viral components that are assembled by the proteins. Tight control of proteolytic cleavages at different sites is required for successful maturation, and the process is a major target of antiretroviral drugs. Here we will describe what is known about the structures of immature and mature retrovirus particles, and about the maturation process by which one transitions into the other. Despite a wealth of available data, fundamental questions about retroviral maturation remain unanswered.
AU - Mattei, Simone
AU - Schur, Florian
AU - Briggs, John AG
ID - 5771
IS - 6
JF - Current Opinion in Virology
SN - 1879-6257
TI - Retrovirus maturation—an extraordinary structural transformation
VL - 18
ER -
TY - CHAP
AU - Sen, Nabhasmita
AU - Biswas, Ranita
AU - Bhowmick, Partha
ID - 5805
SN - 0302-9743
T2 - Computational Topology in Image Context
TI - On Some Local Topological Properties of Naive Discrete Sphere
VL - 9667
ER -
TY - CONF
AB - Although the concept of functional plane for naive plane is studied and reported in the literature in great detail, no similar study is yet found for naive sphere. This article exposes the first study in this line, opening up further prospects of analyzing the topological properties of sphere in the discrete space. We show that each quadraginta octant Q of a naive sphere forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as the functional plane of Q, and hence gives rise to merely mono-jumps during back projection. The other two coordinate planes serve as para-functional and dia-functional planes for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds neither of the two. Owing to this, the quadraginta octants form symmetry groups and subgroups with equivalent jump conditions. We also show a potential application in generating a special class of discrete 3D circles based on back projection and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry, uniqueness, and bounded distance from the underlying real sphere and real plane.
AU - Biswas, Ranita
AU - Bhowmick, Partha
ID - 5806
SN - 0302-9743
T2 - Discrete Geometry for Computer Imagery
TI - On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing
VL - 9647
ER -
TY - CHAP
AB - A discrete spherical circle is a topologically well-connected 3D circle in the integer space, which belongs to a discrete sphere as well as a discrete plane. It is one of the most important 3D geometric primitives, but has not possibly yet been studied up to its merit. This paper is a maiden exposition of some of its elementary properties, which indicates a sense of its profound theoretical prospects in the framework of digital geometry. We have shown how different types of discretization can lead to forbidden and admissible classes, when one attempts to define the discretization of a spherical circle in terms of intersection between a discrete sphere and a discrete plane. Several fundamental theoretical results have been presented, the algorithm for construction of discrete spherical circles has been discussed, and some test results have been furnished to demonstrate its practicality and usefulness.
AU - Biswas, Ranita
AU - Bhowmick, Partha
AU - Brimkov, Valentin E.
ID - 5809
SN - 0302-9743
T2 - Combinatorial image analysis
TI - On the Connectivity and Smoothness of Discrete Spherical Circles
VL - 9448
ER -
TY - JOUR
AB - Quantum metrology exploits entangled states of particles to improve sensing precision beyond the limit achievable with uncorrelated particles. All previous methods required detection noise levels below this standard quantum limit to realize the benefits of the intrinsic sensitivity provided by these states.We experimentally demonstrate a widely applicable method for entanglement-enhanced measurements without low-noise detection. The method involves an intermediate quantum phase magnification step that eases implementation complexity. We used it to perform squeezed-state metrology 8 decibels below the standard quantum limit with a detection system that has a noise floor 10 decibels above the standard quantum limit.
AU - Onur Hosten
AU - Krishnakumar, Rajiv
AU - Engelsen, Nils J
AU - Kasevich, Mark A
ID - 587
IS - 6293
JF - Science
TI - Quantum phase magnification
VL - 352
ER -
TY - JOUR
AB - Quantum metrology uses quantum entanglement - correlations in the properties of microscopic systems - to improve the statistical precision of physical measurements. When measuring a signal, such as the phase shift of a light beam or an atomic state, a prominent limitation to achievable precision arises from the noise associated with the counting of uncorrelated probe particles. This noise, commonly referred to as shot noise or projection noise, gives rise to the standard quantum limit (SQL) to phase resolution. However, it can be mitigated down to the fundamental Heisenberg limit by entangling the probe particles. Despite considerable experimental progress in a variety of physical systems, a question that persists is whether these methods can achieve performance levels that compare favourably with optimized conventional (non-entangled) systems. Here we demonstrate an approach that achieves unprecedented levels of metrological improvement using half a million 87Rb atoms in their 'clock' states. The ensemble is 20.1 ± 0.3 decibels (100-fold) spin-squeezed via an optical-cavity-based measurement. We directly resolve small microwave-induced rotations 18.5 ± 0.3 decibels (70-fold) beyond the SQL. The single-shot phase resolution of 147 microradians achieved by the apparatus is better than that achieved by the best engineered cold atom sensors despite lower atom numbers. We infer entanglement of more than 680 ± 35 particles in the atomic ensemble. Applications include atomic clocks, inertial sensors, and fundamental physics experiments such as tests of general relativity or searches for electron electric dipole moment. To this end, we demonstrate an atomic clock measurement with a quantum enhancement of 10.5 ± 0.3 decibels (11-fold), limited by the phase noise of our microwave source.
AU - Onur Hosten
AU - Engelsen, Nils J
AU - Krishnakumar, Rajiv
AU - Kasevich, Mark A
ID - 588
IS - 7587
JF - Nature
TI - Measurement noise 100 times lower than the quantum-projection limit using entangled atoms
VL - 529
ER -
TY - CONF
AB - We create up to 20 dB spin-squeezed states of atomic ensembles using an optical cavity-based measurement. The prepared states are suitable for atomic sensors that require free space release of the atoms.
AU - Engelsen, Nils
AU - Hosten, Onur
AU - Krishnakumar, Rajiv
AU - Kasevich, Mark
ID - 592
TI - Engineering spin squeezed states for quantum-enhanced atom interferometry
ER -
TY - JOUR
AB - RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species1-3. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins4-10. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation7. Upstream DNA emanates from the active centre cleft at an angle of approximately 105° with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human transcription.
AU - Bernecky, Carrie A
AU - Herzog, Franz
AU - Baumeister, Wolfgang
AU - Plitzko, Jürgen
AU - Cramer, Patrick
ID - 602
IS - 7587
JF - Nature
TI - Structure of transcribing mammalian RNA polymerase II
VL - 529
ER -
TY - JOUR
AB - Consider the transmission of a polar code of block length N and rate R over a binary memoryless symmetric channel W and let P e be the block error probability under successive cancellation decoding. In this paper, we develop new bounds that characterize the relationship of the parameters R, N, P e , and the quality of the channel W quantified by its capacity I(W) and its Bhattacharyya parameter Z(W). In previous work, two main regimes were studied. In the error exponent regime, the channel W and the rate R <; I(W) are fixed, and it was proved that the error probability Pe scales roughly as 2 -√N . In the scaling exponent approach, the channel W and the error probability Pe are fixed and it was proved that the gap to capacity I(W) - R scales as N -1/μ . Here, μ is called scaling exponent and this scaling exponent depends on the channel W. A heuristic computation for the binary erasure channel (BEC) gives μ = 3.627 and it was shown that, for any channel W, 3.579 ≤ μ ≤ 5.702. Our contributions are as follows. First, we provide the tighter upper bound μ <;≤ 4.714 valid for any W. With the same technique, we obtain the upper bound μ ≤ 3.639 for the case of the BEC; this upper bound approaches very closely the heuristically derived value for the scaling exponent of the erasure channel. Second, we develop a trade-off between the gap to capacity I(W)- R and the error probability Pe as the functions of the block length N. In other words, we neither fix the gap to capacity (error exponent regime) nor the error probability (scaling exponent regime), but we do consider a moderate deviations regime in which we study how fast both quantities, as the functions of the block length N, simultaneously go to 0. Third, we prove that polar codes are not affected by error floors. To do so, we fix a polar code of block length N and rate R. Then, we vary the channel W and study the impact of this variation on the error probability. We show that the error probability Pe scales as the Bhattacharyya parameter Z(W) raised to a power that scales roughly like VN. This agrees with the scaling in the error exponent regime.
AU - Mondelli, Marco
AU - Hassani, S. Hamed
AU - Urbanke, Rudiger L.
ID - 6732
IS - 12
JF - IEEE Transactions on Information Theory
SN - 0018-9448
TI - Unified scaling of polar codes: Error exponent, scaling exponent, moderate deviations, and error floors
VL - 62
ER -
TY - CONF
AB - The question whether RM codes are capacity-achieving is a long-standing open problem in coding theory that was recently answered in the affirmative for transmission over erasure channels [1], [2]. Remarkably, the proof does not rely on specific properties of RM codes, apart from their symmetry. Indeed, the main technical result consists in showing that any sequence of linear codes, with doubly-transitive permutation groups, achieves capacity on the memoryless erasure channel under bit-MAP decoding. Thus, a natural question is what happens under block-MAP decoding. In [1], [2], by exploiting further symmetries of the code, the bit-MAP threshold was shown to be sharp enough so that the block erasure probability also converges to 0. However, this technique relies heavily on the fact that the transmission is over an erasure channel. We present an alternative approach to strengthen results regarding the bit-MAP threshold to block-MAP thresholds. This approach is based on a careful analysis of the weight distribution of RM codes. In particular, the flavor of the main result is the following: assume that the bit-MAP error probability decays as N -δ , for some δ > 0. Then, the block-MAP error probability also converges to 0. This technique applies to transmission over any binary memoryless symmetric channel. Thus, it can be thought of as a first step in extending the proof that RM codes are capacity-achieving to the general case.
AU - Kudekar, Shrinivas
AU - Kumar, Santhosh
AU - Mondelli, Marco
AU - Pfister, Henry D.
AU - Urbankez, Rudiger
ID - 6733
T2 - 2016 IEEE International Symposium on Information Theory
TI - Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels
ER -
TY - CONF
AB - We describe a new method to compare the bit-MAP and block-MAP decoding thresholds of Reed-Muller (RM) codes for transmission over a binary memoryless symmetric channel. The question whether RM codes are capacity-achieving is a long-standing open problem in coding theory and it has recently been answered in the affirmative for transmission over
erasure channels. Remarkably, the proof does not rely on specific properties of RM codes, apart from their symmetry. Indeed, the main technical result consists in showing that any sequence of linear codes, with doubly-transitive permutation groups, achieves capacity on the memoryless erasure channel under bit-MAP decoding. A natural question is what happens under block-MAP decoding. If the minimum distance of the code family is close to linear (e.g., of order N/ log(N)), then one can combine an upper bound on the bit-MAP error probability with a lower bound on the minimum distance to show that the code family is also capacity-achieving under block-MAP decoding. This strategy is successful for BCH codes. Unfortunately, the minimum distance of RM codes scales only as √N, which does not suffice to obtain the desired result. Then, one can exploit further symmetries of RM codes to show that the bit-MAP threshold is sharp enough so that the block erasure probability also tends to 0. However, this technique relies heavily on the fact that the transmission is over an erasure channel.
We present an alternative approach to strengthen results regarding the bit-MAP threshold to block-MAP thresholds. This approach is based on a careful analysis of the weight distribution of RM codes. In particular, the flavor of the main result is the following: assume that the bit-MAP error probability decays as N−δ, for some δ > 0. Then, the block-MAP
error probability also converges to 0. This technique applies to the transmission over any binary memoryless symmetric channel. Thus, it can be thought of as a first step in extending the proof that RM codes are capacity-achieving to the general case.
AU - Mondelli, Marco
AU - Kudekar, Shrinivas
AU - Kumar, Santosh
AU - Pfister, Henry D.
AU - Şaşoğlu, Eren
AU - Urbanke, Rüdiger
ID - 6770
T2 - 24th International Zurich Seminar on Communications
TI - Reed-Muller codes: Thresholds and weight distribution
ER -
TY - JOUR
AB - Electrons in materials with linear dispersion behave as massless Weyl- or Dirac-quasiparticles, and continue to intrigue due to their close resemblance to elusive ultra-relativistic particles as well as their potential for future electronics. Yet the experimental signatures of Weyl-fermions are often subtle and indirect, in particular if they coexist with conventional, massive quasiparticles. Here we show a pronounced anomaly in the magnetic torque of the Weyl semimetal NbAs upon entering the quantum limit state in high magnetic fields. The torque changes sign in the quantum limit, signalling a reversal of the magnetic anisotropy that can be directly attributed to the topological nature of the Weyl electrons. Our results establish that anomalous quantum limit torque measurements provide a direct experimental method to identify and distinguish Weyl and Dirac systems.
AU - Moll, Philip J. W.
AU - Potter, Andrew C.
AU - Nair, Nityan L.
AU - Ramshaw, B. J.
AU - Modic, Kimberly A
AU - Riggs, Scott
AU - Zeng, Bin
AU - Ghimire, Nirmal J.
AU - Bauer, Eric D.
AU - Kealhofer, Robert
AU - Ronning, Filip
AU - Analytis, James G.
ID - 7068
JF - Nature Communications
SN - 2041-1723
TI - Magnetic torque anomaly in the quantum limit of Weyl semimetals
VL - 7
ER -
TY - JOUR
AB - The observation of a reconstructed Fermi surface via quantum oscillations in hole-doped cuprates opened a path towards identifying broken symmetry states in the pseudogap regime. However, such an identification has remained inconclusive due to the multi-frequency quantum oscillation spectra and complications accounting for bilayer effects in most studies. We overcome these impediments with high-resolution measurements on the structurally simpler cuprate HgBa2CuO4+δ (Hg1201), which features one CuO2 plane per primitive unit cell. We find only a single oscillatory component with no signatures of magnetic breakdown tunnelling to additional orbits. Therefore, the Fermi surface comprises a single quasi-two-dimensional pocket. Quantitative modelling of these results indicates that a biaxial charge density wave within each CuO2 plane is responsible for the reconstruction and rules out criss-crossed charge stripes between layers as a viable alternative in Hg1201. Lastly, we determine that the characteristic gap between reconstructed pockets is a significant fraction of the pseudogap energy.
AU - Chan, M. K.
AU - Harrison, N.
AU - McDonald, R. D.
AU - Ramshaw, B. J.
AU - Modic, Kimberly A
AU - Barišić, N.
AU - Greven, M.
ID - 7069
JF - Nature Communications
SN - 2041-1723
TI - Single reconstructed Fermi surface pocket in an underdoped single-layer cuprate superconductor
VL - 7
ER -
TY - JOUR
AU - Rolando, Chiara
AU - Erni, Andrea
AU - Grison, Alice
AU - Beattie, Robert J
AU - Engler, Anna
AU - Gokhale, Paul J.
AU - Milo, Marta
AU - Wegleiter, Thomas
AU - Jessberger, Sebastian
AU - Taylor, Verdon
ID - 7141
IS - 5
JF - Cell Stem Cell
SN - 1934-5909
TI - Multipotency of adult hippocampal NSCs in vivo is restricted by Drosha/NFIB
VL - 19
ER -
TY - JOUR
AB - Background: High directional persistence is often assumed to enhance the efficiency of chemotactic migration. Yet, cells in vivo usually display meandering trajectories with relatively low directional persistence, and the control and function of directional persistence during cell migration in three-dimensional environments are poorly understood. Results: Here, we use mesendoderm progenitors migrating during zebrafish gastrulation as a model system to investigate the control of directional persistence during migration in vivo. We show that progenitor cells alternate persistent run phases with tumble phases that result in cell reorientation. Runs are characterized by the formation of directed actin-rich protrusions and tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions or blebs leads to longer or shorter run phases, respectively. Importantly, both reducing and increasing run phases result in larger spatial dispersion of the cells, indicative of reduced migration precision. A physical model quantitatively recapitulating the migratory behavior of mesendoderm progenitors indicates that the ratio of tumbling to run times, and thus the specific degree of directional persistence of migration, are critical for optimizing migration precision. Conclusions: Together, our experiments and model provide mechanistic insight into the control of migration directionality for cells moving in three-dimensional environments that combine different protrusion types, whereby the proportion of blebs to actin-rich protrusions determines the directional persistence and precision of movement by regulating the ratio of tumbling to run times.
AU - Diz Muñoz, Alba
AU - Romanczuk, Pawel
AU - Yu, Weimiao
AU - Bergert, Martin
AU - Ivanovitch, Kenzo
AU - Salbreux, Guillame
AU - Heisenberg, Carl-Philipp J
AU - Paluch, Ewa
ID - 1271
IS - 1
JF - BMC Biology
TI - Steering cell migration by alternating blebs and actin-rich protrusions
VL - 14
ER -
TY - JOUR
AB - We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams.
AU - Held, Martin
AU - Huber, Stefan
AU - Palfrader, Peter
ID - 1272
IS - 5
JF - Computer-Aided Design and Applications
TI - Generalized offsetting of planar structures using skeletons
VL - 13
ER -
TY - JOUR
AB - Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence.
AU - Porco, Silvana
AU - Larrieu, Antoine
AU - Du, Yujuan
AU - Gaudinier, Allison
AU - Goh, Tatsuaki
AU - Swarup, Kamal
AU - Swarup, Ranjan
AU - Kuempers, Britta
AU - Bishopp, Anthony
AU - Lavenus, Julien
AU - Casimiro, Ilda
AU - Hill, Kristine
AU - Benková, Eva
AU - Fukaki, Hidehiro
AU - Brady, Siobhan
AU - Scheres, Ben
AU - Peéet, Benjamin
AU - Bennett, Malcolm
ID - 1273
IS - 18
JF - Development
TI - Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3
VL - 143
ER -
TY - JOUR
AB - Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis.
AU - Mazur, Ewa
AU - Benková, Eva
AU - Friml, Jirí
ID - 1274
JF - Scientific Reports
TI - Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis
VL - 6
ER -