A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to ...navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research.
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Joints tightened Yu, Hung-Hsun Hans; Zhao, Yufei
American journal of mathematics,
04/2023, Volume:
145, Issue:
2
Journal Article
Peer reviewed
Given a set of lines in $\Bbb{R}^3$, a {\it joint} is a point passed through by three lines not all lying in some plane. The joints problem asks for the maximum number of joints formed by $L$ lines. ...Using the polynomial method, Guth and Katz proved that the answer is $O(L^{3/2})$, which is best possible up to a constant factor. We prove a new upper bound of $(\sqrt{2}/3)L^{3/2}$, which matches, up to a $1+o(1)$ factor, the best known construction: place $k$ generic planes, and use their pairwise intersections to form $\smash{\big(\matrix{k\cr 2}\big)}$ lines and their triple-wise intersections to form $\smash{\big(\matrix{k\cr 3}\big)}$ joints. Guth conjectured that this construction is optimal. Our result generalizes to arbitrary dimensions and fields. Our technique builds on the work on Ruixiang Zhang proving the multijoints conjecture via an extension of the polynomial method. We set up a variational problem to control the high order of vanishing of a polynomial at each joint.
We generalize the Guth–Katz joints theorem from lines to varieties. A special case says that
N
planes (2-flats) in 6 dimensions (over any field) have
O
(
N
3
/
2
)
joints, where a joint is a point ...contained in a triple of these planes not all lying in some hyperplane. More generally, we prove the same bound when the set of
N
planes is replaced by a set of 2-dimensional algebraic varieties of total degree
N
, and a joint is a point that is regular for three varieties whose tangent planes at that point are not all contained in some hyperplane. Our most general result gives upper bounds, tight up to constant factors, for joints with multiplicities for several sets of varieties of arbitrary dimensions (known as Carbery’s conjecture). Our main innovation is a new way to extend the polynomial method to higher dimensional objects, relating the degree of a polynomial and its orders of vanishing on a given set of points on a variety.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Major urinary proteins (MUPs) are often suggested to be highly polymorphic, and thereby provide unique chemical signatures used for individual and genetic kin recognition; however, studies on MUP ...variability have been lacking. We surveyed populations of wild house mice (Mus musculus musculus), and examined variation of MUP genes and proteins. We sequenced several Mup genes (9 to 11 loci) and unexpectedly found no inter-individual variation. We also found that microsatellite markers inside the MUP cluster show remarkably low levels of allelic diversity, and significantly lower than the diversity of markers flanking the cluster or other markers in the genome. We found low individual variation in the number and types of MUP proteins using a shotgun proteomic approach, even among mice with variable MUP electrophoretic profiles. We identified gel bands and spots using high-resolution mass spectrometry and discovered that gel-based methods do not separate MUP proteins, and therefore do not provide measures of MUP diversity, as generally assumed. The low diversity and high homology of Mup genes are likely maintained by purifying selection and gene conversion, and our results indicate that the type of selection on MUPs and their adaptive functions need to be re-evaluated.
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Reduced-order models of flame dynamics can be used to predict and mitigate the emergence of thermoacoustic oscillations in the design of gas turbine and rocket engines. This process is hindered by ...the fact that these models, although often qualitatively correct, are not usually quantitatively accurate. As automated experiments and numerical simulations produce ever-increasing quantities of data, the question arises as to how this data can be assimilated into physics-informed reduced-order models in order to render these models quantitatively accurate. In this study, we develop and test a physics-based reduced-order model of a ducted premixed flame in which the model parameters are learned from high-speed videos of the flame. The experimental data is assimilated into a level-set solver using an ensemble Kalman filter. This leads to an optimally calibrated reduced-order model with quantified uncertainties, which accurately reproduces elaborate nonlinear features such as cusp formation and pinch-off. The reduced-order model continues to match the experiments after assimilation has been switched off. Further, the parameters of the model, which are extracted automatically, are shown to match the first-order behavior expected on physical grounds. This study shows how reduced-order models can be updated rapidly whenever new experimental or numerical data becomes available, without the data itself having to be stored.
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Reduced-order models based on level-set methods are widely used tools to qualitatively capture and track the nonlinear dynamics of an interface. The aim of this paper is to develop a ...physics-informed, data-driven, statistically rigorous learning algorithm for state and parameter estimation with level-set methods. A Bayesian approach based on data assimilation is introduced. Data assimilation is enabled by the ensemble Kalman filter and smoother, which are used in their probabilistic formulations. The level-set data assimilation framework is verified in one-dimensional and two-dimensional test cases, where state estimation, parameter estimation and uncertainty quantification are performed. The statistical performance of the proposed ensemble Kalman filter and smoother is quantified by twin experiments. In the twin experiments, the combined state and parameter estimation fully recovers the reference solution, which validates the proposed algorithm. The level-set data assimilation framework is then applied to the prediction of the nonlinear dynamics of a forced premixed flame, which exhibits the formation of sharp cusps and intricate topological changes, such as pinch-off events. The proposed physics-informed statistical learning algorithm opens up new possibilities for making reduced-order models of interfaces quantitatively predictive, any time that reference data is available.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This article presents an integrated circuit (IC) designed to enable low-power long-range backscatter communication with commodity Wi-Fi transceivers. The proposed chip endeavors to improve the most ...critical and difficult specification in Wi-Fi backscatter systems: range. It does so through two proposed techniques: 1) a fully-reflective single-antenna backscatter solution, whereby the termination of a power combiner always has a reflection coefficient near 1 to ensure high reflected power while enabling single-sideband (SSB) quadrature phase shift keying (QPSK) modulation with frequency-translation to separate Wi-Fi channel and 2) a retro-reflective multiple-in-multiple-out (MIMO) approach that redirects incident Wi-Fi signals, after SSB QPSK modulation, back to a colocated access point (AP) with MIMO gain. The proposed chip also implemented a counter-based wake-up scheme within a synchronization receiver (RX) to achieve standards-compatible wake-up with high synchronization accuracy. Implemented in 65-nm CMOS, the wake-up RX consumes 4.5 <inline-formula> <tex-math notation="LaTeX">\mu</tex-math> </inline-formula>W and achieves a sensitivity of <inline-formula> <tex-math notation="LaTeX">-</tex-math> </inline-formula>43.5 dBm, while the synchronization RX consumes an average power of 4.8 <inline-formula> <tex-math notation="LaTeX">\mu</tex-math> </inline-formula>W and achieves a synchronization accuracy of at least 150 ns for input power of <inline-formula> <tex-math notation="LaTeX">-</tex-math> </inline-formula>35 dBm or better. During backscattering, the IC consumes 32 and 38 <inline-formula> <tex-math notation="LaTeX">\mu</tex-math> </inline-formula>W and attains an AP-to-tag range of 13 and 23 m for the fully-reflective and retro-reflective MIMO approaches, respectively.
A sock ordering is a sequence of socks with different colors. A sock ordering is foot-sortable if the sequence of socks can be sorted by a stack so that socks with the same color form a contiguous ...block. The problem of deciding whether a given sock ordering is foot-sortable was first considered by Defant and Kravitz, who resolved the case for alignment-free 2-uniform sock orderings. In this paper, we resolve the problem in a more general setting, where each color appears in the sock ordering at most twice. A key component of the argument is a fast algorithm that determines the foot-sortability of a sock ordering of length \(N\) in time \(O(N\log N)\), which is also an interesting result on its own.
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