VEGA: visual comparison of phylogenetic trees for evolutionary genome analysis (ChinaVis 2019)

In the field of evolutionary genome analysis, biologists seek to identify important genes or chromosome regions by comparing phylogenetic trees and analyzing the mutation at which locus might affect phenotypic traits. Unfortunately, the tree comparison and accompanying analysis are often performed manually. In this paper, we characterize the workflow of evolutionary genome analysis and present a task analysis for the fundamental questions asked by biologists during the analysis procedure. We propose two algorithms to enable quantitative tree comparison. One is to measure the differences between corresponding leaf nodes on two trees, and the other is to compute the classification inconsistency of each leaf node by comparing tree structure with a given biological classification. Configuring with the obtained difference and inconsistency, we present a visual analysis system, visual comparison of phylogenetic trees for evolutionary genome analysis, which not only enables biologists to intuitively explore trees but also identify locus which affects their traits by comparing SNP variants of selected leaf nodes. We conclude with case studies from two biologists who used our system to augment their previous manual analysis workflow and demonstrate that our system can reveal more insight.     

VisAct: a visualization design system based on semantic actions

Current visualization design toolkits help users to explore data and create visualizations. However, most of these systems do not record the executed actions during the visualization construction process with semantic context. In this paper, we present VisAct, a visualization design system based on semantic actions, that helps average users to construct visualizations step by step. Our system contributes a set of action-based visualization components and a high-level grammar for semantic actions. VisAct also guides the visualization construction process and provides an action tracker for history management and data collection. We demonstrate the usability of VisAct by visualizations and a plugin application. Finally, we conduct a user study to evaluate the efficiency and effectiveness of our system.     

Entropic uncertainty relation in neutrino oscillations

The European Physical Journal C - We study the isentropic evolution of the matter produced in relativistic heavy-ion collisions for various values of the entropy-per-baryon ratio of interest for...     

Highly efficient excitation of LP_(01) mode in ring-core fibers by tapering for optimizing OAM generation

We have demonstrated the highly efficient excitation of the linearly polarized mode(LP01)in ring-core fibers(RCFs)by tapering the spliced point between the RCF and the standard single-mode fiber(SMF)to optimize all-fiber orbital angular momentum(OAM)generation.The tapering technique has been investigated theoretically and experimentally.Before tapering,only 50%of light can be coupled from SMFs to RCFs.The modal interference spectrum with an extinction ratio(ER)of～9 dB is observed,showing that higher-order modes are excited in RCF.By tapering the spliced point,90%of light is coupled,and the ER is minimized to be～2 dB,indicating that the higher-order modes are effectively suppressed by tapering.Such tapered spliced points of RCF–SMF are further applied for all-fiber OAM generation.The efficiencies of OAM+1 and OAM?1 generation are found to be enhanced by approximately 11.66%and 12.41%,respectively,showing that the tapered spliced point of the RCF–SMF is a feasible way to optimize OAM generation.     

Overview of finite elements simulation of temperature profile to estimate properties of materials 3D-printed by laser powder-bed fusion

Laser powder bed fusion(LPBF),like many other additive manufacturing techniques,offers flexibility in design expected to become a disruption to the manufacturing industry.The current cost of LPBF process does not favor a try-anderror way of research,which makes modelling and simulation a field of superior importance in that area of engineering.In this work,various methods used to overcome challenges in modeling at different levels of approximation of LPBF process are reviewed.Recent efforts made towards a reliable and computationally effective model to simulate LPBF process using finite element(FE)codes are presented.A combination of ray-tracing technique,the solution of the radiation transfer equation and absorption measurements has been used to establish an analytical equation,which gives a more accurate approximation of laser energy deposition in powder-substrate configuration.When this new analytical energy deposition model is used in in FE simulation,with other physics carefully set,it enables us to get reliable cooling curves and melt track morphology that agree well with experimental observations.The use of more computationally effective approximation,without explicit topological changes,allows to simulate wider geometries and longer scanning time leading to many applications in real engineering world.Different applications are herein presented including:prediction of printing quality through the simulated overlapping of consecutive melt tracks,simulation of LPBF of a mixture of materials and estimation of martensite inclusion in printed steel.     

Predictions of γ(4S)→h_b(1P,2P)π^+π^- transitions

We study the contributions of intermediate bottomonium-like Zb states and the bottom meson loops in the heavy quark spin flip transitionsγ(4 S)→hb(1 P,2 P)π+π-.Depending on the constructive or destructive interferences between the Zb-exchange and the bottom meson loops mechanisms,we predict two possible branching ratios for each process:BRγ(4 S)→hb(1 P)π+π-≈(1.20.40.8×10^-6)or(0.5-0.20.5×10^-6),and BRγ(4 S)→(2 P)π+π-≈(7.1-1.1+1.7×10^-10)or(2.4-0.10.2×10^-10)).The contribution of the bottom meson loops is found to be considerably larger than that of the Zbexchange in the T(4 S)→hb(1 P)ππtransitions,while its decay rates are not comparable to those of heavy quark spin conservedγ(4 S)→γ(1 S,2 S)ππprocesses.We also predict the contribution of the charm meson loops in the branch fractions ofΨ(3 S,4 S)→hc(1 P)ππ.     

An improved evaluation of the neutron background in the PandaX-Ⅱ experiment

In dark matter direct detection experiments,neutron is a serious source of background,which can mimic the dark matter-nucleus scattering signals.In this paper,we present an improved evaluation of the neutron background in the PandaX-II dark matter experiment by a novel approach.Instead of fully relying on the Monte Carlo simulation,the overall neutron background is determined from the neutron-induced high energy signals in the data.In addition,the probability of producing a dark-matter-like background per neutron is evaluated with a complete Monte Carlo generator,where the correlated emission of neutron(s)andγ(s)in the(α,n)reactions and spontaneous fissions is taken into consideration.With this method,the neutron backgrounds in the Run 9(26-ton-day)and Run 10(28-ton-day)data sets of PandaX-II are estimated to be(0.66±0.24)and(0.47±0.25)events,respectively.     

The High Energy X-ray telescope (HE) onboard the Insight-HXMT astronomy satellite

The Insight-Hard X-ray Modulation Telescope(Insight-HXMT) is a broadband X-ray and γ-ray(1-3000 ke V) astronomy satellite. One of its three main telescopes is the High Energy X-ray telescope(HE). The main detector plane of HE comprises 18 Na I(Tl)/Cs I(Na) phoswich detectors, where Na I(Tl) is used as the primary detector to measure ~ 20-250 ke V photons incident from the field of view(FOV) defined by collimators, and Cs I(Na) is used as the active shielding detector to Na I(Tl) by pulse shape discrimination. Additionally, Cs I(Na) is used as an omnidirectional γ-ray monitor. The HE collimators have a diverse FOV,i.e. 1.1°×5.7°(15 units), 5.7°×5.7°(2 units), and blocked(1 unit). Therefore, the combined FOV of HE is approximately5.7°×5.7°. Each HE detector has a diameter of 190 mm resulting in a total geometrical area of approximately 5100 cm2, and the energy resolution is ~15% at 60 ke V. For each recorded X-ray event by HE, the timing accuracy is less than 10 μs and the deadtime is less than 10 μs. HE is used for observing spectra and temporal variability of X-ray sources in the 20-250 ke V band either by pointing observations for known sources or scanning observations to unveil new sources. Additionally, HE is used for monitoring the γ-ray burst in 0.2-3 Me V band. This paper not only presents the design and performance of HE instruments but also reports results of the on-ground calibration experiments.     

Failure analysis with a focus on thermal aspect towards developing safer Na-ion batteries

Safety requirements stimulate Na-based batteries to evolve from high-temperature Na–S batteries to room-temperature Na-ion batteries(NIBs).Even so,NIBs may still cause thermal runaway due to the external unexpected accidents and internal high activity of electrodes or electrolytes,which has not been comprehensively summarized yet.In this review,we summarize the significant advances about the failure mechanisms and related strategies to build safer NIBs from the selection of electrodes,electrolytes and the construction of electrode/electrolyte interfaces.Considering the safety risk,the thermal behaviors are emphasized which will deepen the understanding of thermal stability of different NIBs and accelerate the exploitation of safe NIBs.     

A systematical study of the chiral magnetic effects at the RHIC and LHC energies

Considering the magnetic field response of the QGP medium,we perform a systematical study of the chiral magnetic effect(CME),and make a comparison with the experimental results for the background-subtracted correlator H at the energies of the RHIC Beam Energy Scan(BES)and the LHC energy.The CME signals from our computations show a centrality trend and beam energy dependence that are qualitatively consistent with the experimental measurements of the charge dependent correlations.The time evolution of the chiral electromagnetic current at the RHIC and LHC energies is systematically studied.The dependence of the time-integrated current signal on the beam energy√s with different centralities is investigated.Our phenomenological analysis shows that the time-integrated electromagnetic current is maximal near the collision energy√s≈39 GeV.The qualitative trend of the induced electromagnetic current is in agreement with the CME experimental results at the RHIC and LHC energies.