bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leishmania
allelic selection during experimental sand fly infection correlates with mutational signatures of oxidative DNA damage
Authors: Bussotti Giovanni , Li Blaise , Pescher Pascale , Vojtkova Barbora , Louradour Isabelle , Pruzinova Katerina , Sadlova Jovana , Volf Petr , Späth Gerald F. 
Published: February 2023

Trypanosomatid pathogens are transmitted by blood-feeding insects, causing devastating human infections. These parasites show important phenotypic shifts that often impact parasite pathogenicity, tissue tropism, or drug susceptibility. The evolutionary mechanisms that allow for the selection of such adaptive phenotypes remain only poorly investigated. Here, we use
Leishmania donovani
as a trypanosomatid model pathogen to assess parasite evolutionary adaptation during experimental sand fly infection. Comparing the genome of the parasites before and after sand fly infection revealed a strong population bottleneck effect as judged by allele frequency analysis. Apart from random genetic drift caused by the bottleneck effect, our analyses revealed haplotype and allelic changes during sand fly infection that seem under natural selection given their convergence between independent biological replicates. Our analyses further uncovered signature mutations of oxidative DNA damage in the parasite genomes after sand fly infection, suggesting that
Leishmania
suffers from oxidative stress inside the insect digestive tract. Our results propose a model of
Leishmania
genomic adaptation during sand fly infection, with oxidative DNA damage and DNA repair processes likely driving haplotype and allelic selection. The experimental and computational framework presented here provides a useful blueprint to assess evolutionary adaptation of other eukaryotic pathogens inside their insect vectors, such as
Plasmodium
spp,
Trypanosoma brucei
, and
Trypanosoma cruzi
.
Polarization-multiplexed metaholograms with erasable functionality
Authors: Zhou Shaolin , Liu Liang , Chen Zhijian , Ansari Muhammad Afnan , Chen Xianzhong , Chan Mansun 
Published: February 2023

Abstract
The unprecedented capability of metasurfaces in pixel-wise-level accurate light manipulation has enabled the realization of polarization-multiplexed metasurface holograms in a single or multiple channel. However, most metasurfaces are static and unable to realize active or tunable wave control in many scenarios. We introduce an erasable functionality for multi-channel metasurface holograms based on active phase tuning, which is realized using the nonvolatile chalcogenide phase change alloy of GeSbSeTe (GSST). Upon the incidence of linearly or circularly polarized waves, polarization-dependent holograms constructed using amorphous GSST (a-GSST) elliptical pillars are achieved because of the complete phase control. The a-GSST holograms feature a subwavelength spatial resolution for all elliptical pillars, with local transmittances ranging from 66% to 90%. Benefiting from the amorphous-to-crystalline phase transition of GSST, the hologram functionality can be completely erased because the crystallized pillars cannot provide the effective propagation modes required by the anisotropic phase modulations in the operating wavelength range. The unique properties of the proposed polarization-multiplexed holograms with erasable functionality offer more degrees of freedom and have potential applications in many fields, such as anti-counterfeiting, encryption, and holographic sources.
Asymmetric transmission modular design via direction-dependent absorption of spoof surface plasmon polaritons
Authors: Qiu Tianshuo , Li Weihan , Wang Jiafu , Wang Jianqi , An Qiang , Liu Bingyang , Hou Yangfan , Jiang Juanna , Tang Wenxuan , Cheng Ziru , Qu Shaobo 
Published: February 2023

Abstract
A method of achieving asymmetric transmission is proposed by means of the propagation direction-dependent absorption of spoof surface plasmon polaritons (SSPPs). In this letter, trapezoidal wire arrays which act as absorbers have been combined with cutting metal wires which act as polarization rotators. By combining trapezoidal wire arrays with polarization rotators, the metamaterial can exhibit different properties according to the direction of the incident wave, thereby achieving asymmetric transmission. Incident waves can be efficiently converted to the SSPPs by trapezoidal wire arrays, and their propagation and/or absorption can be controlled by engineering the spatial dispersion of k-vector. Moreover, polarization rotators based on cutting metal wires can customize the polarization rotation performance by changing the length of the metal wire. The simulated and measured results verify the asymmetric transmission effect and design method. The proposed asymmetric transmission structure can be applied in electromagnetic devices for linearly polarized wave or polarization control. Compared with chiral metamaterial structures, this work improves the design customizability and efficiency as well as provides an alternative method of designing asymmetric transmission. In addition, the framework expands the application prospect of asymmetric transmission and builds a bridge from SSPPs to asymmetric transmission, facilitating the asymmetric transmission integrated with other SSPPs devices.
Modeling multi-loop atom interferometers with Co-moving Reference Theory
Authors: Wang Ya-Jie , Zhang Jiao , Hu Qiu-Bo , Wang Ke-Xin , Su Jian-Feng , Tang Chun-Juan , Lu Xiao-Yu 
Published: February 2023

Abstract
With the rapid development of atom interferometry, atom interferometers have been widely used in inertial navigation, resource exploration, basic physics and other fields. For precise measurement experiments with multi-loop atom interferometer configuration, it is urgent to establish a high-precision theoretical model charactering the relationship between target measurement quantities and measurement results. Based on this, we adopt the idea of co-moving reference frame, so as to transfer the gravity, gravity gradient and Earth’s rotation effects to the laser light field interacting with atoms by translating, rotating and stretching the background spacetime. With this method, we not only can simplify the analysis process of the experimental principle, but also give the analytical results of the high-order interference phase of the multi-loop atom interferometer containing the gravity gradient and Earth’s rotation. This work will lay a certain theoretical foundation for higher-precision experiment, and will also help to clearly guide the implementation of the experiment.
The trapping problem on horizontal partitioned level-3 sierpinski gasket networks
Authors: Hu Zhongren , Chen Yun 
Published: February 2023

AbstractRandom walk on complex networks is a research hotspot nowadays. The average trapping time (ATT) is an important property related to the trapping problem, which is a variant of random walk, because it can be used to measure the transmission efficiency of particles randomly walking on the network. In this paper, we consider the trapping problem on the horizontal partitioned level-3 Sierpinski gasket network which is determined by the cutting linelk, that is, by the partition coefficientk. Then through the structure of this research model, we derive the exact analytical expression of theATT. Furthermore, we draw two kinds of numerical simulation diagrams to simulate the relationship between theATTand the iteration number and the partition coefficient, and compare them with theATTon the original graph (uncut). The obtained solution shows that theATTis affected by thek, specifically, the larger thek, the shorter theATT, that is the higher the transmission efficiency.
Density functional theory study of Br doped CsPbI3 perovskite for photovoltaic and optoelectronic applications
Authors: Maleka P M , Dima R S , Ntwaeaborwa O M , Maphanga R R 
Published: February 2023

Abstract
First-principle calculations were used to investigate the structural, optoelectronic, elastic and thermodynamic properties of Br-doped CsPbI3 perovskite material using GGA-PBE, SCAN, and LDA functionals. The computed lattice parameters are consistent with the experimental and theoretical calculations, reported in the literature. The band structure along with the electronic density of states indicated that CsPbI3−xBrx (x = 0, 1, 2, 3) materials are semiconductors with direct band gaps, as projected using the three functionals. The energy band gap of CsPbI3 was tuned by replacing I ions with Br ions, resulting in CsPbI2Br, CsPbBr2I, and CsPbBr3 materials. These perovskite materials were found to be mechanically stable, ductile in nature and elastically anisotropic. The results of optical parameters such as absorption coefficients, refractive index, optical conductivity, optical reflectivity, electron energy loss, and extinction coefficients were calculated and analysed. The thermodynamic parameters including heat capacity, and Debye temperature were calculated. The direct band gap and energy-dependent optical parameters especially the absorption coefficient in the infrared and visible region of these perovskite materials suggest that they might be candidates for potential use in photovoltaic solar cells and optoelectronic applications.
A transient magneto-mechanical numerical model of a tank based on improved jiles-atherton theory
Authors: Zhang Haipeng , Long Jiajie , Ren Li , Xu Ying , Li Xianhao , Tang Yuejin 
Published: February 2023

Abstract
Magnetic field generated by the ferromagnetic material of underwater detectors varies with seawater pressure, which may affect the accuracy of deep-sea resource exploration. The effect of stress on magnetization is cumulative. In order to accurately simulate the influence of deep-sea pressure on the magnetic field around underwater detectors, it is very important to develop a transient magneto-mechanical numerical model. In this paper, a transient magneto-mechanical coupling model of a tank was developed to obtain the magnetic signal deviation caused by the magneto-mechanical coupling effect. By improving the Jiles-Atherton theory for complex stress and calculating the variation in magnetic field with pressure, the hysteresis effect between magnetization and stress was verified. Under different background magnetic fields, the effect of stress on magnetic field was determined by calculating the magnetic field distribution under different pressures.
CosmoGridV1: a simulated 𝗐CDM theory prediction for map-level cosmological inference
Authors: Kacprzak Tomasz , Fluri Janis , Schneider Aurel , Refregier Alexandre , Stadel Joachim 
Published: February 2023

Abstract
We present CosmoGridV1: a large set of lightcone simulations for map-level cosmological inference with probes of large scale structure.
It is designed for cosmological parameter measurement based on Stage-III photometric surveys with non-Gaussian statistics and machine learning.
CosmoGridV1 spans the wCDM model by varying Ωm, σ
8, w
0, H
0, n
s, Ω
b
, and assumes three degenerate neutrinos with fixed ∑ mν
= 0.06 eV.
This space is covered by 2500 grid points on a Sobol sequence.
At each grid point, we run 7 simulations with PkdGrav3 and store 69 particle maps at nside = 2048 up to z = 3.5, as well as halo catalog snapshots.
The fiducial cosmology has 200 independent simulations, along with their stencil derivatives.
An important part of CosmoGridV1 is the benchmark set of 28 simulations, which include larger boxes, higher particle counts, and higher redshift resolution of shells.
They allow for testing if new types of analyses are sensitive to choices made in CosmoGridV1.
We add baryon feedback effects on the map level, using shell-based baryon correction model.
The shells are used to create maps of weak gravitational lensing, intrinsic alignment, and galaxy clustering, using the UFalcon code.
The main part of CosmoGridV1 are the raw particle count shells that can be used to create full-sky maps for a given n(z).
We also release projected maps for a Stage-III forecast, as well as maps used previously in KiDS-1000 deep learning constraints with CosmoGridV1.
The data is available at http://www.cosmogrid.ai/.
Velocity reconstruction with the cosmic microwave background and galaxy surveys
Authors: Cayuso Juan , Bloch Richard , Hotinli Selim C. , Johnson Matthew C. , McCarthy Fiona 
Published: February 2023

Abstract
The kinetic Sunyaev Zel'dovich (kSZ) and moving lens effects, secondary contributions to
the cosmic microwave background (CMB), carry significant cosmological information due to their
dependence on the large-scale peculiar velocity field. Previous work identified a promising means
of extracting this cosmological information using a set of quadratic estimators for the radial and
transverse components of the velocity field. These estimators are based on the statistically
anisotropic components of the cross-correlation between the CMB and a tracer of large scale
structure, such as a galaxy redshift survey. In this work, we assess the challenges to the program
of velocity reconstruction posed by various foregrounds and systematics in the CMB and galaxy
surveys, as well as biases in the quadratic estimators. To do so, we further develop the quadratic
estimator formalism and implement a numerical code for computing properly correlated spectra for
all the components of the CMB (primary/secondary blackbody components and foregrounds) and a
photometric redshift survey, with associated redshift errors, to allow for accurate
forecasting. We create a simulation framework for generating realizations of properly correlated
CMB maps and redshift binned galaxy number counts, assuming the underlying fields are Gaussian,
and use this to validate a velocity reconstruction pipeline and assess map-based systematics such
as masking. We highlight the most significant challenges for velocity reconstruction, which
include biases associated with: modelling errors, characterization of redshift errors, and coarse
graining of cosmological fields on our past light cone. Despite these challenges, the outlook for
velocity reconstruction is quite optimistic, and we use our reconstruction pipeline to confirm
that these techniques will be feasible with near-term CMB experiments and photometric galaxy
redshift surveys.
Boltzmann equations for astrophysical Stochastic Gravitational Wave Backgrounds scattering off of massive objects
Authors: Pizzuti Lorenzo , Tomella Alessandro , Carbone Carmelita , Calabrese Matteo , Baccigalupi Carlo 
Published: February 2023

Abstract
The goal of this work is to present a set of coupled Boltzmann equations describing the intensity and polarisation Stokes parameters of the SGWB. Collision terms (as discussed e.g. in ref. [1]) which account for gravitational Compton scattering off of massive objects, are also included. This set resembles that for the CMB Stokes parameters, but the different spin nature of the gravitational radiation and the physics involved in the scattering process determine crucial differences. In the case of gravitational Compton scattering, due to the Rutherford angular dependence of the cross section, all the SGWB intensity multipoles of order ℓ are scattered out, therefore producing outgoing intensity anisotropies of any order ℓ if they are present in the incoming radiation. On the other hand, as already outlined in [1], SGWB linear polarisation modes can be expanded in a basis of spherical harmonics with m = ±4 and ℓ ≥ 4. This means that SGWB polarisation modes can be generated from unpolarised anisotropic radiation only with m = ±4, therefore requiring at least a hexadecapole anisotropy (ℓ ≥ 4) in the incoming intensity. Assuming a simplified toy model where scattering targets are localised in a small redshift range, we solve analytically the set of coupled Boltzmann equations to get explicit expressions for the intensity and polarisation angular power spectra. We confirm the contribution of the gravitational Compton scattering to the SGWB anisoptropies is extremely small for collisions with massive compact objects (BH and SMBH) in the frequency range of current and upcoming surveys. The system of coupled Boltzmann equations presented here provides a way to accurate estimate the total amount of anisotropies generated by multiple SGWB scattering processes off of massive objects, as well as the interplay between polarisation and intensity, during the GW propagation across the LSS of the universe. These results will be useful for the full treatment of the astrophysical SWGB anisotropies in view of upcoming gravitational waves observatories.
Triaxially deformed relativistic Hartree–Bogoliubov theory in Woods–Saxon basis
Authors: Xia X W , Shi Z 
Published: February 2023

Abstract
A triaxially deformed relativistic Hartree–Bogoliubov theory in the Woods–Saxon basis is developed with the aim of treating the triaxial deformation, pairing correlations and continuum in a unified way. In order to consider the triaxial deformation, the deformed potentials are expanded in terms of spherical harmonic functions in the coordinate space. In order to take the pairing correlations into account and treat the continuum properly, by using the Dirac Woods–Saxon basis, which has correct asymptotic behavior, the relativistic Hartree–Bogoliubov equation with triaxial deformation is solved. The formalism of triaxially deformed relativistic Hartree–Bogoliubov theory in Woods–Saxon basis is presented. Taking an axially deformed nucleus 24Ne and a triaxially deformed nucleus 76Ge as examples, the numerical checks are performed. A weakly bound nucleus 112Ge is taken as an example to carry out the necessary converge checks for the numerical parameters. In addition, the ground-state properties of even–even germanium isotopes are investigated. The evolutions of two-neutron separation energy, deformation, root-mean-square radii and density distribution with mass number are analyzed. The comparison between the calculations from the relativistic Hartree–Bogoliubov theory based on harmonic-oscillator basis and the triaxially deformed relativistic Hartree–Bogoliubov theory in Woods–Saxon basis is performed. It is found that the neutron drip line is extended from 114Ge to 118Ge in the triaxially deformed relativistic Hartree–Bogoliubov theory in Woods–Saxon basis.
Theoretical investigations on a variable-coefficient generalized forced–perturbed Korteweg–de Vries–Burgers model for a dilated artery, blood vessel or circulatory system with experimental support
Authors: Gao Xin-Yi , Guo Yong-Jiang , Shan Wen-Rui 
Published: February 2023

Abstract
Recent theoretical physics efforts have been focused on the probes for nonlinear pulse waves in, for example, variable-radius arteries. With respect to the nonlinear waves in an artery full of blood with certain aneurysm, pulses in a blood vessel, or features in a circulatory system, this paper symbolically computes out an auto-Bäcklund transformation via a noncharacteristic movable singular manifold, certain families of the solitonic solutions, as well as a family of the similarity reductions for a variable-coefficient generalized forced–perturbed Korteweg–de Vries–Burgers equation. Aiming, e.g., at the dynamical radial displacement superimposed on the original static deformation from an arterial wall, our results rely on the axial stretch of the injured artery, blood as an incompressible Newtonian fluid, radius variation along the axial direction or aneurysmal geometry, viscosity of the fluid, thickness of the artery, mass density of the membrane material, mass density of the fluid, strain energy density of the artery, shear modulus, stretch ratio, etc. We also highlight that the shock-wave structures from our solutions agree well with those dusty-plasma-experimentally reported.
Post-explant profiling of subcellular-scale carbon fiber intracortical electrodes and surrounding neurons enables modeling of recorded electrophysiology
Authors: Letner Joseph G , Patel Paras R , Hsieh Jung-Chien , Smith Flores Israel M , della Valle Elena , Walker Logan A , Weiland James D , Chestek Cynthia A , Cai Dawen 
Published: February 2023

Abstract

Objective. Characterizing the relationship between neuron spiking and the signals that electrodes record is vital to defining the neural circuits driving brain function and informing clinical brain-machine interface design. However, high electrode biocompatibility and precisely localizing neurons around the electrodes are critical to defining this relationship. Approach. Here, we demonstrate consistent localization of the recording site tips of subcellular-scale (6.8 µm diameter) carbon fiber electrodes and the positions of surrounding neurons. We implanted male rats with carbon fiber electrode arrays for 6 or 12+ weeks targeting layer V motor cortex. After explanting the arrays, we immunostained the implant site and localized putative recording site tips with subcellular-cellular resolution. We then 3D segmented neuron somata within a 50 µm radius from implanted tips to measure neuron positions and health and compare to healthy cortex with symmetric stereotaxic coordinates. Main results. Immunostaining of astrocyte, microglia, and neuron markers confirmed that overall tissue health was indicative of high biocompatibility near the tips. While neurons near implanted carbon fibers were stretched, their number and distribution were similar to hypothetical fibers placed in healthy contralateral brain. Such similar neuron distributions suggest that these minimally invasive electrodes demonstrate the potential to sample naturalistic neural populations. This motivated the prediction of spikes produced by nearby neurons using a simple point source model fit using recorded electrophysiology and the mean positions of the nearest neurons observed in histology. Comparing spike amplitudes suggests that the radius at which single units can be distinguished from others is near the fourth closest neuron (30.7 ± 4.6 µm,

X
ˉ

± S) in layer V motor cortex. Significance. Collectively, these data and simulations provide the first direct evidence that neuron placement in the immediate vicinity of the recording site influences how many spike clusters can be reliably identified by spike sorting.
Development and analysis of solid lubricant coating on M2 high-speed steel using the EDC process
Authors: Muralidharan B , Kumaran V , Barathsuriya R D 
Published: February 2023

Abstract
This paper reports solid lubricant coating on the M2 high-speed steel substrate with MoS2:Cu (50:50) green compact electrode by electric discharge coating (EDC) process. The influence of input parameters (peak current(I) and pulse duration(ton)) on the coating responses (thickness, microhardness, and surface roughness) have been investigated. The coated materials atomic weight percentage and chemical compounds are examined through EDS and XRD analysis. The maximum coating thickness (695.3μm) was reported at ton − 750 μs and I- 5 A. The coated samples microhardness exhibit between 217.8 HV—669.43 HV, which is lesser than the substrate (750 HV). The adhesive strength of the coating surface was examined using the scratch test with the progressive load. The result shows, adhesive strength increased at higher current level.