bluuebunny/crossref_metadata_2025 huggingface dataset:
Examination of optimized ultrashort three-color waveforms for generating short and intense isolated attosecond pulses in soft x rays
Authors: Zhang Chi , Li Baochang , Tang Xiangyu , Wang Kan , Chen Yanbo , Han Jiaxin , Li Xiaoyong , Jin Cheng
Published: July 2024

Isolated attosecond pulses (IAPs) can be readily generated via high-order harmonic generation driven by an ultrashort laser pulse. Here, it is shown that the best way to obtain the ultrashort waveform for producing a short and intense IAP in the soft x rays is to optimize the three-color (TC) laser pulse consisting of the fundamental field and its second and third harmonic fields. To calibrate it, another way of constructing the ultrashort waveform directly in time using a truncated basis set of B-spline functions is first proposed. The calibration waveform (CW) contains more frequency components up to the eighth harmonic order. It is found that the IAP by the TC waveform has a shorter duration after macroscopic propagation in a nonlinear gas medium compared to that by the CW field. It is uncovered that the CW field is additionally modified by the higher-order frequency components during propagation, dominated by the neutral atom dispersion. The effect of phase jitter in the TC waveform and the extension of the TC scheme into higher photon energies are also discussed. Currently, precise control of TC laser waveform synthesis is already achievable in the labs, thus paving an effective way for generating a useful attosecond light source in the soft x rays.
Axial confinement of wire array Z-pinch precursor plasmas by a pulsed magnetic mirror field
Authors: Chen C. , Lavine E. S. , Potter W. M. , Seyler C. E. , Kusse B. R.
Published: July 2024

A novel wire-array Z-pinch platform has been developed to study the effect of a pulsed magnetic mirror field on a collisional high energy density plasma. The mirror is driven in series with the Z-pinch target and, therefore, scales with driver current. Axial confinement is observed based on visible imaging and axial flow velocity measurements. The presence of axial compressing J ×B force is determined indirectly based on Thomson scattering and interferometry measurements and corroborated by three-dimensional extended-MHD simulations. Compared to non-magnetized wire array Z-pinch, a modified pulsed mirror configuration is observed to increase precursor plasma thermal energy density by about 30%. If optimized, such a configuration could potentially improve magnetized liner inertial fusion performance by reducing axial plasma end loss.
Nonlinear shifts and dislocations in financial market structure and composition
Authors: James Nick , Menzies Max
Published: July 2024

This paper develops new mathematical techniques to identify temporal shifts among a collection of US equities partitioned into a new and more detailed set of market sectors. Although conceptually related, our three analyses reveal distinct insights about financial markets, with meaningful implications for investment managers. First, we explore a variety of methods to identify nonlinear shifts in a market sector structure and describe the mathematical connection between the measure used and the captured phenomena. Second, we study a network structure with respect to our new market sectors and identify meaningfully connected sector-to-sector mappings. Finally, we conduct a series of sampling experiments over different sample spaces and contrast the distribution of Sharpe ratios produced by long-only, long-short, and short-only investment portfolios. In addition, we examine the sector composition of the top-performing portfolios for each of these portfolio styles. In practice, the methods proposed in this paper could be used to identify regime shifts, optimally structured portfolios, and better communities of equities.
Defects and oxygen impurities in ferroelectric wurtzite Al1−xScxN alloys
Authors: Lee Cheng-Wei , Din Naseem Ud , Brennecka Geoff L. , Gorai Prashun
Published: July 2024

III-nitrides and related alloys are widely used for optoelectronics and as acoustic resonators. Ferroelectric wurtzite nitrides are of particular interest because of their potential for direct integration with Si and wide bandgap semiconductors and unique polarization switching characteristics; such interest has taken off since the first report of ferroelectric Al1−xScxN alloys. However, the coercive fields needed to switch polarization are on the order of MV/cm, which are 1–2 orders of magnitude larger than oxide perovskite ferroelectrics. Atomic-scale point defects are known to impact the dielectric properties, including breakdown fields and leakage currents, as well as ferroelectric switching. However, very little is known about the native defects and impurities in Al1−xScxN and their effect on the dielectric and ferroelectric properties. In this study, we use first-principles calculations to determine the formation energetics of native defects and unintentional oxygen incorporation and their effects on the polarization switching barriers in Al1−xScxN alloys. We find that nitrogen vacancies are the dominant native defects, and unintentional oxygen incorporation on the nitrogen site is present in high concentrations. They introduce multiple mid-gap states that can lead to premature dielectric breakdown and increased temperature-activated leakage currents in ferroelectrics. We also find that nitrogen vacancy and substitutional oxygen reduce the switching barrier in Al1−xScxN at low Sc compositions. The effect is minimal or even negative (increases barrier) at higher Sc compositions. Unintentional defects are generally considered to adversely affect ferroelectric properties, but our findings reveal that controlled introduction of point defects by tuning synthesis conditions can instead benefit polarization switching in ferroelectric Al1−xScxN at certain compositions.
Effects of turbulence integral length scales on aerodynamic characteristics and displacement responses of a square prism
Authors: Lu Bin , Li Qiusheng , Han Xuliang , Wang Xincong
Published: July 2024

This paper investigates the influence of the inflow turbulence integral length scales on the aerodynamic forces on a surface-mounted finite-length square prism and its displacement responses by computational fluid dynamics simulations. Four turbulent inflow conditions with the same mean wind speed and turbulence intensity but different longitudinal and transverse turbulence integral length scales are generated for the simulations. First, the wind pressures and forces on a rigid square prism model and the shear layer characteristics are simulated by large eddy simulations. The simulation results show that the mean characteristics of the wind pressures and shear layers are not sensitive to the turbulence integral length scales. However, the root mean square (RMS) wind pressures on side faces and RMS across-wind forces are increased with the longitudinal turbulence integral length scale, and the mechanism is analyzed by the proper orthogonal decomposition. Second, the displacement responses at the mean wind speed of vortex-induced resonance are computed based on an aeroelastic square prism model by fluid–solid interaction simulations. The RMS displacements of the model are observed to be more sensitive to the transverse turbulence integral length scale rather than the longitudinal turbulence integral length scale. Finally, the influence of the turbulence integral length scales on the Reynolds stresses around the square prism is presented and discussed.
Experimental study on dynamic characteristics of shock train in an isolator with different types of incident shocks
Authors: Wang Dayi , Wang Ziao , Chang Juntao , Huang Renzhe , Xin Xuanan
Published: July 2024

The hypersonic mixed-compression inlet, operating in an off-design state, can be categorized into low-speed and over-speed regimes based on whether the external compression shock is incident into the internal flow channel. In this study, we investigate the movement process of the shock train within an inlet/isolator under both low-speed and over-speed conditions by generating various incident shocks using wedges installed in a direct-connected ground wind tunnel. Experimental investigations are conducted to examine the dynamic characteristics of the shock train in an isolator subjected to different types of incident shocks at an incoming Mach number of 2.7. The findings reveal that varying levels of backpressure resistance for the shock train are observed with different types of incident shocks. Through the movement trajectory of the shock train leading shock (STLS) and power spectral density analysis, it is found that unilateral incident shocks result in a more intense oscillation process for the shock train with a lower dominant oscillation frequency. The dynamic mode decomposition method identifies different oscillation structures within the unsteady shock train flow field and highlights that dominant mode energy primarily concentrates at the STLS, while its symmetry is influenced by the type of incident shock. Specifically, the symmetric bilateral incident shock tends to promote a higher degree of symmetry in the STLS structure while reducing its oscillation strength; however, when the STLS passes over the reflection point of the incident shock, the rapid upstream movement of the shock train still occurs in this situation, thereby inducing inlet unstart and compromising engine safety.
Implementation of energy and gradient for the TDDFT-approximate auxiliary function (aas) method
Authors: Wang Yuchen , Havenridge Shana , Aikens Christine M.
Published: July 2024

In this work, we have implemented the time-dependent density functional theory approximate auxiliary s function (TDDFT-aas) method, which is an approximate TDDFT method. Instead of calculating the exact two-center electron integrals in the K coupling matrix when solving the Casida equation, we approximate the integrals, thereby reducing the computational cost. In contrast to the related TDDFT plus tight-binding (TDDFT+TB) method, a new type of gamma function is used in the coupling matrix that does not depend on the tight-binding parameters. The calculated absorption spectra of silver and gold nanoparticles using TDDFT-aas show good agreement with TDDFT and TDDFT+TB results. In addition, we have implemented the analytical excited-state gradients for the TDDFT-aas method, which makes it possible to calculate the emission energy of molecular systems.
Wehnelt photoemission in an ultrafast electron microscope: Stability and usability
Authors: Willis Simon A. , Curtis Wyatt A. , Flannigan David J.
Published: July 2024

We tested and compared the stability and usability of three different cathode materials and configurations in a thermionic-based ultrafast electron microscope: (1) on-axis thermionic and photoemission from a custom 100 μm diameter LaB6 source with a graphite guard ring, (2) off-axis photoemission from the Ni aperture surface of the Wehnelt electrode, and (3) on-axis thermionic and photoemission from a custom 200 μm diameter polycrystalline Ta source. For each cathode type and configuration, including the Ni Wehnelt aperture, we illustrate how the photoelectron beam-current stability is deleteriously impacted by simultaneous cooling of the source following thermionic heating. Furthermore, we demonstrate usability via collection of parallel- and convergent-beam electron diffraction patterns and by formation of the optimum probe size. We find that usability of the off-axis Ni Wehnelt-aperture photoemission is at least comparable to on-axis LaB6 thermionic emission, as well as to on-axis photoemission [the heretofore conventional approach to ultrafast electron microscopy (UEM) in thermionic-based instruments]. However, the stability and achievable beam currents for off-axis photoemission from the Wehnelt aperture were superior to that of the other cathode types and configurations, regardless of the electron-emission mechanism. Beam-current stability for this configuration was found to be ±1% (one standard deviation from the mean) for 70 min (longest duration tested), and steady-state beam current was reached within the sampling-time resolution used here (∼1 s) for 15 pA beam currents (i.e., 460 electrons per packet for a 200 kHz repetition rate). Repeatability and robustness of the steady-state condition were also found to be within ±1% of the mean. We discuss the implications of these findings for UEM imaging and diffraction experiments, for pulsed-beam damage measurements, and for practical switching between optimum conventional TEM and UEM operation within the same instrument.
Energies of Fröhlich surface optical phonon in Q1D nanostructures: Curvature and dielectric effects
Authors: Zhang Li , Liang Z. W. , Wang Qi , Shi J. J.
Published: July 2024

Energy of Fröhlich surface optical (SO) phonon in quasi-one-dimensional (Q1D) nanostructures remains doubtful in terms of Raman and photoluminescence experimental data. Based on a notion of the curvature proposed, the confusion is clearly clarified. It is found that the energy interval of SO modes previously accepted in the quantum system could be further divided into two sub-intervals based on the positive and negative curvature of nanowire (NW) and nanohole (NH). Furthermore, the cutoff energy and width of energy sub-intervals in NW and NH can be modulated by altering the dielectric constant of the surrounding medium. Moreover, the physical mechanism of curvature and dielectric effects on the energies of SO phonon in NW and NH are comprehended reasonably from a perspective of electrostatic potential distribution. The calculated energies of SO modes in low-energy sub-interval are fully consistent with the Raman and PL experimental results for AlN, GaN, and InN NWs. It is predicted that SO modes of high-energy sub-interval could be observed in the NH structure. The current theoretical scheme and numerical results not only extend and deepen the knowledge of the energy of the SO phonon but also can be used in the design and development of optical and optoelectronic devices based on SO modes of Q1D nanostructures.
Global expansion of marine protected areas and the redistribution of fishing effort
Authors: McDonald Gavin , Bone Jennifer , Costello Christopher , Englander Gabriel , Raynor Jennifer
Published: July 2024

The expansion of marine protected areas (MPAs) is a core focus of global conservation efforts, with the “30x30” initiative to protect 30% of the ocean by 2030 serving as a prominent example of this trend. We consider a series of proposed MPA network expansions of various sizes, and we forecast the impact this increase in protection would have on global patterns of fishing effort. We do so by building a predictive machine learning model trained on a global dataset of satellite-based fishing vessel monitoring data, current MPA locations, and spatiotemporal environmental, geographic, political, and economic features. We then use this model to predict future fishing effort under various MPA expansion scenarios compared to a business-as-usual counterfactual scenario that includes no new MPAs. The difference between these scenarios represents the predicted change in fishing effort associated with MPA expansion. We find that regardless of the MPA network objectives or size, fishing effort would decrease inside the MPAs, though by much less than 100%. Moreover, we find that the reduction in fishing effort inside MPAs does not simply redistribute outside—rather, fishing effort outside MPAs would also decline. The overall magnitude of the predicted decrease in global fishing effort principally depends on where networks are placed in relation to existing fishing effort. MPA expansion will lead to a global redistribution of fishing effort that should be accounted for in network design, implementation, and impact evaluation.
Kinesin-1-transported liposomes prefer to go straight in 3D microtubule intersections by a mechanism shared by other molecular motors
Authors: Bensel Brandon M. , Previs Samantha Beck , Bookwalter Carol , Trybus Kathleen M. , Walcott Sam , Warshaw David M.
Published: July 2024

Kinesin-1 ensembles maneuver vesicular cargoes through the three-dimensional (3D) intracellular microtubule (MT) network. To define how such cargoes navigate MT intersections, we first determined how many kinesins from an ensemble on a lipid-based cargo simultaneously engage a MT, and then determined the directional outcomes (straight, turn, terminate) for liposome cargoes at perpendicular MT intersections. Run lengths of 350-nm diameter liposomes decorated with up to 20, constitutively active, truncated kinesin-1 KIF5B (K543) were longer than single motor transported cargo, suggesting multiple motor engagement. However, detachment forces of lipid-coated beads with ~20 kinesins, measured using an optical trap, showed no more than three simultaneously engaged motors, with a single engaged kinesin predominating, indicating anticooperative MT binding. At two-dimensional (2D) and 3D in vitro MT intersections, liposomes frequently paused (~2 s), suggesting kinesins simultaneously bind both MTs and engage in a tug-of-war. Liposomes showed no directional outcome bias in 2D (1.1 straight:turn ratio) but preferentially went straight (1.8 straight:turn ratio) in 3D intersections. To explain these data, we developed a mathematical model of liposome transport incorporating the known mechanochemistry of kinesins, which diffuse on the liposome surface, and have stiff tails in both compression and extension that impact how motors engage the intersecting MTs. Our model predicts the ~3 engaged motor limit observed in the optical trap and the bias toward going straight in 3D intersections. The striking similarity of these results to our previous study of liposome transport by myosin Va suggests a “universal” mechanism by which cargoes navigate 3D intersections.
Beyond homogenates: New tool available for estimating glycogen’s numerical subcellular distribution
Authors: Nielsen Joachim
Published: July 2024

This Commentary discusses the implications of a recent JGP study (Ríos et al. https://www.doi.org/10.1085/jgp.202413595) demonstrating an AI model to quantify glycogen granules.
Nonlinear-Optical Analogies in Nuclear-Like Soliton Reactions: Selection Rules, Nonlinear Tunneling and Sub-Barrier Fusion–Fission
Authors: Belyaeva T. L. , Serkin V. N.
Published: July 2024

The main goal of our study is to reveal unexpected but intriguing analogies arising between optical solitons and nuclear physics, which still remain hidden from us. We consider the main cornerstones of the concept of nonlinear optics of nuclear reactions and the well-dressed repulsive-core solitons. On the base of this model, we reveal the most intriguing properties of the nonlinear tunneling of nucleus-like solitons and the soliton self-induced sub-barrier transparency effect. We describe novel interesting and stimulating analogies between the interaction of nucleus-like solitons on the repulsive barrier and nuclear sub-barrier reactions. The main finding of this study concerns the conservation of total number of nucleons (or the baryon number) in nuclear-like soliton reactions. We show that inelastic interactions among well-dressed repulsive-core solitons arise only when a “cloud” of “dressing” spectral side-bands appears in the frequency spectra of the solitons. This property of nucleus-like solitons is directly related to the nuclear density distribution described by the dimensionless small shape-squareness parameter. Thus the Fourier spectra of nucleus-like solitons are similar to the nuclear form factors. We show that the nuclear-like reactions between well-dressed solitons are realized by “exchange” between “particle-like” side bands in their spectra.
Structural and Ferroelectric Transition in Few-Layer HfO2 Films by First Principles Calculations
Authors: Gao 高 Ruiling 瑞灵 , Liu 刘 Chao 超 , Shi 施 Bowen 博文 , Li 李 Yongchang 永昌 , Luo 罗 Bing 兵 , Chen 陈 Rui 睿 , Ouyang 欧 Wenbin 阳文彬 , Gao 高 Heng 恒 , Hu 胡 Shunbo 顺波 , Wang 王 Yin 音 , Li 李 Dongdong 东栋 , Ren 任 Wei 伟
Published: July 2024

The discovery of ferroelectricity in HfO2-based materials with high dielectric constant has inspired tremendous research interest for next-generation electronic devices. Importantly, films structure and strain are key factors in exploration of ferroelectricity in fluorite-type oxide HfO2 films. Here we investigate the structures and strain-induced ferroelectric transition in different phases of few-layer HfO2 films (layer number N = 1–5). It is found that HfO2 films for all phases are more stable with increasing films thickness. Among them, the Pmn21 (110)-oriented film is most stable, and the films of N = 4, 5 occur with a P21 ferroelectric transition under tensile strain, resulting in polarization about 11.8 μC/cm2 along in-plane a-axis. The ferroelectric transition is caused by the strain, which induces the displacement of Hf and O atoms on the surface to non-centrosymmetric positions away from the original paraelectric positions, accompanied by the change of surface Hf–O bond lengths. More importantly, three new stable HfO2 2D structures are discovered, together with analyses of computed electronic structures, mechanical, and dielectric properties. This work provides guidance for theoretical and experimental study of the new structures and strain-tuned ferroelectricity in freestanding HfO2 films.
A comparative study of the Au/n-Si (MS) and Au/(ZnO:CeO2:PVP)/n-Si (MPS) Schottky structures by using current/voltage characteristics in dark and under illumination
Authors: Üstün Oray , Özçelik Uğur , Azizian-Kalandaragh Yashar , Altındal Şemsettin , Özçelik Süleyman
Published: July 2024

In the present study, both metal/semiconductor (MS) and metal/polymer/semiconductor (MPS) Schottky Diodes (SDs) were grown onto the same n-Si wafer to compare their electrical and optical characteristics. Firstly, ZnO and CeO2 nanostructures were synthesized by ultrasonic-assisted method (UAM), and structurally characterized by utilizing x-ray diffraction (XRD), Ultraviolet-visible spectroscopy (UV–vis), and Fourier-Transform-IR (FTIR) methods. The mean submicron crystallite sizes were estimated to be below 11.39 nm for CeO2 and 54.37 nm for ZnO nanostructures through the Debye–Scherrer method. The optical bandgap was calculated as 3.84 eV for CeO2 and 3.88 eV for ZnO nanostructures via Tauc plot. Electrical parameters such as reverse-saturation current (Io), ideality-factor (n), zero-bias barrier height (ΦBo), and rectification-ratio (RR) were found as 0.596 μA, 5.45, 0.64 eV, 2.74 × 105 in dark and 5.54 μA, 5.88, 0.59 eV, 8.60 × 103 under illumination for the MS SD and 0.027 μA, 4.36, 0.72 eV, 1.85 × 107 in dark and 0.714 μA, 5.18, 0.64 eV, 7.61 × 104 under illumination for the MPS SD, respectively. The energy-dependent profile of surface-states was obtained via the Card-Rhoderick method, by considering ΦB(V) and n. RR of the MPS SD is almost sixty-seven times the RR of the MS SD in the dark. The sensitivity of the MPS SD (=710) is nineteen and five-tenths the sensitivity of the MS SD (=36.4), so the MPS SD is considerably more sensitive to illumination. These results indicate that the (ZnO:CeO2:PVP) organic interlayer significantly improves the performance of the MS SD.
Compact magneto-optical traps using planar optics
Authors: Tan 谭 Zhi 智 , Lu 鹿 Bo 博 , Han 韩 Chengyin 成银 , Lee 李 Chaohong 朝红
Published: July 2024

Magneto-optical traps (MOTs) composed of magnetic fields and light fields have been widely utilized to cool and confine microscopic particles. Practical technology applications require miniaturized MOTs. The advancement of planar optics has promoted the development of compact MOTs. In this article, we review the development of compact MOTs based on planar optics. First, we introduce the standard MOTs. We then introduce the grating MOTs with micron structures, which have been used to build cold atomic clocks, cold atomic interferometers, and ultra-cold sources. Further, we introduce the integrated MOTs based on nano-scale metasurfaces. These new compact MOTs greatly reduce volume and power consumption, and provide new opportunities for fundamental research and practical applications.
Interaction between the core and the edge for ion cyclotron resonance heating based on artificial absorption plasma model
Authors: LIU 刘 Zhuoqi 卓琪 , ZHANG 张 Jiahui 珈珲 , WU 吴 Kaibang 凯邦 , ZHANG 张 Xinjun 新军 , QIN 秦 Chengming 成明 , WANG 王 Feng 丰 , WANG 王 Zhengxiong 正汹
Published: July 2024

In numerical simulations of the ion cyclotron range of frequencies (ICRF) wave heating scheme, core solvers usually focus on wave propagation and absorption mechanisms within the core plasma region. However, the realistic scrape-off layer (SOL) plasma is usually simplified, making it difficult to have deeper understanding of wave propagation and absorption within the SOL. In this work, we employ a cold plasma assumption and an artificial absorption mechanism based on the approach of reference (Zhang et al 2022 Nucl. Fusion
62 076032), to study wave propagation and absorption in the realistic SOL plasma of the EAST. During the exponential decay of the total coupled power with respect to the toroidal mode numbers, several fluctuations are observed in the case of low collisional frequencies. The fluctuations may be caused by the cavity modes associated with specific toroidal mode numbers. Due to the presence of cut-off densities, the edge power losses and the total coupled power exhibit different behaviors before and after the cut-off layer is “open”. Furthermore, the simulation results obtained from the kinetic model in reference (Zhang et al 2022 Nucl. Fusion
62 076032) is discussed. This suggests that both the core-edge combined model and the artificial mechanism are capable of simulating wave propagation and absorption.
Approaching periodic systems in ensemble density functional theory via finite one-dimensional models
Authors: Leano Remi J , Pribram-Jones Aurora , Strubbe David A
Published: July 2024

Ensemble density functional theory (EDFT) is a generalization of ground-state DFT, which is based on an exact formal theory of finite collections of a system’s ground and excited states. EDFT in various forms has been shown to improve the accuracy of calculated energy level differences in isolated model systems, atoms, and molecules, but it is not yet clear how EDFT could be used to calculate band gaps for periodic systems. We extend the application of EDFT toward periodic systems by estimating the thermodynamic limit with increasingly large finite one-dimensional ‘particle in a box’ systems, which approach the uniform electron gas (UEG). Using ensemble-generalized Hartree and local spin density approximation exchange-correlation functionals, we find that corrections go to zero in the infinite limit, as expected for a metallic system. However, there is a correction to the effective mass, with results comparable to other calculations on 1D, 2D, and 3D UEGs, which indicates promise for non-trivial results from EDFT on periodic systems.
Structural health monitoring of a swivel bridge for evaluating builder comfort under train-induced vibration
Authors: Huaxi Lu , Yuting Deng , Xiang Wang
Published: July 2024

The swivel bridge being built overcrossing the railway service line, the builder’s comfort level under the train-induced vibration is one of the critical issues in the bridge construction process. This study compares the applicability and usage limits of existing vibration comfort evaluation indicators for reasonably selected vibration comfort evaluation criteria. A framework is therefore proposed to evaluate builder comfort under train-induced vibrations during the construction process. Taking a swivel bridge overcrossing the Shanghai-Kunming railway line as an example, the structural health monitoring system is performed in three construction stages of the swivel bridge. Then, the acceleration response is measured, the acceleration-based evaluation indicators are compared, and the builder comfort level is evaluated in the three construction stages. The results demonstrate that the on-site measured indicators are close to the standard limits, and the builder comfort on the swivel bridge under the excitation of passing trains should be given attention.
Set values for mean field games
Authors: İşeri̇ Meli̇h , Zhang Jianfeng
Published: July 2024

In this paper we study mean field games with possibly multiple mean field equilibria. Instead of focusing on the individual equilibria, we propose to study the set of values over all possible equilibria, which we call the set value of the mean field game. When the mean field equilibrium is unique, typically under certain monotonicity conditions, our set value reduces to the singleton of the standard value function which solves the master equation. The set value is by nature unique, and we shall establish two crucial properties: (i) the dynamic programming principle, also called time consistency; and (ii) the convergence of the set values of the corresponding

N
N

-player games, which can be viewed as a type of stability result. To our best knowledge, this is the first work in the literature which studies the dynamic value of mean field games without requiring the uniqueness of mean field equilibria. We emphasize that the set value is very sensitive to the type of the admissible controls. In particular, for the convergence one has to restrict to corresponding types of equilibria for the N-player game and for the mean field game. We shall illustrate this point by investigating three cases, two in finite state space models and the other in a continuous time model with controlled diffusions.
Restrictions on Anosov subgroups of 𝑆𝑝(2𝑛,ℝ)
Authors: Dey Subhadip , Greenberg Zachary , Riestenberg J.
Published: July 2024

Let

n
∈

N

n\in \mathbb {N}

and let

Θ
⊂
{
1
,
…
,
n
}

\Theta \subset \{1,\dots ,n\}

be a nonempty subset. We prove that if

Θ
\Theta

contains an odd integer, then any

P
Θ

P_\Theta

-Anosov subgroup of

Sp
⁡
(
2
n
,

R

)

\operatorname {Sp}(2n,\mathbb {R})

is virtually isomorphic to a free group or a surface group. In particular, any Borel Anosov subgroup of

Sp
⁡
(
2
n
,

R

)

\operatorname {Sp}(2n,\mathbb {R})

is virtually isomorphic to a free or surface group. On the other hand, if

Θ
\Theta

does not contain any odd integers, then there exists a

P
Θ

P_\Theta

-Anosov subgroup of

Sp
⁡
(
2
n
,

R

)

\operatorname {Sp}(2n,\mathbb {R})

which is not virtually isomorphic to a free or surface group. We also exhibit new examples of maximally antipodal subsets of certain flag manifolds; these arise as limit sets of rank

1
1

subgroups.
Morse boundaries of 3-manifold groups
Authors: Zbinden Stefanie
Published: July 2024

We classify the homeomorphism types of the Morse boundaries of all 3-manifold groups into 9 different possible homeomorphism types, and show how the Morse boundary depends on the geometric decomposition.
‘A movie about flowers?’ Notes on the ecological turn in adaptation studies
Authors: Elliott Tomas
Published: July 2024

This article takes up and responds to the recent ecological turn in adaptation studies, exploring the discipline’s widespread interest in the overlap between the notion of adaptation in evolutionary biology and the notion of adaptation in literature, film, and media studies. It argues that in order to develop a historically and ecocritically alert approach to adaptation studies, it is necessary to unpack what is at stake in using biological terms and paradigms to study adaptation in art. Firstly, it offers a survey of several studies that have explored the overlap between adaptation in nature and adaptation in culture, arguing that these have been overly influenced by the notions of neo-Darwinism that were popularized by Richard Dawkins in The Selfish Gene (1976). Secondly, it offers a rereading of the film that has become a primary case study among theorists who have reached for biological metaphors to explain cultural change: Adaptation (2002). It argues that whereas scholars have often tended to use Adaptation as a springboard from which to launch an exploration of the purported homology between adaptation in nature and adaptation in art, in fact, the film’s evolutionary themes are clearly historicizable, tied to a set of values coordinated around ideas of heteronormative reproductivity, dissemination, and growth. Examining those values helps to demonstrate how the film’s evolutionary themes are deployed as part of its representational strategies, thereby challenging the idea that they might be unproblematically used to describe the overlap between adaptation in biology and adaptation in art.
RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies
Authors: Ianevski Aleksandr , Kushnir Aleksandr , Nader Kristen , Miihkinen Mitro , Xhaard Henri , Aittokallio Tero , Tanoli Ziaurrehman
Published: July 2024

RepurposeDrugs (https://repurposedrugs.org/) is a comprehensive web-portal that combines a unique drug indication database with a machine learning (ML) predictor to discover new drug-indication associations for approved as well as investigational mono and combination therapies. The platform provides detailed information on treatment status, disease indications and clinical trials across 25 indication categories, including neoplasms and cardiovascular conditions. The current version comprises 4314 compounds (approved, terminated or investigational) and 161 drug combinations linked to 1756 indications/conditions, totaling 28 148 drug–disease pairs. By leveraging data on both approved and failed indications, RepurposeDrugs provides ML-based predictions for the approval potential of new drug–disease indications, both for mono- and combinatorial therapies, demonstrating high predictive accuracy in cross-validation. The validity of the ML predictor is validated through a number of real-world case studies, demonstrating its predictive power to accurately identify repurposing candidates with a high likelihood of future approval. To our knowledge, RepurposeDrugs web-portal is the first integrative database and ML-based predictor for interactive exploration and prediction of both single-drug and combination approval likelihood across indications. Given its broad coverage of indication areas and therapeutic options, we expect it accelerates many future drug repurposing projects.
Comparative analysis of integrative classification methods for multi-omics data
Authors: Novoloaca Alexei , Broc Camilo , Beloeil Laurent , Yu Wen-Han , Becker Jérémie
Published: July 2024

Recent advances in sequencing, mass spectrometry, and cytometry technologies have enabled researchers to collect multiple ’omics data types from a single sample. These large datasets have led to a growing consensus that a holistic approach is needed to identify new candidate biomarkers and unveil mechanisms underlying disease etiology, a key to precision medicine. While many reviews and benchmarks have been conducted on unsupervised approaches, their supervised counterparts have received less attention in the literature and no gold standard has emerged yet. In this work, we present a thorough comparison of a selection of six methods, representative of the main families of intermediate integrative approaches (matrix factorization, multiple kernel methods, ensemble learning, and graph-based methods). As non-integrative control, random forest was performed on concatenated and separated data types. Methods were evaluated for classification performance on both simulated and real-world datasets, the latter being carefully selected to cover different medical applications (infectious diseases, oncology, and vaccines) and data modalities. A total of 15 simulation scenarios were designed from the real-world datasets to explore a large and realistic parameter space (e.g. sample size, dimensionality, class imbalance, effect size). On real data, the method comparison showed that integrative approaches performed better or equally well than their non-integrative counterpart. By contrast, DIABLO and the four random forest alternatives outperform the others across the majority of simulation scenarios. The strengths and limitations of these methods are discussed in detail as well as guidelines for future applications.
DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations
Authors: Lei Yahui , Huang Xiao-Tai , Guo Xingli , Hang Katie Chan Kei , Gao Lin
Published: July 2024

Inferring gene regulatory networks (GRNs) allows us to obtain a deeper understanding of cellular function and disease pathogenesis. Recent advances in single-cell RNA sequencing (scRNA-seq) technology have improved the accuracy of GRN inference. However, many methods for inferring individual GRNs from scRNA-seq data are limited because they overlook intercellular heterogeneity and similarities between different cell subpopulations, which are often present in the data. Here, we propose a deep learning-based framework, DeepGRNCS, for jointly inferring GRNs across cell subpopulations. We follow the commonly accepted hypothesis that the expression of a target gene can be predicted based on the expression of transcription factors (TFs) due to underlying regulatory relationships. We initially processed scRNA-seq data by discretizing data scattering using the equal-width method. Then, we trained deep learning models to predict target gene expression from TFs. By individually removing each TF from the expression matrix, we used pre-trained deep model predictions to infer regulatory relationships between TFs and genes, thereby constructing the GRN. Our method outperforms existing GRN inference methods for various simulated and real scRNA-seq datasets. Finally, we applied DeepGRNCS to non-small cell lung cancer scRNA-seq data to identify key genes in each cell subpopulation and analyzed their biological relevance. In conclusion, DeepGRNCS effectively predicts cell subpopulation-specific GRNs. The source code is available at https://github.com/Nastume777/DeepGRNCS.
Using citizen science data for predicting the timing of ecological phenomena across regions
Authors: Capinha César , Ceia-Hasse Ana , de-Miguel Sergio , Vila-Viçosa Carlos , Porto Miguel , Jarić Ivan , Tiago Patricia , Fernández Néstor , Valdez Jose , McCallum Ian , Pereira Henrique Miguel
Published: July 2024

The scarcity of long-term observational data has limited the use of statistical or machine-learning techniques for predicting intraannual ecological variation. However, time-stamped citizen-science observation records, supported by media data such as photographs, are increasingly available. In the present article, we present a novel framework based on the concept of relative phenological niche, using machine-learning algorithms to model observation records as a temporal sample of environmental conditions in which the represented ecological phenomenon occurs. Our approach accurately predicts the temporal dynamics of ecological events across large geographical scales and is robust to temporal bias in recording effort. These results highlight the vast potential of citizen-science observation data to predict ecological phenomena across space, including in near real time. The framework is also easily applicable for ecologists and practitioners already using machine-learning and statistics-based predictive approaches.
Do Patients with Inflammatory Bowel Disease Really Know What Other Immune-mediated Inflammatory Diseases They Are Diagnosed with?
Authors: de Francisco Ruth , Pérez-Martínez Isabel , Castaño-García Andrés , Carballo-Folgoso Lorena , Flórez-Díez Pablo , García-Pérez Cristina , Fernández-González Emilia , Rolle Valeria , Chiminazzo Valentina , Queiro Rubén , Alonso-Castro Sara , Santos-Juanes Jorge , Gueimonde Miguel , Riestra Sabino
Published: July 2024

Background and Aims

The association of inflammatory bowel disease [IBD] with other immune-mediated inflammatory diseases [IMIDs] in the same patient is well known. We aimed to evaluate the degree of knowledge that patients with IBD have regarding the coexistence of other IMIDs, and to analyse the factors associated with concordance between self-reported and confirmed medical information.

Methods

Patients with IBD at a tertiary hospital answered a questionnaire on the presence of 54 IMIDs [self-reported diagnosis], and their IMID diagnosis was confirmed in their medical records [reference diagnosis]. Agreement between the self-reported IMID and IMID according to medical records was evaluated. The association between concordance and different predictors was evaluated using logistic regression models.

Results

A total of 1,620 patients were included; 626 [39%] patients were diagnosed with at least one IMID, and 177 [11%] with two or more. Overall agreement between patients´ self-report and medical records was k:0.61. When we grouped IMIDs according to affected organs or systems, agreement on rheumatic IMIDs was moderate [k:0.58], whereas agreement on cutaneous [k:0.66], endocrine [k: 0.74,] and ocular [k:0.73] IMIDs was substantial. Among patients who had IMIDs, the factor associated with greater concordance was female gender; less concordance was associated with a lower educational level and the fact that the IMID had been diagnosed at the same time or later than IBD.

Conclusion

The knowledge that patients with IBD have regarding the coexistence of other IMIDs is poor, particularly in rheumatic IMIDs.
An assemblage-level comparison of genetic diversity and population genetic structure between island and mainland ant populations
Authors: Naughton Ida , Tsutsui Neil D , Ward Philip S , Holway David A
Published: July 2024

Island biotas provide unparalleled opportunities to examine evolutionary processes. Founder effects and bottlenecks, e.g., typically decrease genetic diversity in island populations, while selection for reduced dispersal can increase population structure. Given that support for these generalities mostly comes from single-species analyses, assemblage-level comparisons are needed to clarify how (i) colonization affects the gene pools of interacting insular organisms, and (ii) patterns of genetic differentiation vary within assemblages of organisms. Here, we use genome-wide sequence data from ultraconserved elements (UCEs) to compare the genetic diversity and population structure of mainland and island populations of nine ant species in coastal southern California. As expected, island populations (from Santa Cruz Island) had lower expected heterozygosity and Watterson’s theta compared to mainland populations (from the Lompoc Valley). Island populations, however, exhibited smaller genetic distances among samples, indicating less population subdivision. Within the focal assemblage, pairwise Fst values revealed pronounced interspecific variation in mainland-island differentiation, which increases with gyne body size. Our results reveal population differences across an assemblage of interacting species and illuminate general patterns of insularization in ants. Compared to single-species studies, our analysis of nine conspecific population pairs from the same island-mainland system offers a powerful approach to studying fundamental evolutionary processes.
Low-energy building insulation through external wall modification: a case study on Lanzhou Academy of Painting in China
Authors: Wang Xiaoxiao , Xing Kun , Feng Xinshu , Li Ziyi
Published: July 2024

This study analyzes the external wall insulation of Lanzhou Academy of Painting, China, clarifies the thermal storage performance and characteristics of insulation materials according to local conditions, and proposes an insulation technique that combines external insulation of external walls with a double-skin façade. Based on the characteristics of passive low-energy buildings, the passive façade design with high-performance insulation materials was selected according to local conditions. The insulation performance of such buildings is studied under the conditions of no thermal bridge, high air tightness, waterproof and vapor isolation, and a sunlight shield. Our findings can promote the implementation of passive ultra-low energy-consumption designs in China. Based on the design of double outer skin, the use of thermal insulation and environmental protection materials as well as the control of air flow rate is used to improve the thermal insulation performance of the wall, through the computer simulation to compare the new design of the outer skin to Lanzhou Painting Academy as a pilot. It is proved that the composite double outer surface can be used in a large area of public buildings in cold regions. The low energy consumption double composite exterior skin designed in this article can be adjusted through its own air inlet and outlet size, the reasonable use of natural conditions to achieve the effect of heat preservation and heat dissipation. Through the simulation of the spectral diagram to compare the traditional outer skin and the innovative double skin heat storage performance differences, the simulation shows that the traditional thermal insulation outer skin heat storage capacity is uniform and need to be combined with other devices to achieve indoor thermal insulation, double skin through its own regulation using the control of air convection combined with the new thermal insulation materials to achieve lower energy consumption, heat storage effect is better. In order to compare the effect, the Swire room temperature simulation is carried out using the design of local double-layer exterior and traditional outer skin splicing, and the difference in spectral performance of the two types of walls is obtained intuitively. The use of double skin can regulate the heat storage capacity of the wall to directly affect the room temperature, which can be used in large public buildings in cold regions of China to achieve energy saving and carbon reduction.
Selector of amino-acid scales set
Authors: Vrdoljak Anton , Vukičević Damir
Published: July 2024

Experimental and theoretical properties of amino acids as building blocks of peptides and proteins have been extensively researched. Each such method assigns a number to each amino acid, and one such assignment is called amino-acid scale. Their usage in bioinformatics to explain and predict behaviour of peptides and proteins is of essential value. The number of such scales is very large. There are more than a hundred scales related just to hydrophobicity. A large number of scales can be a computational burden for algorithms that try to define peptide descriptors combining several of these scales. Hence, it is of interest to construct a smaller, but still representative set of scales. Here, we present software that does this. We test it on the set of scales using a database constructed by Kawashima and collaborators and show that it is possible to significantly reduce the number of scales observed without losing much of the information. An algorithm is implemented in C#. As a result, we provide a smaller database that might be a very useful tool for the analyses and construction of new peptides. Another interesting application of this database would be to compare the artificial intelligence construction of peptides having as an input the complete Kawashima database and this reduced one. Obtaining in both cases similar results would give much credibility to the constructs of such AI algorithms.