bluuebunny/crossref_metadata_2025 huggingface dataset:
Production of positronium chloride: A study of the charge exchange reaction between Ps and Cl−
Authors: Lévêque-Simon K. , Camper A. , Taïeb R. , Caillat J. , Lévêque C. , Giner E.
Published: March 2024

We present cross sections for the formation of positronium chloride (PsCl) in its ground state from the charge exchange between positronium (Ps) and chloride (Cl−) in the range of 10 meV–100 eV Ps energy. We have used theoretical models based on the first Born approximation in its three-body formulation. We simulated the collisions between Ps and Cl− using ab initio binding energies and positronic wave functions at both the mean-field and correlated levels extrapolated to the complete basis set limit. The accuracy of these ab initio data was benchmarked on the PsF system with the existing highly accurate results, including the very recent quantum Monte Carlo results. We have investigated Ps excited states up to n = 4. The results suggest that the channel Ps(n = 2) is of particular interest for the production of PsCl in the ground state and shows that an accurate treatment of correlation effects (i.e., electron–electron and electron–positron correlations) leads to a significant change in the magnitude of the PsCl production cross section with respect to the mean-field level.
Super-resolution reconstruction for subsurface defects of optical elements based on CdSe/ZnS quantum dots fluorescence dichroism
Authors: Li Rong , Wang Chunyang , Wu Yajie , Liu Xuelian , Cui Yana , Xiao Bo , Deng Linzhe
Published: March 2024

The subsurface defects (SSD) of optical elements have a significant impact on the service life and laser damage threshold of the inertial confinement nuclear fusion optical system. Due to the optical diffraction limit, fluorescence microscopy has limited image resolution for detecting SSD in optical elements, making it challenging to meet the requirements for precision detection. A super-resolution method is proposed in this paper for detecting SSD in optical elements based on the fluorescence polarization characteristics of CdSe/ZnS quantum dots fluorescence dichroism. By enhancing the imaging sparsity of adjacent fluorophores through a polarization modulated excitation laser and utilizing the fluorescence polarization modulation algorithm, the resolution is achieved beyond the optical diffraction limit. The results demonstrate that the proposed method in this paper can obtain super-resolution images of SSD in optical elements with at least a two-fold increase in lateral resolution. This approach effectively improves detection accuracy for SSD and holds significant guiding significance. In addition, it also has application value for assessing the quality of high-precision optical elements.
Island myriads in periodic potentials
Authors: Lazarotto Matheus J. , Caldas Iberê L. , Elskens Yves
Published: March 2024

A phenomenon of emergence of stability islands in phase space is reported for two periodic potentials with tiling symmetries, one square and the other hexagonal, inspired by bidimensional Hamiltonian models of optical lattices. The structures found, here termed as island myriads, resemble web-tori with notable fractality and arise at energy levels reaching that of unstable equilibria. In general, the myriad is an arrangement of concentric island chains with properties relying on the translational and rotational symmetries of the potential functions. In the square system, orbits within the myriad come in isochronous pairs and can have different periodic closure, either returning to their initial position or jumping to identical sites in neighbor cells of the lattice, therefore impacting transport properties. As seen when compared to a more generic case, i.e., the rectangular lattice, the breaking of square symmetry disrupts the myriad even for small deviations from its equilateral configuration. For the hexagonal case, the myriad was found but in attenuated form, mostly due to extra instabilities in the potential surface that prevent the stabilization of orbits forming the chains.
Driven electron g-factor anisotropy in layered III–V semiconductors: Interfacing, tunnel coupling, and structure inversion asymmetry effects
Authors: Toloza Sandoval M. A. , Leon Padilla J. E. , Wanderley A. B. , Sipahi G. M. , Diniz Chubaci J. F. , Ferreira da Silva A.
Published: March 2024

A key piece for spintronic applications, the so-called electron g-factor engineering is still predominantly based on the semiconductor bulk g factor and its dependence on the bandgap energy. In nanostructures, however, the mesoscopic confinement introduces exclusive anisotropies, transforming scalar g factors into tensors, enabling different renormalization mechanisms as routes for fine-tuning the electron g factor. These questions we address in this comparative theoretical analysis between the obtained electron g-factor (tensor) anisotropies for realistic InAs|AlSb- and In0.53Ga0.47As|InP-based multilayers. The electron g-factor anisotropy, i.e., the difference between g factors for magnetic fields parallel and perpendicular to the interfaces, is analytically calculated via perturbation theory using the envelope-function approach based on the eight-band Kane model. Effects from bulk, interfacing, tunnel coupling, and structure inversion asymmetry are systematically introduced within a transparent comparative view; differences between obtained anisotropies, such as in the magnitude, sign, and other fine details, are analyzed in terms of the heterostructure parameters, mapped over different confining and tunnel-coupling regimes without requiring elaborated numerical computations.
Fast and high-precision compressible flowfield inference method of transonic airfoils based on attention UNet
Authors: Zhu Zhijie , Zhao Guoqing , Zhao Qijun
Published: March 2024

Traditional numerical simulation methods for airfoil flowfields are complex and time-consuming, and deep learning-based inference methods for Reynolds-averaged Navier–Stokes equations (RANS) solutions of transonic airfoils have limitations in terms of their robustness and generalization. A novel data-driven inference method named as attention UNet (AU)-RANS is proposed for efficient and accurate prediction of flowfields around airfoils with strong compressibility and large-scale turbulent separation. First, to enhance the learning the boundary flow information and inference of the entire flowfield solution, an innovative data preprocessing method is proposed to convert the physical quantities and coordinate information of RANS solutions into neural network spatial information. Second, an attention mechanism is introduced in UNet to suppress feature responses in irrelevant background regions and enhance sensitivity to the geometrical features of the input airfoil and varying inflow conditions. The quantitative and qualitative analyses of AU-RANS inference results demonstrate that the well-trained model can effectively infer RANS solutions for airfoil flowfield and can accurately predict the shock waves and flow separation phenomena under high Mach number conditions with a large angle of attack.
Study of dielectric-based thermal management of second-life battery packs with rectangular vortex generators
Authors: Joy Jibin M. , Kumar Ashish , Rakshit Dibakar
Published: March 2024

The performance of lithium-ion battery (LiB) is influenced by the operational temperature. The thermal management of the battery module depends upon the interaction between coolant and battery surface. The study focuses on analysis of vortex interactions as a commercial dielectric coolant (FC 3283) circulates within battery module. The analysis indicates that the arrangement reduces the maximum average temperature by 26 °C in comparison with the conventional methods. However, a maximum temperature difference of 4 °C persists at final row of battery cells. Therefore, the vortex generators (V.G.) are deployed to alter the flow behavior to achieve uniform cooling of LiB. Rectangular V.G. alleviates the temperature difference by stretching primary vortices. The V.G.s promote smaller induced vortices, enabling a multiscale distribution of turbulent kinetic energy, reducing the concentration of turbulence near central region of the cell. The induced vortices ensure uniform heat transfer along the cell length. Furthermore, a 15% increase in vorticity magnitude and a 33% rise in an average Nusselt number in the region near the last-row cells is achieved. Overall, employment of V.G.s results in a 2.5 °C reduction in maximum cell temperature difference. A novel metric, the operational effectiveness factor (OEF), is coined to assess the combined effect of heat transfer enhancement and additional pumping requirements resulting from the different positions of the V.G. A high OEF value implies the ability of the configuration to maintain a more uniform cell temperature while ensuring lower parasitic power. Middle V.G. configuration achieved highest OEF of 1.35, while bottom V.G. configuration exhibited lowest OEF of 1.11.
Fluid–rigid body coupling simulations with the passively moving solid model based on a physically consistent particle method
Authors: Negishi Hideyo , Kondo Masahiro , Takahashi Hidenao , Amakawa Hiroaki , Obara Shingo , Kurose Ryoichi
Published: March 2024

Fluid–rigid body interaction is a significant topic in research on particle methods. This study developed a fluid–rigid body coupling method based on a physically consistent particle method, i.e., the moving particle hydrodynamics (MPH) method, incorporating the passively moving solid (PMS) model. When the discrete particle system satisfies the fundamental laws of physics, i.e., mass conservation, linear and angular momentum conservation, and the second law of thermodynamics, the method is asserted physically consistent, and this feature is important for robust dynamic calculations. The PMS model is a pioneering approach that is practical for particle methods in which fluid and rigid-body particles are initially calculated as a fluid. Then, only rigid-body particles are modified to restore the initial shape by applying rigid-body constraints. Thus, combining the MPH method and the PMS model realizes a fluid–rigid body coupling method that satisfies fundamental physical laws. The proposed method was first verified via the fundamental rigid body and fluid–rigid body coupling problems: the Dzhanibekov effect on a T-shaped rigid body, a floating rectangular solid, a floating cylinder, and water entry of a two-dimensional cylinder. Second, the proposed method was validated via calculating a cylinder rolling on a liquid film as a fluid–rigid body coupling problem with rotation. By using a potential-based surface tension model, the computed results showed reasonable agreement with the experimental data obtained in this study. Overall, it was confirmed that the proposed method is a promising fluid–rigid body coupling approach, in which the surface tension and wettability can be considered as well.
Statistical characterization of the collective synchrotron radiation power emitted by non-ideal magnetized plasma fluids in relativistic jets
Authors: Cremaschini Claudio , Kovář Jiří
Published: March 2024

The problem of determining the collective synchrotron radiation power emitted by non-ideal magnetized plasma fluids at kinetic equilibrium in relativistic jets is addressed. A covariant statistical kinetic approach is implemented based on a novel solution for the corresponding non-isotropic kinetic distribution function (KDF). This is expressed by a Gaussian-like solution that is consistent with relativistic magnetic moment conservation holding in collisionless magnetized plasmas and predicts tensorial equation of state and pressure anisotropy which are specific for these systems. Notably, the same equilibrium admits also a convergent integrable Chapman–Enskog series expansion around a leading-order Juttner distribution, which affords the analytical calculation of continuum fluid fields. In this reference, it is shown that the statistical average of total synchrotron power evaluated over the non-isotropic KDF differs significantly from the corresponding ensemble estimate that would be trivially obtained if the underlying velocity distribution were purely isotropic. It is pointed out that the knowledge of such a statistical discrepancy on the radiation-power curve could provide an independent framework for the characterization of the physical properties of the relativistic plasma state or of the background magnetic field that permeates these astrophysical scenarios.
Superancillary Equations for the Multiparameter Equations of State in REFPROP 10.0
Authors: Bell Ian H.
Published: March 2024

Superancillary equations have been developed for the recommended (by NIST) multiparameter equations of state (EOS) for all 147 pure fluids in NIST REFPROP 10.0. These superancillary equations represent the orthobaric densities and saturation pressure of the EOS as a function of temperature by Chebyshev expansions to an accuracy better than the iterative calculations in REFPROP and are hundreds to thousands of times faster to evaluate than a full iterative solution of Maxwell’s criteria. The C++ code required to develop and test the superancillary equations is provided as open-source material. The methodology is straightforwardly extensible to new multiparameter EOS, establishing a new paradigm for the evaluation of vapor–liquid equilibria for pure fluids.
Tuning methods for multigap drift tube linacs
Authors: Shelbaya O. , Baartman R. , Braun P. , Jung P. M. , Kester O. , Planche T. , Podlech H. , Rädel S. D.
Published: March 2024

Multigap cavities are used extensively in linear accelerators to achieve velocities up to a few percent of the speed of light, driving nuclear physics research around the world. Unlike for single-gap structures, there is no closed-form expression to calculate the output beam parameters from the cavity voltage and phase. To overcome this, we propose to use a method based on the integration of the first and second moments of the beam distribution through the axially symmetric time-dependent fields of the cavity. A beam-based calibration between the model’s electric field scaling and the machine’s rf amplitudes is presented, yielding a fast online energy change method, returning cavity amplitude and phase necessary for a desired output beam energy and energy spread. The method is validated with 23Na6+ beam energy measurements.
Effect of surface peak-valley features on the fluid flow performance in rough contact interface
Authors: Ji Jiawei , Liu Kun , Sun Wei , Zheng Cheng , Liu Xiaojun , Du Yu , Ye Jiaxin , Jiao Yunlong
Published: March 2024

In this work, two kinds of microtextured surfaces with different surface peak-valley features, namely positively skewed surface with micropillar array and negatively skewed surface with micropit array, are prepared to explore the effect of peak-valley features on the fluid flow performance in rough contact interface. The distribution and connectivity of microchannels is analyzed, and the physical mechanism of peak-valley features inducing different fluid flow processes is also derived through constructing a kinetic model of fluid spreading. It is found that when the surface skewness Ssk > 0, the positively skewed surface forms the void regions with better connectivity in the interface compared with the negatively skewed surface (Ssk < 0), despite both the surfaces having nearly the same roughness (Sa ∼ 3.6 mm). The formed microchannels are defined as crossed open microchannel and semi-closed microchannel, respectively, and the feature length of the microchannel decreases with the increase in load. The quantitative results of fluid flow demonstrate that the liquid has a better spreading and flow ability in the contact interface of the positively skewed surface. Even under the same microchannel feature length (nearly 48 mm), the fluid spread area ratio of the positively skewed surface has an order of magnitude higher than that of the negatively skewed surface. The mechanism of different flow characteristics induced by surface peak-valley features is believed as the variation of the microchannel shape, leading to the change in the capillary pressure at the meniscus. We believe the present work would lay a theoretical foundation for regulating the microscopic flow behavior in the contact interface.
Intelligent prediction of non-Newtonian hybrid nanoparticle-enhanced fluid flow and heat transfer behaviours in a trapezoidal enclosure: Integrated simulation approach
Authors: Bibi Aneela , Xu Hang , Ullah Naeem
Published: March 2024

This study investigates the utilization of a trapezoidal cavity with a corrugated bottom wall containing a Carreau hybrid nanofluid composed of water, aluminum, and copper nanoparticles. A heated, rotating cylinder is placed at the center of the enclosure in the presence of an external magnetic field. The impact of Forchheimer and Brinkman porous medium models on the hybrid nanofluid is examined. Three different inlet–outlet placement configurations are considered to investigate their influence on heat transfer. The governing equations for fluid flow and heat transfer are solved numerically. Through simulations, a range of flow-controlling variables is systematically adjusted, including the Darcy number, Reynolds number, Hartmann number, nanoparticle volume fraction, undulation on the hot bottom wall, power law index, and rotational speed of the inner heated cylinder. The results demonstrate that the hybrid nanofluid and rotating cylinder significantly enhance heat transfer within the trapezoidal cavity. Higher values of the Darcy number, Reynolds number, and nanoparticle volume fraction lead to increased heat transfer rates. The placement configuration of the inlet and outlet ports also affects heat transfer performance, with the bottom-top configuration yielding the best results. Furthermore, a comparative analysis of flow profiles and heat distribution is conducted using the multiple expression programing technique. The proposed model accurately predicts the flow and heat transfer characteristics in the trapezoidal cavity, as validated through comparison with provided data sets.
Ion evaporation-induced tip streaming from liquid drops of ionic liquids
Authors: Chen Chong , Fan Yipeng , Xia Guangqing , Lu Chang , Sun Bin , Han Yajie
Published: March 2024

Ion evaporation from charged surfaces of ionic liquids has aroused significant interest due to its wide range of applications in various fields, such as ionic liquid ion sources (ILIS), electrospray thrusters, and high-precision etching, among others. This study delves into the transient electrohydrodynamics of ionic liquid drops undergoing ion evaporation with the assistance of an externally applied electric field. A transient electrohydrodynamic (EHD) model is developed to make up for the dearth of direct observation (visualization). A structure morphologically resembling the traditional cone-jet is depicted, featuring charged jets emitted from the drop's ends that subsequently break into tiny droplets. In contrast to the traditional cone-jet, this structure forms through a distinct mechanism, with charge depletion induced by ion evaporation playing a crucial role. A comprehensive exploration of parameter influences reveals the following key findings: (a) the normalized radius of the jets increases with the augmentation of the dimensionless number Ξ, which is defined as the ratio of the electric potential energy of ions to their activation energy for evaporation; (b) enhancing the electric Bond number Bo, which quantifies the ratio of Maxwell stress to surface tension, expedites the temporal evolution of tip streaming.
Sisal and jute composite containing carbon nanotubes for improved mechanical and thermal performance
Authors: Sathish T. , Giri Jayant , R. Saravanan , Makki Emad
Published: March 2024

Natural fiber composites are often sought after in industries, such as automotive and aerospace, due to their low density compared to traditional synthetic composites. Sisal and jute are renewable and biodegradable resources, making them attractive from a sustainability standpoint. The effect of carbon nanotube (CNT) insertion of a composed sisal and jute fiber composite material on the thermal and mechanical characteristics is investigated in this study. The primary objective of this research is to determine the exceptional mechanical strength and heat resistance that allows the composite-filled filling CNT to perform better than others. The methodical experimental approach was used to evaluate the effect of sisal and jute matrix and different amounts of CNTs’ mechanical and thermal properties. Thermal behavior is found by thermogravimetric analysis, and mechanical performance is used to qualify tensile strength, flexural strength, and impact resistance. The result suggests that CNTs may have reinforcing properties and significant tensile and flexural strength improvement. Impact resistance improved and increased the toughness of the composite material. The 7% CNT composite exhibited improvements in tensile strength of 63.9% and flexural strength of 46.6%, suggesting the synergistic reinforcing effect of CNTs. The high temperature from the use of need resistance shows promise for the composite material based on the tests of its capability for heat absorption and thermal stability. Various technical contexts are potentially useful in focusing on environmentally friendly material creation that exhibits exceptional thermal and mechanical properties.
Phenomenology of transition to quantum turbulence in flows of superfluid helium
Authors: Skrbek Ladislav , Schmoranzer David , Sreenivasan Katepalli R.
Published: March 2024

Transition from laminar to turbulent states of classical viscous fluids is complex and incompletely understood. Transition to quantum turbulence (QT), by which we mean the turbulent motion of quantum fluids such as helium II, whose physical properties depend on quantum physics in some crucial respects, is naturally more complex. This increased complexity arises from superfluidity, quantization of circulation, and, at finite temperatures below the critical, the two-fluid behavior. Transition to QT could involve, as an initial step, the transition of the classical component, or the intrinsic or extrinsic nucleation of quantized vortices in the superfluid component, or a simultaneous occurrence of both scenarios—and the subsequent interconnected evolution. In spite of the multiplicity of scenarios, aspects of transition to QT can be understood at a phenomenological level on the basis of some general principles, and compared meaningfully with transition in classical flows.
Interactional multimodal metadiscourse in public health posters during the COVID-19 pandemic
Authors: Al-Subhi Aisha Saadi
Published: March 2024

While language remains a constant channel of communication, visual information also plays a significant role in
contemporary communication. This study explores the application of interactional metadiscourse and meaning-making in public health
posters issued during the COVID-19 crisis. It examines both the textual and visual communicative strategies adopted in the
multimodal texts of 60 COVID-19 posters published on the official websites of the World Health Organization and the Ministry of
Health in Saudi Arabia. Principally, the study is framed within the theories of interactional metadiscourse by Hyland (2005b) and multimodality by Kress and van Leeuwen (1996/ 2006/ 2010), as investigated through their work on
visual grammar. The frequency and functions of interactional metadiscourse resources and socio-semiotic resources were scrutinized
and analyzed. The findings reveal that reader pronouns and directives were the most frequently used interactional metadiscourse to
explicitly engage the target audience and guide them toward physical acts that maintain the application of health-protective
procedures. The results further demonstrate that framing, salience, and images were the socio-semiotic resources most commonly
utilized to achieve compositional meaning, explain content visually, and make information more readily comprehensible to the
public.
Soliton dynamics and stability in the ABS spinor model with a
PT
-symmetric periodic complex potential
Authors: Mertens Franz G , Sánchez-Rey Bernardo , Quintero Niurka R
Published: March 2024

We investigate the effects on solitons dynamics of introducing a

PT

-symmetric complex potential in a specific family of the cubic Dirac equation in (1+1)-dimensions, called the Alexeeva–Barashenkov–Saxena model. The potential is introduced taking advantage of the fact that the nonlinear Dirac equation admits a Lagrangian formalism. As a consequence, the imaginary part of the potential, associated with gains and losses, behaves as a spatially periodic damping (changing from positive to negative, and back) that acts at the same time on the two spinor components. A collective coordinates (CCs) theory is developed by making an ansatz for a moving soliton where the position, rapidity, momentum, frequency, and phase are all functions of time. We consider the complex potential as a perturbation and verify that numerical solutions of the equation of motions for the CCs are in agreement with simulations of the nonlinear Dirac equation. The main effect of the imaginary part of the potential is to induce oscillations in the charge and energy (they are conserved for real potentials) with the same frequency and phase as the momentum. We find long-lived solitons even with very large charge and energy oscillations. Additionally, we extend to the nonlinear Dirac equation an empirical stability criterion, previously employed successfully in the nonlinear Schrödinger equation.
Emotion recognition with reduced channels using CWT based EEG feature representation and a CNN classifier
Authors: Mahmud Md Sultan , Fattah Shaikh Anowarul , Saquib Mohammad , Saha Oishy
Published: March 2024

Objective. Although emotion recognition has been studied for decades, a more accurate classification method that requires less computing is still needed. At present, in many studies, EEG features are extracted from all channels to recognize emotional states, however, there is a lack of an efficient feature domain that improves classification performance and reduces the number of EEG channels. Approach. In this study, a continuous wavelet transform (CWT)-based feature representation of multi-channel EEG data is proposed for automatic emotion recognition. In the proposed feature, the time-frequency domain information is preserved by using CWT coefficients. For a particular EEG channel, each CWT coefficient is mapped into a strength-to-entropy component ratio to obtain a 2D representation. Finally, a 2D feature matrix, namely CEF2D, is created by concatenating these representations from different channels and fed into a deep convolutional neural network architecture. Based on the CWT domain energy-to-entropy ratio, effective channel and CWT scale selection schemes are also proposed to reduce computational complexity. Main results. Compared with previous studies, the results of this study show that valence and arousal classification accuracy has improved in both 3-class and 2-class cases. For the 2-class problem, the average accuracies obtained for valence and arousal dimensions are 98.83% and 98.95%, respectively, and for the 3-class, the accuracies are 98.25% and 98.68%, respectively. Significance. Our findings show that the entropy-based feature of EEG data in the CWT domain is effective for emotion recognition. Utilizing the proposed feature domain, an effective channel selection method can reduce computational complexity.
Importance profiles. Visualization of atomic basis set requirements
Authors: Lehtola Susi
Published: March 2024

Recent developments in fully numerical methods promise interesting opportunities for new, compact atomic orbital (AO) basis sets that maximize the overlap to fully numerical reference wave functions, following the pioneering work of Richardson and coworkers from the early 1960s. Motivated by this technique, we suggest a way to visualize the importance of AO basis functions employing fully numerical wave functions computed at the complete basis set limit: the importance of a normalized AO basis function

|
α
⟩

centered on some nucleus can be visualized by projecting

|
α
⟩

on the set of numerically represented occupied orbitals

|

ψ

i

⟩

as

I

0

(
α
)
=

∑

i

⟨
α

|

ψ

i

⟩
⟨

ψ

i

|

α
⟩

. Choosing α to be a continuous parameter describing the AO basis, such as the exponent of a Gaussian-type orbital or Slater-type orbital basis function, one is then able to visualize the importance of various functions. The proposed visualization

I

0

(
α
)

has the important property

0
⩽

I

0

(
α
)
⩽
1

which allows unambiguous interpretation. We also propose a straightforward generalization of the importance profile for polyatomic applications

I
(
α
)

, in which the importance of a test function

|
α
⟩

is measured as the increase in projection from the atomic minimal basis. We exemplify the methods with importance profiles computed for atoms from the first three rows, and for a set of chemically diverse diatomic molecules. We find that the importance profile offers a way to visualize the atomic basis set requirements for a given system in an a priori manner, provided that a fully numerical reference wave function is available.
On Wronskians and 𝑞𝑞-systems
Authors: Zeitlin Anton
Published: March 2024

We discuss the

q
q

qq

-systems, the functional form of the Bethe ansatz equations for the twisted Gaudin model from a new geometric point of view. We use a concept of

G
G

-Wronskians, which are certain meromorphic sections of principal

G
G

-bundles on the projective line. In this context, the

q
q

qq

-system, similar to its difference analog, is realized as the relation between generalized minors of the

G
G

-Wronskian. We explain the link between

G
G

-Wronskians and twisted

G
G

-oper connections, which are the traditional source for the

q
q

qq

-systems.
Quasi-experimental methods for pharmacoepidemiology: difference-in-differences and synthetic control methods with case studies for vaccine evaluation
Authors: Kennedy-Shaffer Lee
Published: March 2024

Difference-in-differences and synthetic control methods have become common study designs for evaluating the effects of changes in policies, including health policies. They also have potential for providing real-world effectiveness and safety evidence in pharmacoepidemiology. To effectively add to the toolkit of the field, however, designs—including both their benefits and drawbacks—must be well understood. Quasi-experimental designs provide an opportunity to estimate the average treatment effect on the treated without requiring the measurement of all possible confounding factors, and to assess population-level effects. This requires, however, other key assumptions, including the parallel trends or stable weighting assumptions, a lack of other concurrent events that could alter time trends, and an absence of contamination between exposed and unexposed units. The targeted estimands are also highly specific to the settings of the study, and combining across units or time periods can be challenging. Case studies are presented for 3 vaccine evaluation studies, showcasing some of these challenges and opportunities in a specific field of pharmacoepidemiology. These methods provide feasible and valuable sources of evidence in various pharmacoepidemiologic settings and can be improved through research to identify and weigh the advantages and disadvantages in those settings.

This article is part of a Special Collection on Pharmacoepidemiology.
Oligofluorene main-chain length-dependence on one-pot extraction of chirality-selective semiconducting single-walled carbon nanotubes
Authors: Shindome Shoichiro , Shiraki Tomohiro , Toshimitsu Fumiyuki , Fujigaya Tsuyohiko , Nakashima Naotoshi
Published: March 2024

Polyfluorene and their derivatives are noted for being fascinating dispersants for single-walled carbon nanotubes (SWCNTs) because they selectively solubilize semiconducting (sem-) SWCNTs. However, the selective extraction mechanism of this unique behavior has not yet been fully clarified. In this paper, we describe a unique SWCNT solubilization behavior using 12 fluorene oligomers with different main-chain lengths (FOn, n = 2∼30), in which n is the number of fluorene-repeating unit. Sonication of SWCNTs using these oligofluorenes in toluene was found to solubilize SWCNTs when the main-chain length was longer than n = 12. Raman spectra revealed that selective sem-SWCNT extraction occurred when using the FOn with n ≥ 18, while, when using FOn (n = 12, 15), both sem- and metallic (met-) SWCNTs were solubilized. The (n,m)chiralites of the extracted SWCNTs using the fluorene oligomers differed from those using a homopolymer, poly(9,9′-di-n-octylfluorene) (PFO); that is, PFO extracted (9,7)SWCNTs well, while only FO30 slightly dissolved the (9,7)tubes, and when using other FOn (n = 12∼27), no (9,7)tubes were solubilized. The present study demonstrated the importance of the main-chain length of the oligofluorenes on selected chirality extraction of sem-SWCNTs, which is useful for designing fluorene-based compounds with selective extraction of sem-SWCNTs with a specific (n,m) chirality.
GPVI inhibition: Advancing antithrombotic therapy in cardiovascular disease
Authors: Slater Alexandre , Khattak Sophia , Thomas Mark R
Published: March 2024

Glycoprotein (GP) VI (GPVI) plays a major role in thrombosis but not haemostasis, making it a promising antithrombotic target. The primary role of GPVI on the surface of platelets is a signalling receptor for collagen, which is one of the most potent thrombotic sub-endothelial components that is exposed by atherosclerotic plaque rupture. Inhibition of GPVI has therefore been investigated as a strategy for treatment and prevention of atherothrombosis, such as during stroke and acute coronary syndromes. A range of specific GPVI inhibitors have been characterized, and two of these inhibitors, glenzocimab and revacept, have completed Phase II clinical trials in ischaemic stroke. In this review, we summarize mechanisms of GPVI activation and the latest progress of clinically tested GPVI inhibitors, including their mechanisms of action. By focusing on what is known about GPVI activation, we also discuss whether alternate strategies could be used to target GPVI.
A genome-wide cytotoxicity screen of cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth
Authors: Pollenz Richard S , Barnhill Kaylee , Biggs Abbigail , Bland Jackson , Carter Victoria , Chase Michael , Clark Hayley , Coleman Caitlyn , Daffner Marshall , Deam Caitlyn , Finocchiaro Alyssa , Franco Vanessa , Fuller Thomas , Pinera Juan Gallardo , Horne Mae , Howard Zoe , Kanahan Olivia , Miklaszewski Christopher , Miller Sydney , Morgan Ryan , Onalaja Oluwatobi , Otero Louis , Padhye Shivani , Rainey Emily , Rasul Fareed , Robichaux Kobe , Rodier Alexandra , Schlosser Sydni , Sciacchitano Ava , Stewart Emma , Thakkar Rajvi , Heller Danielle M
Published: March 2024

Over the past decade, thousands of bacteriophage genomes have been sequenced and annotated. A striking observation from this work is that known structural features and functions cannot be assigned for >65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes of interest like inhibition of host growth. This study describes the results of a screen evaluating the effects of overexpressing each gene encoded by the temperate Cluster F1 mycobacteriophage Girr on the growth of the host bacterium Mycobacterium smegmatis. Overexpression of 29 of the 102 Girr genes (~28% of the genome) resulted in mild to severe cytotoxicity. Of the 29 toxic genes described, 12 have no known function and are predominately small proteins of <125 amino acids. Overexpression of the majority of these 12 cytotoxic no known functions proteins resulted in moderate to severe growth reduction and represent novel antimicrobial products. The remaining 17 toxic genes have predicted functions, encoding products involved in phage structure, DNA replication/modification, DNA binding/gene regulation, or other enzymatic activity. Comparison of this dataset with prior genome-wide cytotoxicity screens of mycobacteriophages Waterfoul and Hammy reveals some common functional themes, though several of the predicted Girr functions associated with cytotoxicity in our report, including genes involved in lysogeny, have not been described previously. This study, completed as part of the HHMI-supported SEA-GENES project, highlights the power of parallel, genome-wide overexpression screens to identify novel interactions between phages and their hosts.
Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases
Authors: Brock Daniel C , Wang Meng , Hussain Hafiz Muhammad Jafar , Rauch David E , Marra Molly , Pennesi Mark E , Yang Paul , Everett Lesley , Ajlan Radwan S , Colbert Jason , Porto Fernanda Belga Ottoni , Matynia Anna , Gorin Michael B , Koenekoop Robert K , Lopez Irma , Sui Ruifang , Zou Gang , Li Yumei , Chen Rui
Published: March 2024

Inherited retinal diseases (IRDs) are a group of rare genetic eye conditions that cause blindness. Despite progress in identifying genes associated with IRDs, improvements are necessary for classifying rare autosomal dominant (AD) disorders. AD diseases are highly heterogenous, with causal variants being restricted to specific amino acid changes within certain protein domains, making AD conditions difficult to classify. Here, we aim to determine the top-performing in-silico tools for predicting the pathogenicity of AD IRD variants. We annotated variants from ClinVar and benchmarked 39 variant classifier tools on IRD genes, split by inheritance pattern. Using area-under-the-curve (AUC) analysis, we determined the top-performing tools and defined thresholds for variant pathogenicity. Top-performing tools were assessed using genome sequencing on a cohort of participants with IRDs of unknown etiology. MutScore achieved the highest accuracy within AD genes, yielding an AUC of 0.969. When filtering for AD gain-of-function and dominant negative variants, BayesDel had the highest accuracy with an AUC of 0.997. Five participants with variants in NR2E3, RHO, GUCA1A, and GUCY2D were confirmed to have dominantly inherited disease based on pedigree, phenotype, and segregation analysis. We identified two uncharacterized variants in GUCA1A (c.428T>A, p.Ile143Thr) and RHO (c.631C>G, p.His211Asp) in three participants. Our findings support using a multi-classifier approach comprised of new missense classifier tools to identify pathogenic variants in participants with AD IRDs. Our results provide a foundation for improved genetic diagnosis for people with IRDs.
Development and utility of a clinical research informatics application for participant recruitment and workflow management for a return of results pilot trial in familial hypercholesterolemia in the Million Veteran Program
Authors: Brunette Charles A , Yi Thomas , Danowski Morgan E , Cardellino Mark , Harrison Alicia , Assimes Themistocles L , Knowles Joshua W , Christensen Kurt D , Sturm Amy C , Sun Yan V , Hui Qin , Pyarajan Saiju , Shi Yunling , Whitbourne Stacey B , Gaziano J Michael , Muralidhar Sumitra , Vassy Jason L
Published: March 2024

Objective

The development of clinical research informatics tools and workflow processes associated with re-engaging biobank participants has become necessary as genomic repositories increasingly consider the return of actionable research results.

Materials and Methods

Here we describe the development and utility of an informatics application for participant recruitment and enrollment management for the Veterans Affairs Million Veteran Program Return Of Actionable Results Study, a randomized controlled pilot trial returning individual genetic results associated with familial hypercholesterolemia.

Results

The application is developed in Python-Flask and was placed into production in November 2021. The application includes modules for chart review, medication reconciliation, participant contact and biospecimen logging, survey recording, randomization, and documentation of genetic counseling and result disclosure. Three primary users, a genetic counselor and two research coordinators, and 326 Veteran participants have been integrated into the system as of February 23, 2023. The application has successfully handled 3367 task requests involving greater than 95 000 structured data points. Specifically, application users have recorded 326 chart reviews, 867 recruitment telephone calls, 158 telephone-based surveys, and 61 return of results genetic counseling sessions, among other available study tasks.

Conclusion

The development of usable, customizable, and secure informatics tools will become increasingly important as large genomic repositories begin to return research results at scale. Our work provides a proof-of-concept for developing and using such tools to aid in managing the return of results process within a national biobank.
Evaluating cross-reactivity of new psychoactive substances (NPS) in human whole blood by enzyme-linked immunosorbent assay (ELISA)
Authors: Cieri Grace , Mohr Amanda L A , Mastrovito Rebecca , Logan Barry K
Published: March 2024

Due to the increase in the use of novel psychoactive substances (NPS) and their overall prevalence, it is important to have effective and reliable screening technologies to detect NPS in biological matrices. Enzyme-linked immunosorbent assays (ELISA) are among the most popular screening methods. To evaluate the effectiveness of ELISA for NPS detection, five subclasses of NPS (novel synthetic opioids, fentanyl analogs, stimulants, benzodiazepines and hallucinogens) were evaluated in whole blood for their cross-reactivity on commercially available ELISA kits. A variety of novel synthetic opioids were tested at concentrations of 1–80 ng/mL and 50–2000 ng/mL and demonstrated no cross-reactivity to a morphine ELISA plate at either concentration range. Fentanyl analogs were tested at concentrations ranging from 0.01 to 1 ng/mL and had cross-reactivities ranging from 8% to 178% on the fentanyl ELISA kit used. Both para-chloro fentanyl (178%) and acryl fentanyl (164%) showed cross-reactivities well above that of fentanyl. Novel stimulants were tested at concentrations of 0.5–40 ng/mL and 20–2,000 ng/mL. 4-Fluoroamphetamine was the only novel stimulant with cross-reactivity (3,354%) to the amphetamine ELISA plate. Novel benzodiazepines were tested at concentrations of 1–40 ng/mL on a benzodiazepine plate. Cross-reactivities ranged from 36.1% to 263%, with desalkylflurazepam having the highest cross-reactivity. Finally, novel hallucinogens were tested at concentrations of 0.5–10 ng/mL on a phencyclidine (PCP) ELISA plate, which produced no cross-reactivity and then with 10–1,000 ng/mL, which gave results from 56.6% to 151%. Both hydroxy-PCP (151%) and chloro-PCP (137%) showed cross-reactivities above that of PCP. This research has demonstrated the utility of using ELISA-based screening for novel benzodiazepines, hallucinogens and for fentanyl analogs; however, there is limited application and risk of false-negative results for the other drug classes due to low or non-existent cross-reactivities.
Genetic and epigenetic basis of phytohormonal control of floral transition in plants
Authors: Li Xiaoxiao , Lin Chuyu , Lan Chenghao , Tao Zeng
Published: March 2024

The timing of the developmental transition from the vegetative to the reproductive stage is critical for angiosperms, and is fine-tuned by the integration of endogenous factors and external environmental cues to ensure successful reproduction. Plants have evolved sophisticated mechanisms to response to diverse environmental or stress signals, and these can be mediated by hormones to coordinate flowering time. Phytohormones such as gibberellin, auxin, cytokinin, jasmonate, abscisic acid, ethylene, and brassinosteroids and the cross-talk among them are critical for the precise regulation of flowering time. Recent studies of the model flowering plant Arabidopsis have revealed that diverse transcription factors and epigenetic regulators play key roles in relation to the phytohormones that regulate floral transition. This review aims to summarize our current knowledge of the genetic and epigenetic mechanisms that underlie the phytohormonal control of floral transition in Arabidopsis, offering insights into how these processes are regulated and their implications for plant biology.
Variations in milk, udder skin, and fecal microbiota and their relationships with blood metabolites and milk composition in dairy cows
Authors: AoDaohu  , Karin Akada , Kiiru Gathinji Peter , Naoki Nishino
Published: March 2024

This study examined the milk, udder skin, feces, and bedding microbiota in a dairy farm. Blood metabolites concentration and milk composition were also determined to examine their relationship with variations in the microbiota. Samples were collected from 10 healthy cows during the summers of 2018 and 2020. Milk protein, fat, and solid-not-fat contents were higher, and blood urea nitrogen and nonesterified fatty acid levels were lower in the 2020 samples. Principal coordinate analysis demonstrated that milk, udder skin, and fecal microbiota were separate groups. Year-to-year differences were distinct for milk and udder skin microbiota; however, the fecal microbiota of the 2018 and 2020 samples were similar. The bedding microbiota grouped with the udder skin microbiota of the 2018 samples. Although nonpathogens found as prevalent taxa in udder skin microbiota were likely to be found as abundant taxa in milk microbiota, selection and elimination occurred during transmission. Network analysis suggested that bacterial taxa of milk, udder skin, and fecal microbiota were unrelated to blood metabolites and milk composition, regardless of pathogens or nonpathogens.
X-ray stacking reveals average SMBH accretion properties of star-forming galaxies and their cosmic evolution over 4 ≲ z ≲ 7
Authors: Matsui Suin , Shimasaku Kazuhiro , Ito Kei , Ando Makoto , Tanaka Takumi S
Published: March 2024

With an X-ray stacking analysis of $\simeq 12\, 000$ Lyman-break galaxies (LBGs) using the Chandra Legacy Survey image, we investigate average supermassive black hole (SMBH) accretion properties of star-forming galaxies (SFGs) at 4 ≲ z ≲ 7. Although no X-ray signal is detected in any stacked image, we obtain strong 3σ upper limits for the average black hole accretion rate (BHAR) as a function of star formation rate (SFR). At z ∼ 4 (5) where the stacked image is deeper, the 3σ BHAR upper limits per SFR are ∼1.5 (1.0) dex lower than the local black hole-to-stellar mass ratio, indicating that the SMBHs of SFGs in the inactive (BHAR $\lesssim 1 \, \mathrm{M}_\odot$ yr−1) phase are growing much more slowly than expected from simultaneous evolution. We obtain a similar result for BHAR per dark halo accretion rate. QSOs from the literature are found to have ∼1 dex higher SFRs and ≳ 2 dex higher BHARs than LBGs with the same dark halo mass. We also make a similar comparison for dusty starburst galaxies and quiescent galaxies from the literature. A duty-cycle corrected analysis shows that for a given dark halo, the SMBH mass increase in the QSO phase dominates over that in the much longer inactive phase. Finally, a comparison with the TNG300, TNG100, SIMBA100, and EAGLE100 simulations finds that they overshoot our BHAR upper limits by ≲ 1.5 dex, possibly implying that simulated SMBHs are too massive.