bluuebunny/crossref_metadata_2025 huggingface dataset:
Motion compensated cone-beam CT reconstruction using an a priori motion model from CT simulation: a pilot study
Authors: Lauria Michael , Miller Claudia , Singhrao Kamal , Lewis John , Lin Weicheng , O’Connell Dylan , Naumann Louise , Stiehl Bradley , Santhanam Anand , Boyle Peter , Raldow Ann C , Goldin Jonathan , Barjaktarevic Igor , Low Daniel A
Published: March 2024

Objective. To combat the motion artifacts present in traditional 4D-CBCT reconstruction, an iterative technique known as the motion-compensated simultaneous algebraic reconstruction technique (MC-SART) was previously developed. MC-SART employs a 4D-CBCT reconstruction to obtain an initial model, which suffers from a lack of sufficient projections in each bin. The purpose of this study is to demonstrate the feasibility of introducing a motion model acquired during CT simulation to MC-SART, coined model-based CBCT (MB-CBCT). Approach. For each of 5 patients, we acquired 5DCTs during simulation and pre-treatment CBCTs with a simultaneous breathing surrogate. We cross-calibrated the 5DCT and CBCT breathing waveforms by matching the diaphragms and employed the 5DCT motion model parameters for MC-SART. We introduced the Amplitude Reassignment Motion Modeling technique, which measures the ability of the model to control diaphragm sharpness by reassigning projection amplitudes with varying resolution. We evaluated the sharpness of tumors and compared them between MB-CBCT and 4D-CBCT. We quantified sharpness by fitting an error function across anatomical boundaries. Furthermore, we compared our MB-CBCT approach to the traditional MC-SART approach. We evaluated MB-CBCT’s robustness over time by reconstructing multiple fractions for each patient and measuring consistency in tumor centroid locations between 4D-CBCT and MB-CBCT. Main results. We found that the diaphragm sharpness rose consistently with increasing amplitude resolution for 4/5 patients. We observed consistently high image quality across multiple fractions, and observed stable tumor centroids with an average 0.74 ± 0.31 mm difference between the 4D-CBCT and MB-CBCT. Overall, vast improvements over 3D-CBCT and 4D-CBCT were demonstrated by our MB-CBCT technique in terms of both diaphragm sharpness and overall image quality. Significance. This work is an important extension of the MC-SART technique. We demonstrated the ability of a priori 5DCT models to provide motion compensation for CBCT reconstruction. We showed improvements in image quality over both 4D-CBCT and the traditional MC-SART approach.
Enhancements of electrical properties and positive bias instability in self-aligned top-gate a-IGZO TFTs by hydrogen incorporation
Authors: Liu Yuan-Ming , Chiu Jih-Chao , Chen Yu-Ciao , Fan Yu-Cheng , Ma Rong-Wei , Yen Chia-Chun , Chen Tsang-Long , Chou Cheng-Hsu , Liu C W
Published: March 2024

Flow rate effects of the silane (SiH4) and ammonia (NH3) on the top gate insulator and the cap layer in self-aligned top-gate amorphous InGaZnO thin film transistors are investigated. The hydrogen density increases with increasing SiH4 and NH3 flow rates. Hydrogen passivation can improve the field-effect mobility, subthreshold swing (S.S.), hysteresis. The positive bias instability is also improved by hydrogen incorporation. However, the overabundance of hydrogen causes the significant negative threshold voltage shift under negative bias illumination stress (NBIS). Moreover, the most deteriorated S.S. and hysteresis shift after NBIS occur in the TFT with the most hydrogen source.
Enhanced scintillation performance of Cu-doped β-Ga2O3 single crystals grown by floating-zone method
Authors: Fan Qing , Wang Lixiang , Gao Xu , Yan Yuchao , Li Ming , Jin Zhu , Fang Yanjun , Xia Ning , Zhang Hui , Yang Deren
Published: March 2024

As a booming semiconductor material, β-Ga2O3 with an ultra-wide bandgap of 4.8 eV exhibits several advantages in scintillators including high stability and low self-absorption. To further improve the scintillator performance, we grew unintentionally doped, Cu-, Fe-, Mg-, and Si-doped β-Ga2O3 substrates using the floating zone method. The 0.1 mol% Cu-doped β-Ga2O3 exhibits the highest light yield of 6957 ph MeV−1 with a good linear response, which represents better predictability and stability for the input x-ray energy. Photoluminescence shows peak emission around 425 nm under the excitation of 254 nm. All the results show that Cu-doped β-Ga2O3 makes an effective scintillator with excellent light yield, and is an alternative for the high-performance ionizing radiation detectors.
Model-based linear control of nonlinear pneumatic soft bending actuators
Authors: Wang Jiajin , Xu Baoguo , Lai Jianwei , Wang Xin , Lu Ye , Hu Cong , Li Huijun , Song Aiguo
Published: March 2024

Advanced model-based control techniques hold great promise for the precise control of pneumatic soft bending actuators (PSBAs) with strong nonlinearities. However, most previous controllers were designed in a cumbersome nonlinear form. Considering the simplicity of linear system theory, this paper presents a novel perspective on using model-based linear control to handle nonlinear PSBAs, and for the first time, summarizes two methodologies, global linearization and pseudo-linear construction. Derived from them, Koopman-based and hysteresis-based linear control approaches are proposed, respectively. For the former, a novel fusion prediction equation is developed to build a high-fidelity Koopman model, realizing global linearization, and then the linear model predictive control (MPC) is deployed. For the latter, the inverse of the generalized Prandtl–Ishlinskii (GPI) model cascades with the PSBA to construct a pseudo-linear system, eliminating the asymmetric hysteresis, which activates the linear proportional-integral-derivative (PID) control. It is worth noting that the above two are based on data-driven models adapted to various PSBAs with material and structural customization. Finally, the two model-based linear control approaches are verified and compared through a series of experiments. The results show that the proposed linear controls, with more concise designs, achieve comparable or even superior performance than nonlinear controls.
Research on a rotary piezoelectric energy harvester based on movable magnets
Authors: Han Yuhang , Wang Chensheng , Sun Lei , Wang Hongxin , Yang Bowen , He Lipeng
Published: March 2024

A hybrid energy harvester (HEH) is designed using a movable magnet to harvest the mechanical energy for rotational motion. One movement of the movable magnet can generate electricity from piezoelectric nanogenerators (PENG) and electromagnetic generators (EMG), improving the energy conversion efficiency of HEH. The main factors affecting the motion characteristics of active magnets (number of magnets and magnet diameter) are illustrated through theoretical modeling and simulation, and the voltage characteristics of EMG and vibration characteristics of PENG are analyzed. According to the main factors affecting the motion characteristics, the experimental testing system was set up. The results show that the voltage of PENG and EMG can be up to 6.55 V and 1.37 V, respectively as the magnet diameter is 10 mm and the number of magnets is 5. The maximum power of PENG is 2.4 mW at 30 kΩ, and the power of EMG is 0.49 mW at 4 kΩ. The application experiment also proves the feasibility of the practical application of R-PEH, which provides a new solution for the research of hybrid energy harvesting systems.
Tunable chiral bound states in a dimer chain of coupled resonators
Authors: Li Jing , Lu Jing , Gong Z R , Zhou Lan
Published: March 2024

We study an excitation hopping on a one-dimensional (1D) dimer chain of coupled resonators with the alternate on-site photon energies, which interacts with a two-level emitter (TLE) by a coupling point or two adjacent coupling points. In the single-excitation subspace, this system not only possesses two energy bands with propagating states, but also possesses photonic bound states. The number of bound states depends on the coupling forms between the TLE and the dimer chain. It is found that when the TLE is locally coupled to one resonator of the dimer chain, the bound-state that has mirror reflection symmetry. When the TLE is nonlocally coupled to two adjacent resonators, three bound states with preferred direction arise due to the mirror symmetry breaking. By using chirality to measure the asymmetry, it is found that the chirality of these bound states can be tuned by changing the energy differences of single photon in the adjacent resonators, the coupling strengths and the transition energy of the TLE.
Nonlocal correlations in quantum networks distributed with different entangled states
Authors: Hsu Li-Yi
Published: March 2024

We initiate the study of the nonlocal correlations in generic asymmetric quantum networks in a star configuration. Therein, the diverse unrelated sources can emit either partially or maximally entangled states, while the observers employ varying numbers of measurement settings. We propose nonlinear Bell inequalities tailored to the distributed entangled states. Specifically, we demonstrate that the algebraic maximal violations of the proposed nonlinear Bell inequalities are physically achievable within the quantum region. To achieve this, we construct the segmented Bell operators through the cut-graft-mix method applied to the Bell operators in the standard Bell tests. Furthermore, we devise the fitting Bell operators using the sum-of-square approach.
Characteristics of low-pressure-plasma-processed NiRu-MOFs/nickel foam for Hydrogen evolution reaction
Authors: Yu Shuo-En , Wang Ying-Chyi , Tseng Chia-Yun , Cheng I-Chun , Chen Jian-Zhang
Published: March 2024

NiRu bimetallic metal–organic frameworks (NiRu-MOFs) are grown by a simple hydrothermal method on nickel foam (NF) as an the electrocatalyst for the hydrogen evolution reaction. Low-pressure plasmas of pure Ar, 95%Ar + 5%H2, and 95% Ar + 5%O2 are used for the post-treatment of the NiRu-MOFs. NiRu-MOFs-AO with post-plasma treatment with 95%Ar + 5%O2 show the lowest overpotential of 123.3 mV at a current density of 10 mA cm−2 and a Tafel slope of 72.0 mV dec−1 in 1 M KOH electrolyte. Electrochemical impedance spectroscopy results indicate that post-plasma treatment can further reduce the charge transfer resistance. Moreover, the electric double-layer capacitance (Cdl) is calculated based on the cyclic voltammetry results, and the electrocatalyst subjected to 95%Ar + 5%O2 post-plasma treatment shows a 2Cdl value of 3.69 mF/cm2, suggesting a larger electrochemically active surface area after oxygen-containing-plasma treatment.
Molecular dynamics simulation of intergranular fracture in austenitic steel containing precipitation
Authors: Wei Limin , Wang Shuo , Hao Weixun , Liu Yong , Zhu Jingchuan
Published: March 2024

Molecular dynamics simulation is applied to study the crack propagation in austenitic steel containing precipitation. Based on the experimental results, models containing precipitation with two shapes and three volume fractions are constructed. The interactions of the crack with precipitation, dislocation, twin and stacking faults are investigated. It demonstrates that the crack propagation process is strongly related to the temperature and the characteristic parameter of the precipitation. However, the microstructure evolution and dislocation emission are more affected by the temperature. At the same temperature, the initial emission position of the dislocation is changed due to the variation of the precipitation shape. It also indicates that the peak dislocation density is weakly correlated with the single characteristic parameter of the precipitation. Combined with the variation of the crack propagation rate and the peak dislocation density with temperature, it illustrates a negative relationship between these two results.
Nonlinear delay difference equation with bistability as a new traffic flow model
Authors: Okamoto Kazuya , Miyaji Tomoyuki , Tomoeda Akiyasu
Published: March 2024

We propose an improved version of the Rule-184 fuzzy cellular automaton model for describing the key properties of real-world traffic flow. A crucial aspect of modeling involves incorporating the time delay caused by vehicles’ inertia and reaction time in a nonlinear difference equation. Specifically, the effect of time delay was incorporated into the model’s transition rates as an internal form. We then conducted a bifurcation analysis to investigate whether this model has important properties for representing traffic flow. The analysis results indicate that the proposed model exhibits bistability at a certain density region, in which both free and jamming flows coexist. Furthermore, the uniform solution was stable at all densities depending on the values of the parameters included in the model.
High-performance rGO@CNTs@AgNbS nanocomposite electrode material for hybrid supercapacitor and electrochemical glucose sensor
Authors: Yasmeen Aneeqa , Imran Muhammad , Akram Javaria , Afzal Amir Muhammad , Iqbal Muhammad Waqas , Mumtaz Sohail , Muzaffar Nimra , Habila Mohamed A , Safdar Samia , Ahmad Zubair
Published: March 2024

Due to its outstanding ability to store energy, the hybrid energy storage system known as the supercapattery has attained a lot of attention. These devices give extraordinary power and energy densities than supercapacitors and batteries. In this research, a hydrothermal method is used to synthesize a composite material with equal amounts of both components (a 50/50 weight ratio) of silver niobium sulfide and doped with rGO@CNT. Its potential is evaluated using a variety of electrochemical investigations, including galvanostatic charge–discharge and cyclic voltammetry measurements. The rGO@CNT@AgNbS is considered the most attractive material for electrodes based on the electrochemical analysis results, with a specific capacity of 2750 C/g. Additional investigations, including cyclic voltammetry (CV), galvanostatic charge–discharge (GCD), XRD, SEM, and a 15000-cycle stability test, are carried out to better understand this asymmetric device. The device displayed a significant energy density of 65 Wh kg−1 and a fantastic power density of 2229 W /k g . Besides, the composite devices are used as an electrochemical glucose sensor to detect glucose. The device showed an extraordinary sensitivity (greater than 95%) up to a small level of glucose. This study demonstrates the excellent achievement of composite rGO@CNT@AgNbS electrodes for supercapattery applications, with tremendous power and energy densities.
Enhanced structural, optical and electrical properties of polycrystalline WO3 thin films achieved by aluminum nanosheets coating
Authors: Qasrawi A F , Khanfar Hazem K
Published: March 2024

Herein the effects of aluminum nanosheets on the structural, morphological, optical and electrical properties of tungsten oxide thin films are reported. Polycrystalline phase of the thermally evaporated WO3 was achieved by the pulsed laser welding technique. The polycrystalline films are then coated with Al nanosheets of thicknesses of 100 nm and 150 nm by the ion coating technique. It is observed that Al induces the domination of the hexagonal structure of WO3 over the tetragonal. Associated with the enhanced crystallinity the light absorption in the films increased by more than 60% and the energy band gap narrowed significantly. Namely the energy band gap of the as grown WO3 decreased from 3.15 eV to 2.85 eV and 2.59 eV as the Al layer thickness increased from 100 to 150 nm, respectively. It is also observed that crystalline films of WO3 exhibited lower electrical resistivity compared to films fabricated by other techniques. The temperature dependent electrical resistivity measurement was carried out in the temperature range of 310–420 K. It showed room temperature values of 2.5 (

Ω

cm), 2.2 (

Ω

cm) and 1.9 (

Ω

cm) and impurity levels centered at 0.25 eV, 0.34 eV and 0.16 eV for uncoated and films coated with Al nanosheets of thicknesses of 100 nm and 150 nm, respectively. The enhanced crystallinity that is accompanied with narrower energy band gap and lower electrical resistivity values make crystalline WO3 films promising for optoelectronic applications.
Cross sections of cascade production of photoions after photoionization of the iodine atom in the 0.01–100 keV incident photon energy range
Authors: Chaynikov A P , Kochur A G , Dudenko A I
Published: March 2024

Ion yields upon the cascade decays of single vacancies in K to O shells of an isolated iodine atom are calculated by the method of construction and analysis of the cascade decay trees. Branching ratios needed for the simulations are calculated based on Pauli–Fock partial transition widths. Partial photoionization cross sections are calculated with accounting for the core relaxation effect and used to calculate the cross sections of I
q+ photoions production in the 0.01–100 keV incident photon energy range. Accounting for the spin–orbit splitting and the splitting due to electron–electron interaction is shown to be important when calculating mean energies and probabilities of the transitions between energetically closely lying ionic configurations. On the other hand, inclusion of the additional shake-off electron ejections, in spite of complicating severely the decay trees, is found to affect little calculated cascade ions production probabilities.
Kinetic numerical analysis of electromagnetic ion cyclotron instability in non-thermal Vasyliunas-Cairns distributed plasmas
Authors: Shahzad Muhammad Ahsan , Rehman Aman-ur , Ahmad Mushtaq , Sarfraz Muhammad , Bilal Muhammad , Mahmood Shahzad
Published: March 2024

Enhanced fluctuations driven by non-thermal features of particle-distributions are reported frequently in the variety of space plasma observations. In the rare-collisional plasmas, these amplified fluctuations scatter the particles in various direction and governs the dynamics of space plasma environments effectively. Electromagnetic ion cyclotron (EMIC) waves usually responsible for low frequency interplanetary magnetic field fluctuations. These are natural emissions in numerous natural environments of plasmas which usually operates underneath the ion/proton cyclotron frequencies. These are identified as left hand circular polarization (L-mode) with a propagation directed towards the ambient magnetic field. Various space missions and in situ measurements unveil the perpendicular temperature anisotropies of non-thermal populations of ions/protons i.e. in heliospheric regions and solar wind. These proton temperature anisotropies excite EMIC instability which in turn the pitch angle scatters the ions and restrained the anisotropy in certain ranges. In Vasyliunas-Cairns distributed hybrid non-thermal electromagnetic proton plasma, the transverse dielectric response function (TDERF) is calculated for L-mode. It is then numerically solved in order to show the impact of non-thermal populations due to non-thermal parameters α and κ on the dispersion and growth rates of EMIC instability in low and high plasma beta β regimes. Possible variation in the real oscillatory and imaginary frequencies spectrum is also analyzed with the variation in the values of other pertinent parameters i.e. temperature anisotropy τ and β. The parametric numerical analysis of the present work has relevance about that plasma phenomena of space regions where non-thermal distributed populations are prevalent.
Novel setup for detecting short-range anisotropic corrections to gravity
Authors: Bobowski Jake S , Patel Hrishikesh , Faizal Mir
Published: March 2024

In this paper we argue that, even though there are strong theoretical and empirical reasons to expect a violation of spatial isotropy at short distances, contemporary setups for probing gravitational interactions at short distances have not been configured to measure such spatial anisotropies. We propose a simple modification to the state-of-the-art torsion pendulum design and numerically demonstrate that it suppresses signals due to the large spatially-isotropic component of the gravitational force while maintaining a high sensitivity to short-range spatial anisotropies. We incorporate anisotropy using both Yukawa-type and power-law-type short-distance corrections to gravity. The proposed differential torsion pendulum is shown to be capable of making sensitive measurements of small gravitational anisotropies and the resulting anisotropic torques are largely independent of the details of the underlying short-distance modification to gravity. Thus, if there is an anisotropic modification to gravity, from any theory, in any form of the modified potential, the proposed setup provides a practical means of detecting it.
The Science Performance of the Gemini High Resolution Optical Spectrograph
Authors: McConnachie Alan W. , Hayes Christian R. , Robertson J. Gordon , Pazder John , Ireland Michael , Burley Greg , Churilov Vladimir , Lothrop Jordan , Zhelem Ross , Kalari Venu , Anthony André , Baker Gabriella , Berg Trystyn , Chapin Edward L. , Chin Timothy , Densmore Adam , Diaz Ruben , Dunn Jennifer , Edgar Michael L. , Farrell Tony , Firpo Veronica , Fuentes Javier , Gomez-Jimenez Manuel , Hardy Tim , Henderson David , Hill Alexis , Labrie Kathleen , Jensen Jaclyn , Lambert Sam , Lawrence Jon , Macdonald G. Scott , Margheim Steven , Millar Bryan , Muller Rolf , Nielsen Jon G. , Pérez Gabriel , Quiroz Carlos , Ruiz-Carmona Roque , Sebo Kim M. , Sestito Federico , Silva Kareleyne , Simpson Chris , Smith Greg , Venkatesan Sudharshan , Waller Fletcher , Waller Lewis , Wevers Ivan , Venn Kim A. , Young Peter , Silversides Katherine
Published: March 2024

The Gemini High Resolution Optical Spectrograph (GHOST) is a fiber-fed spectrograph system on the Gemini South telescope that provides simultaneous wavelength coverage from 348 to 1061 nm, and is designed for optimal performance between 363 and 950 nm. It can observe up to two objects simultaneously in a 7.′5 diameter field of regard at R ≃ 56,000 or a single object at R ≃ 75,000. The spectral resolution modes are obtained by using integral field units to image slice a 1.″2 aperture by a factor of five in width using 19 fibers in the high resolution mode and by a factor of three in width using 7 fibers in the standard resolution mode. GHOST is equipped with hardware to allow for precision radial velocity measurements, expected to approach meters per second precision. Here, we describe the basic design and operational capabilities of GHOST, and proceed to derive and quantify the key aspects of its on-sky performance that are of most relevance to its science users.
Pattern effect suppression of pulse signals based on pre-signal control method
Authors: Wang Yifan , Guo Meng , Lu Zehui , Yao Yuan , Zhang Hao , Liu Bo , Duan Shaoxiang , Liu Haifeng , Lin Wei
Published: March 2024

By using the pre-signal light as the control light, we propose a method to suppress the transient effect of erbium-doped fiber amplifiers for low-frequency pulse signals. The pattern effect of the pulse signals within the low frequency range (400–1000 Hz) and 1550 nm band is relieved, and the optical surge coefficient Cs decreases to about 0.54 dB. Experimental results show that the proposed method has better performances in suppressing pattern effect in comparison with the conventional continuous light control scheme and higher output gain compared to the compensation pulsed light method. Our proposed pattern effect suppression approach based on the pre-signal control method is anticipated to find promising applications in the field of optical communications.
Pattern-dependent resistivity variations in inkjet-printed conductors due to non-uniform ink drying
Authors: Ghalamboran Milad , Nazeri Mohammad , Grau Gerd
Published: March 2024

When fabricating inkjet-printed electronic devices and circuits, inkjet-printed conductive materials require drying and sintering to improve electrical conductivity. Electrical conductivity should be the same irrespective of pattern design, size, location, or density of adjacent patterns. However, we demonstrate that spatial variations in the drying process for inkjet-printed patterns with proximity to others cause resistivity variations. These resistivity variations are studied here experimentally for different circuit patterns and in arrays of inkjet-printed square electrodes. This variation depends not only on the location of each electrode in an array but also on the number of electrodes. This means that for the same drying temperature and duration, the array with a larger number of electrodes exhibits a larger resistivity variation. The sooner an electrode dries, the lower resistivity it achieves. The resistivity variation between an individual electrode and the center electrode in a 7 × 7 electrode array can be a factor of seven. This variation decreases for lower numbers of electrodes to a factor of three for a 3 × 3 array. Furthermore, x-ray photoelectron spectroscopy analyses provide evidence for the residual presence of carbon-based materials within electrodes after the drying process. These results confirm that the location of electrodes within an array significantly influences the amount of residual carbon-based materials, thereby contributing to resistivity variations. Although intense pulsed light sintering can decrease this variation, its optimal parameters depend on the printed designs, and our simulation results show a non-uniform temperature profile over the electrode arrays. Temperature increases more at the center of patterns than the corners, which can be useful in this case to improve resistivity uniformity. In this study, for the first time, we show how different printed shapes and designs can result in non-uniform resistivity after drying and sintering.
High flux strontium atom source
Authors: Feng C-H , Robert P , Bouyer P , Canuel B , Li J , Das S , Kwong C C , Wilkowski D , Prevedelli M , Bertoldi A
Published: March 2024

We present a novel cold strontium atom source designed for quantum sensors. We optimized the deceleration process to capture a large velocity class of atoms emitted from an oven and achieved a compact and low-power setup capable of generating a high atomic flux. Our approach involves velocity-dependent transverse capture of atoms using a two-dimensional magneto-optical trap. To enhance the atomic flux, we employ tailored magnetic fields that minimize radial beam expansion and incorporate a cascaded Zeeman-slowing configuration utilizing two optical frequencies. The performance is comparable to that of conventional Zeeman slower sources, and the scheme is applicable to other atomic species. Our results represent a significant advancement towards the deployment of portable and, possibly, space-based cold atom sensors.
Projections and patterns of heat-related mortality impacts from climate change in Southeast Asia
Authors: Amnuaylojaroen Teerachai , Parasin Nichapa , Limsakul Atsamon
Published: March 2024

This study aims to investigate the impact of climate change on heat-related mortality in Southeast Asia in the future. The ensemble mean from five General Circulation Models (GCMs) including the Flexible Global Ocean-Atmosphere-Land System Model: Grid-Point Version 3 (FGOALS-g3), Max Planck Institute Earth System Model Version 1.2 (MPI-ESM1-2-LR), EC-Earth3, The Meteorological Research Institute Earth System Model Version 2.0 (MRI-ESM2-0), and Geophysical Fluid Dynamics Laboratory Earth System Model Version 4 (GFDL-ESM4) was used to project severe temperatures and heat indices in Southeast Asia under the Coupled Model Intercomparison Projects Phase 6 (CMIP6). This data was used to correlate with mortality data from the Global Burden of Disease database to quantify heat-related mortality in the region. The ensemble mean results show a reasonable level of accuracy in capturing temperature patterns in the Southeast Asian region with an R2of 0.96, root mean square error (RMSE) of 0.84 and a standard deviation of residual (SDR) of 0.02. When compared to the baseline (1990–2019), temperature extreme indices are rising across all climatic scenarios, with a substantial increase in the SSP3–7.0 and SSP5–8.5 scenarios, ranging from 10% to 50% over the regions, with the heat index predicted to peak in the middle of the century. The two low-emission scenarios, SSP1-2.6 and SSP2-4.5, on the other hand, anticipate more moderate increases, indicating a potentially less severe impact on the region. As a result, under high-emission scenarios, there is expected to be a significant increase in heat-related mortality across Southeast Asia. The expected impact is estimated to affect between 200 and 300 people per 100,000 people from 2030 to 2079, accordingly. Our results highlight the critical need to address health-related impacts of climate change in this region.
Onshore methane emissions measurements from the oil and gas industry: a scoping review
Authors: Vollrath Coleman , Hugenholtz Chris H , Barchyn Thomas E
Published: March 2024

Research on methane (CH4) emissions from the oil and gas (O&G) industry informs policies, regulations, and international initiatives that target reductions. However, there has been little integration and synthesis of the literature to document the state of knowledge, identify gaps, and determine key insights that can guide research priorities and mitigation. To address this, we performed a scoping review of 237 English-language peer-reviewed articles on CH4 emissions from onshore O&G sources, charting data on five research themes: publication trends, geography, measurement levels and methods, emissions sources, and emissions rates. Almost all articles (98%) were published between 2012 and 2022 with an increasing publication rate, indicating a nascent and evolving understanding of the science. Most articles (72%) focused on CH4 emissions from the U.S. O&G industry and were written by U.S.-based authors (69%), while other major O&G-producing countries like Saudi Arabia, Russia, and China were under-represented. Upstream was the most frequently studied supply chain segment, where U.S.-focused articles accounted for 75% of the research. Nearly half the articles (43%) included in the review reported site-level measurements, limiting the identification of equipment- and component-level emissions sources and root cause. Articles that measured or identified equipment-level sources (18%) noted high emissions from tanks, unlit flares, and compressors. The most common stand-off measurement platforms were vehicles and aircraft, while the use of satellites increased in articles published since 2019. Reported emissions profiles were consistently heavy-tailed and indicate method-based and geographic differences in magnitude and skew. All articles (n = 26) that compared inventory- to measurement-based estimates of emissions found large discrepancies in that inventories under-estimated the latter by a factor of 1.2–10 times. We recommend future research focus on: (i) field-based emissions studies for under-represented regions and source categories, (ii) identifying root causes and linking measurements to mitigation, and (iii) multi-level measurement integration.
Interlinking electronic band properties in catalysts with electrochemical nitrogen reduction performance: a direct influence
Authors: Biswas Ashmita , Samui Surajit , Dey Ramendra Sundar
Published: March 2024

The wordwide energy demands and the surge towards a net-zero sustainable society let the researchers set a goal towards the end of carbon cycle. This has enormously exaggerated the electrocatalytic processes such as water splitting, CO2 capture and reduction and nitrogen reduction reaction (NRR) as a safe and green alternative as these involve the utilization of renewable green power. Interestingly, the NH3 produced from NRR has been realized as a future fuel in terms of safer green H2 storage and transportation. Nevertheless, to scale up the NH3 production electrochemically, a benevolent catalyst needs to be developed. More interestingly, the electronic features of the catalyst that actually contribute to the interaction and binding between the adsorbate and reaction intermediates should be analyzed such that these can be tuned based on our requirements to obtain the desired high-standard goals of NH3 synthesis. The current topical review aims to provide an illustrative understanding on the experimental and theoretical descriptors that are likely to influence the electronic structure of catalysts for NRR. We have widely covered a detailed explanation regarding work function, d-band center and electronic effect on the electronic structures of the catalysts. While summarizing the same, we realized that there are several discrepancies in this field, which have not been discussed and could be misleading for the newcomers in the field. Thus, we have briefed the limitations and diverging explanations and have provided a few directions that could be looked upon to overcome the issues.
A novel auxetic stator winding to improve the performance of permanent magnet synchronous electric motors
Authors: Ravanbod Mohammad , Montazeri Allahyar
Published: March 2024

High efficiency and torque density in permanent magnet synchronous motors (PMSMs) have contributed to their increasing popularity. Nonetheless, these advantages are compromised by higher vibration levels resulting from the torque ripple issue and magnetic flux density in the stator, causing magnetic forces on the stator surface. In this study, a new smart shape for the stator winding is proposed which reduces unwanted torque vibration and the overall magnetic flux density while keeping the same motor efficiency. The proposed windings shape is designed based on the auxetic principle and a locally resonant mechanism (LRM). Afterward, the proposed and original PMSM models are compared by looking at the average torque, total losses, torque ripple, flux density, output power, and motor efficiency under different speed operating conditions. In addition, the sensitivity analyses of the proposed model reveal the influence of auxetic structural parameters and initial mechanical angle on the system’s performance, which can be utilized to control the physical and mechanical properties of the system. According to the results, the designed model reduces torque ripple and magnetic flux density in the stator region by 41.38% and 4.70%, respectively, while the motor efficiency remains unaffected. The present work offers a potentially robust and affordable solution for regulating the vibration behavior of electric motors without impacting power efficiency.
Harlem, USSR: Black Modernism in the Soviet Union, 1923–1937
Authors: Karmanov Fedor
Published: March 2024

The following essay tracks the translation of African-American poetry in the first two decades of the Soviet Union. Because the concept of race had no direct correlate in the Soviet Union, this essay argues that the translation of African-American poetry allowed Russian translators to publish modernist poetry that challenged the aesthetic imperatives of the Bolshevik party. To that end, the translation of Black modernist poetry—work by Langston Hughes, Claude McKay, and others—maps on to a canon of “socialist modernism,” an assembly of work that was both aesthetically and politically radical and one that pushed back against the Soviet conceptualizations of “socialist realism” and “bourgeois modernism.”
nanoBERT: a deep learning model for gene agnostic navigation of the nanobody mutational space
Authors: Hadsund Johannes Thorling , Satława Tadeusz , Janusz Bartosz , Shan Lu , Zhou Li , Röttger Richard , Krawczyk Konrad
Published: March 2024

Motivation

Nanobodies are a subclass of immunoglobulins, whose binding site consists of only one peptide chain, bestowing favorable biophysical properties. Recently, the first nanobody therapy was approved, paving the way for further clinical applications of this antibody format. Further development of nanobody-based therapeutics could be streamlined by computational methods. One of such methods is infilling—positional prediction of biologically feasible mutations in nanobodies. Being able to identify possible positional substitutions based on sequence context, facilitates functional design of such molecules.

Results

Here we present nanoBERT, a nanobody-specific transformer to predict amino acids in a given position in a query sequence. We demonstrate the need to develop such machine-learning based protocol as opposed to gene-specific positional statistics since appropriate genetic reference is not available. We benchmark nanoBERT with respect to human-based language models and ESM-2, demonstrating the benefit for domain-specific language models. We also demonstrate the benefit of employing nanobody-specific predictions for fine-tuning on experimentally measured thermostability dataset. We hope that nanoBERT will help engineers in a range of predictive tasks for designing therapeutic nanobodies.

Availability and implementation

https://huggingface.co/NaturalAntibody/.
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes
Authors: Gisdon Florian J , Zunker Mariella , Wolf Jan Niclas , Prüfer Kai , Ackermann Jörg , Welsch Christoph , Koch Ina
Published: March 2024

Motivation

The functional complexity of biochemical processes is strongly related to the interplay of proteins and their assembly into protein complexes. In recent years, the discovery and characterization of protein complexes have substantially progressed through advances in cryo-electron microscopy, proteomics, and computational structure prediction. This development results in a strong need for computational approaches to analyse the data of large protein complexes for structural and functional characterization. Here, we aim to provide a suitable approach, which processes the growing number of large protein complexes, to obtain biologically meaningful information on the hierarchical organization of the structures of protein complexes.

Results

We modelled the quaternary structure of protein complexes as undirected, labelled graphs called complex graphs. In complex graphs, the vertices represent protein chains and the edges spatial chain–chain contacts. We hypothesized that clusters based on the complex graph correspond to functional biological modules. To compute the clusters, we applied the Leiden clustering algorithm. To evaluate our approach, we chose the human respiratory complex I, which has been extensively investigated and exhibits a known biological module structure experimentally validated. Additionally, we characterized a eukaryotic group II chaperonin TRiC/CCT and the head of the bacteriophage Φ29. The analysis of the protein complexes correlated with experimental findings and indicated known functional, biological modules. Using our approach enables not only to predict functional biological modules in large protein complexes with characteristic features but also to investigate the flexibility of specific regions and coformational changes. The predicted modules can aid in the planning and analysis of experiments.

Availability and implementation

Jupyter notebooks to reproduce the examples are available on our public GitHub repository: https://github.com/MolBIFFM/PTGLtools/tree/main/PTGLmodulePrediction.
AbFlex: designing antibody complementarity determining regions with flexible CDR definition
Authors: Jeon Woosung , Kim Dongsup
Published: March 2024

Motivation

Antibodies are proteins that the immune system produces in response to foreign pathogens. Designing antibodies that specifically bind to antigens is a key step in developing antibody therapeutics. The complementarity determining regions (CDRs) of the antibody are mainly responsible for binding to the target antigen, and therefore must be designed to recognize the antigen.

Results

We develop an antibody design model, AbFlex, that exhibits state-of-the-art performance in terms of structure prediction accuracy and amino acid recovery rate. Furthermore, >38% of newly designed antibody models are estimated to have better binding energies for their antigens than wild types. The effectiveness of the model is attributed to two different strategies that are developed to overcome the difficulty associated with the scarcity of antibody–antigen complex structure data. One strategy is to use an equivariant graph neural network model that is more data-efficient. More importantly, a new data augmentation strategy based on the flexible definition of CDRs significantly increases the performance of the CDR prediction model.

Availability and implementation

The source code and implementation are available at https://github.com/wsjeon92/AbFlex.
iNGNN-DTI: prediction of drug–target interaction with interpretable nested graph neural network and pretrained molecule models
Authors: Sun Yan , Li Yan Yi , Leung Carson K , Hu Pingzhao
Published: March 2024

Motivation

Drug–target interaction (DTI) prediction aims to identify interactions between drugs and protein targets. Deep learning can automatically learn discriminative features from drug and protein target representations for DTI prediction, but challenges remain, making it an open question. Existing approaches encode drugs and targets into features using deep learning models, but they often lack explanations for underlying interactions. Moreover, limited labeled DTIs in the chemical space can hinder model generalization.

Results

We propose an interpretable nested graph neural network for DTI prediction (iNGNN-DTI) using pre-trained molecule and protein models. The analysis is conducted on graph data representing drugs and targets by using a specific type of nested graph neural network, in which the target graphs are created based on 3D structures using Alphafold2. This architecture is highly expressive in capturing substructures of the graph data. We use a cross-attention module to capture interaction information between the substructures of drugs and targets. To improve feature representations, we integrate features learned by models that are pre-trained on large unlabeled small molecule and protein datasets, respectively. We evaluate our model on three benchmark datasets, and it shows a consistent improvement on all baseline models in all datasets. We also run an experiment with previously unseen drugs or targets in the test set, and our model outperforms all of the baselines. Furthermore, the iNGNN-DTI can provide more insights into the interaction by visualizing the weights learned by the cross-attention module.

Availability and implementation

The source code of the algorithm is available at https://github.com/syan1992/iNGNN-DTI.
Rapid generation of high-quality structure figures for publication with PyMOL-PUB
Authors: Chen Yuting , Zhang Haoling , Wang Wen , Shen Yue , Ping Zhi
Published: March 2024

Motivation

The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/or program call commands. Therefore, providing interfaces based on established software instead of manual editing becomes a significant necessity.

Results

We developed PyMOL-PUB, based on the original design of PyMOL, to effectively create publication-quality figures from molecular structure data. It provides functions including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions allow users to easily generate high-quality figures, demonstrate structural differences, illustrate inter-molecular interactions, and predict performances of biomacromolecules.

Availability and implementation

Our tool is publicly available at https://github.com/BGI-SynBio/PyMOL-PUB.
Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS
Authors: Trimbour Remi , Deutschmann Ina Maria , Cantini Laura
Published: March 2024

Motivation

The molecular identity of a cell results from a complex interplay between heterogeneous molecular layers. Recent advances in single-cell sequencing technologies have opened the possibility to measure such molecular layers of regulation.

Results

Here, we present HuMMuS, a new method for inferring regulatory mechanisms from single-cell multi-omics data. Differently from the state-of-the-art, HuMMuS captures cooperation between biological macromolecules and can easily include additional layers of molecular regulation. We benchmarked HuMMuS with respect to the state-of-the-art on both paired and unpaired multi-omics datasets. Our results proved the improvements provided by HuMMuS in terms of transcription factor (TF) targets, TF binding motifs and regulatory regions prediction. Finally, once applied to snmC-seq, scATAC-seq and scRNA-seq data from mouse brain cortex, HuMMuS enabled to accurately cluster scRNA profiles and to identify potential driver TFs.

Availability and implementation

HuMMuS is available at https://github.com/cantinilab/HuMMuS.
Cerebellar degeneration in gluten ataxia is linked to microglial activation
Authors: Floare Mara-Luciana , Wharton Stephen B , Simpson Julie E , Aeschlimann Daniel , Hoggard Nigel , Hadjivassiliou Marios
Published: March 2024

Gluten sensitivity has long been recognized exclusively for its gastrointestinal involvement; however, more recent research provides evidence for the existence of neurological manifestations that can appear in combination with or independent of the small bowel manifestations. Amongst all neurological manifestations of gluten sensitivity, gluten ataxia is the most commonly occurring one, accounting for up to 40% of cases of idiopathic sporadic ataxia. However, despite its prevalence, its neuropathological basis is still poorly defined. Here, we provide a neuropathological characterization of gluten ataxia and compare the presence of neuroinflammatory markers glial fibrillary acidic protein, ionized calcium-binding adaptor molecule 1, major histocompatibility complex II and cluster of differentiation 68 in the central nervous system of four gluten ataxia cases to five ataxia controls and seven neurologically healthy controls. Our results demonstrate that severe cerebellar atrophy, cluster of differentiation 20+ and cluster of differentiation 8+ lymphocytic infiltration in the cerebellar grey and white matter and a significant upregulation of microglial immune activation in the cerebellar granular layer, molecular layer and cerebellar white matter are features of gluten ataxia, providing evidence for the involvement of both cellular and humoral immune-mediated processes in gluten ataxia pathogenesis.