bluuebunny/crossref_metadata_2025 huggingface dataset:
Infrared image target detection for substation electrical equipment based on improved faster region-based convolutional neural network algorithm
Authors: Wu Changdong , Wu Yanliang , He Xu
Published: April 2024

Substation electrical equipment generates a massive number of infrared images during operation. However, the overall quality of the infrared images is low and it lacks image detail information. When using traditional target detection algorithms for detection, feature extraction poses great difficulties. Therefore, to address this problem, this paper proposes a target detection algorithm based on the improved faster region-based convolutional neural network (Faster R-CNN). It achieves the correct identification of different types of electrical equipment in infrared images. First, the algorithm improves the backbone network of Faster R-CNN for feature extraction. An InResNet structure is proposed to replace the residual block structure of the original ResNet-34 network, which enhances the richness of feature extraction. Second, the rectified linear unit activation function in the original feature extraction network is replaced by the exponential linear unit activation function, and group normalization is used instead of batch normalization as the network normalization method. Then, the dense connection structure is introduced into the ResNet-34 network, and the whole network is called residual dense connection network. Finally, the improved Faster R-CNN is compared to the original Faster R-CNN, a single-shot multibox detector, and you only look once v3 plus spatial pyramid pooling. The experimental results show that the improved algorithm has the highest mean average precision and average recall for most of the substation electrical equipment in infrared images. Moreover, from the confidence level of the detected electrical equipment and the accuracy of the prediction box, the improved Faster R-CNN has the best performance.
Coupled cluster-inspired geminal wavefunctions
Authors: Gaikwad Pratiksha B. , Kim Taewon D. , Richer M. , Lokhande Rugwed A. , Sánchez-Díaz Gabriela , Limacher Peter A. , Ayers Paul W. , Miranda-Quintana Ramón Alain
Published: April 2024

Electron pairs have an illustrious history in chemistry, from powerful concepts to understanding structural stability and reactive changes to the promise of serving as building blocks of quantitative descriptions of the electronic structure of complex molecules and materials. However, traditionally, two-electron wavefunctions (geminals) have not enjoyed the popularity and widespread use of the more standard single-particle methods. This has changed recently, with a renewed interest in the development of geminal wavefunctions as an alternative to describing strongly correlated phenomena. Hence, there is a need to find geminal methods that are accurate, computationally tractable, and do not demand significant input from the user (particularly via cumbersome and often ill-behaved orbital optimization steps). Here, we propose new families of geminal wavefunctions inspired by the pair coupled cluster doubles ansatz. We present a new hierarchy of two-electron wavefunctions that extends the one-reference orbital idea to other geminals. Moreover, we show how to incorporate single-like excitations in this framework without leaving the quasiparticle picture. We explore the role of imposing seniority restrictions on these wavefunctions and benchmark these new methods on model strongly correlated systems.
Nonlinear Hall effect and scaling law in Sb-doped topological insulator MnBi4Te7
Authors: Wang Shaoyu , Li Xiubing , Zhang Heng , Chen Bo , Xie Hangkai , Li Congcong , Fei Fucong , Zhang Shuai , Song Fengqi
Published: April 2024

The nonlinear Hall effect (NLHE), as a new member of Hall effect family, has been realized in many materials, attracting a great deal of attention. Here, we report the observation of NLHE in magnetic topological insulator Sb-doped MnBi4Te7 flakes. The NLHE generation efficiency can reach up to 0.06 V−1, which is comparable to that observed in MnBi2Te4. Differently, the NLHE can survive up to 200 K, much larger than the magnetic transition temperature. We further study the scaling behavior of the NLHE with longitudinal conductivity. The linear relationship with opposite slope when temperature is below and above the magnetic transition temperature is uncovered. It reveals that the NLHE originates from skew scattering. Our work provides a platform to search NLHE with larger generation efficiency at higher temperatures.
Multiexcitonic and optically bright states in subunits of pentacene crystals: A hybrid DFT/MRCI and molecular mechanics study
Authors: Schulz Timo , Hédé Simon , Weingart Oliver , Marian Christel M.
Published: April 2024

A hybrid quantum mechanics/molecular mechanics setup was used to model electronically excited pentacene in the crystal phase. Particularly interesting in the context of singlet fission (SF) is the energetic location of the antiferromagnetically coupled multiexcitonic singlet state, 1(TT), and the ferromagnetically coupled analog in relation to the optically bright singlet state. To provide photophysical properties of the accessible spin manifold, combined density functional theory and multi-reference configuration interaction calculations were performed on pentacene dimers and a trimer, electrostatically embedded in the crystal. The likelihood of a quintet intermediate in the SF process was estimated by computing singlet–quintet electron spin–spin couplings employing the Breit–Pauli Hamiltonian. The performance of the applied methods was assessed on the pentacene monomer. The character of the optically bright state and the energetic location of the 1(TT) state depend strongly on the relative orientation of the pentacene units. In the V-shaped dimers and in the trimer, the optically bright state is dominated by local and charge transfer (CT) excitations, with admixtures of doubly excited configurations. The CT excitations gain weight upon geometry relaxation, thus supporting a CT-mediated SF mechanism as the primary step of the SF process. For the slip-stacked dimer, the energetic order of the bright and the 1(TT) states swaps upon geometry relaxation, indicating strong nonadiabatic coupling close to the Franck–Condon region—a prerequisite for a coherent SF process. The multiexcitonic singlet, triplet, and quintet states are energetically too far apart and their spin–spin couplings are too small to bring about a noteworthy multiplicity mixing.
Fault diagnosis of drone motors driven by current signal data with few samples
Authors: Chen Guanglin , Li Shaobo , He Qiuchen , Zhou Peng , Zhang Qianfu , Yang Guilin , Lv Dongchao
Published: April 2024

Multi rotor unmanned aerial vehicles (UAVs) are extensively utilized across various domains, and the motor constitutes a pivotal element in the UAV power system. The majority of UAV failures and crashes stem from motor malfunctions, underscoring the imperative need for comprehensive research on fault diagnosis in UAV motors to ensure the stable and reliable execution of flight tasks. This study focuses on quadrotor UAVs as the research subject and devises targeted fault simulation experiments based on the structural features and operational characteristics of the DC brushless motor used in quadrotor UAVs, specifically examining the stator, rotor, and bearings. To address challenges related to the UAV’s own loads, limited space for redundant parts, and the high cost and difficulty associated with installing sensors for traditional fault diagnostic signals such as vibration and temperature, this study opts to use current signals as a substitute. This approach resolves the issue of challenging data collection for UAVs and investigates a current signal based fault diagnosis method for UAV motors. Lastly, in response to the limited training samples available for fault data due to the UAV’s highly sensitive characteristics regarding the health status of its components and flight stability, traditional machine learning and deep learning methods encounter difficulties in identifying representative features with a small number of training samples, leading to the risk of overfitting and reduced model accuracy in fault diagnosis. To overcome this challenge, we propose a hybrid neural network fault diagnosis model that incorporates a width learning system and a convolutional neural network (CNN). The width learning system eliminates temporal characteristics from the original current signal, capturing more comprehensive and representative sample features in the width feature space. Subsequently, the CNN is employed for feature extraction and classification tasks. In empirical small sample fault diagnosis experiments using current signal data for UAV motors, our proposed model outperforms other models used for comparison.
Correlations for an anisotropic polarized stochastic gravitational wave background in pulsar timing arrays
Authors: Bernardo Reginald Christian , Liu Guo-Chin , Ng Kin-Wang
Published: April 2024

The recent compelling observation of the nanohertz stochastic gravitational wave
background has brought to light a new galactic arena to test gravity. In this paper, we derive a
formula for the most general expression of the stochastic gravitational wave background
correlation that could be tested with pulsar timing and future square kilometer arrays. Our
expressions extend the harmonic space analysis, also often referred to as the power spectrum
approach, to predict the correlation signatures of an anisotropic polarized stochastic
gravitational wave background with subluminal tensor, vector, and scalar gravitational degrees of
freedom. We present the first few nontrivial anisotropy and polarization signatures in the
correlation and discuss their dependence on the gravitational wave speed and pulsar distances. Our
results set up tests that could potentially be used to rigorously examine the isotropy of the
stochastic gravitational wave background and strengthen the existing constraints on possible
non-Einsteinian polarizations in the nanohertz gravitational wave regime.
Simulation analysis of the entire construction process of the sunflower shaped continuous arch bridge
Authors: Meng Sichao , Zhang Zhanyi
Published: April 2024

At present, there is a lot of research on the structural system of the completion stage of the Kuihua arch bridge in China, but there is a lack of research on the risks existing in each stage of the construction of the Kuihua arch bridge. Therefore, it is necessary to conduct a full process simulation analysis of the construction process of the sunflower shaped continuous arch bridge. The following conclusions were drawn from this study: (1) After analysis, the construction method of first removing the support below the main arch ring and then pouring the main beam can ensure the safety of construction. (2) The maximum axial force of the support pole below the main arch is -17.67kN, located in rows 10 and 50. The maximum vertical displacement of the main arch is -4.998mm, which is much smaller than the allowable deflection. Therefore, the shape of the main arch is within the safe range. (3) The tensile stress of the main arch and continuous longitudinal beam are both less than the design value of C40 concrete tensile strength of 1.71MPa, so the main arch and continuous longitudinal beam have not cracked, and are in a safe state throughout the construction process.
Analysis of the Impact of Shield Tunneling Under Existing Subway Station
Authors: Li Zonggen , Li Fei
Published: April 2024

To ensure the safety of existing subway station structures and the normal operation of the metro, this study focuses on a specific engineering case in Suzhou’s metro, where shield tunnels were initiated at a close distance to pass beneath an existing subway station. Numerical simulation method was employed to analysis the impact of shield tunneling parameters on the deformation of the existing station structure under conditions with and without pre-reinforcement boundaries. Additionally, the study involved a comparison with monitoring data to validate the reliability of the numerical simulation approach. The results indicate that: 1) Controlling the shield tunneling parameters, such as setting appropriate shield tunneling face support force and tail grouting pressure, is beneficial in managing the deformation of the existing station; 2) The elastic modulus of an equivalent grouting layer has the greatest impact on settlement. Choosing the appropriate grouting material during construction is a key approach to control settlement. 3) Strengthening the soil strength in the reinforcement area and increasing the thickness of the track slab have a minimal impact on the settlement of the track slab at the existing station. However, the former is beneficial for the stability of the shield excavation face. The latter enhances the existing structure’s resistance to deformation.
Research on Reinforcement Technology for Cover Beam Structures of in-service Bridge
Authors: Liu Ran , Wu Xiaoguang , Zhang Haijun , Li Hang , Quan Wei
Published: April 2024

In order to determine a suitable reinforcement technology for the cover beam structure of a bridge in service, a model of a bridge in Shanxi Province was created and analyzed. Three different reinforcement methods were simulated using the finite element method, and these methods were then compared and analyzed. The results indicate that all three reinforcement methods can enhance the bridge’s performance, with the effectiveness ranked as follows: increasing the cross-section, applying external prestress, and attaching steel sheets. Considering factors such as economy, feasibility, and safety, it is recommended to reinforce the cover beam of the bridge by strengthening the external prestressed ribs in combination with affixing steel plates. This approach not only effectively reduces the stress and displacement of the cover beam structure but also redistributes the stress on the cover beam. Importantly, this method does not hinder bridge traffic and minimizes the impact on the clearance under the bridge.
Numerical Modelling and Analysis of Post-Tensioned Precast Prestressed Slab-Beam-Column Composite Joint
Authors: Guo Zhipeng , Li Liming , Shi Pengfei , Li Siyao , Zhang Yunfeng , Zhou Jian , Su Yanjiang
Published: April 2024

In order to study the seismic performance of post-tensioned precast prestressed slab-beam-column composite joint under low cycle loads, ABAQUS was used to simulate the quasi-static behavior of the composite joint. On the premise of verifying the accuracy of the FEM for post-tensioned precast prestressed concrete joints, a comparative analysis was conducted on the hysteresis performance, bearing capacity, energy consumption performance, and deformation capacity differences between concrete joint and composite joints. The seismic performance of the post-tensioned prestressed composite joint has been obtained, providing assistance for the design of the joint.
Research on deep foundation excavation of rail transit station under water-rich soft soil
Authors: Jia Jianwei , Gao Ruiqi , Wang Huigang , Huo Zexian , Zhang Yandong
Published: April 2024

During the excavation of deep foundation, the deformation of surrounding structure usually occurs due to soil unloading, while in water-rich soft soil, the deformation becomes complex and diversified due to the increase of influencing factors. Therefore, the study of Influencing factors and control methods of excavation deformation should be carried out. Based on a rail transit station of Tianjin B1 Rail Line, considering the characteristics of water-rich soft soil, combining relevant monitoring data, the influence of deformation, stress and stability under various excavation stage will be analyzed, providing a guidance for similar project.
Research on vibration isolation optimization design technology for the articulated link mount of turbofan engine
Authors: Chen Yonghui , Wang Jianqiang , Zhou Runeng , Chen Chunlan , Yan Qun , Zhang Zhenxing
Published: April 2024

As an important structure connecting the aircraft and the engine, the turbofan engine mount often adopts a hinged multi-link mechanism, and its dynamic performance directly affects the transmission of engine vibrations to the fuselage. To study and improve the vibration isolation performance of this type of mount system, this paper proposes an optimization strategy based on modal design ideas, which takes the minimum distance between the natural frequencies of the mount system and the excitation frequency as the optimization objective, seeks the parameter solution that maximizes the optimization objective, and uses genetic algorithms to carry out optimization analysis. The results show that through optimization analysis, the effective vibration isolation range of the system is increased by approximately 125% near the excitation frequency of the low-pressure rotor; at the excitation frequency of the low-pressure rotor, the system transfer rate is reduced by approximately 58.4%; after optimization, due to the overall frequency deviation of the installation section system from the excitation frequency, the impact of small perturbations of the main parameters on its transfer rate is generally lower, with a maximum decrease of approximately 17.3%, greatly improving the robustness of the system.
Structural displacement and deformation of adjacent shield tunnel induced by foundation pit excavation
Authors: Feng S. , Wang M. , Jiang Y.X. , Li Y.D. , Wang H.L. , Ran L. , Jin T.
Published: April 2024

Excavating a foundation pit close to a tunnel will unavoidably impact the nearby soil, causing the tunnel to shift and deform. Examining the longitudinal displacement and convergence deformation of a nearby shield tunnel during foundation pit excavation is crucial for maintaining safe operations. Nevertheless, most of the current research primarily focuses on the effects of a single foundation pit excavation on existing tunnels. This study examines and analyzes the effects of multiple foundation pit excavations on the displacement and deformation of pre-existing tunnels, using a project at a subway station as a case study. By employing the PLAXIS three-dimensional finite element software, a large-scale computational model based on the HS model is established, and then five dangerous working conditions are selected for simulation analysis. The research findings delineate that: (i) The displacement of the tunnel is affected by various factors. These encompass the magnitude of the foundation pit excavation, the positioning of the foundation pit excavation in relation to the tunnel, and the closeness of the tunnel to the foundation pit. (ii) The deformation encountered by the tunnel is largely influenced by external loads, where the scale of the unloading load primarily determines the deformation characteristics of the tunnel.
Exploring the potential of pretrained CNNs and time-frequency methods for accurate epileptic EEG classification: a comparative study
Authors: Jamil Mudasir , Aziz Muhammad Zulkifal , Yu Xiaojun
Published: April 2024

Prompt diagnosis of epilepsy relies on accurate classification of automated electroencephalogram (EEG) signals. Several approaches have been developed to characterize epileptic EEG data; however, none of them have exploited time-frequency data to evaluate the effect of tweaking parameters in pretrained frameworks for EEG data classification. This study compares the performance of several pretrained convolutional neural networks (CNNs) namely, AlexNet, GoogLeNet, MobileNetV2, ResNet-18 and SqueezeNet for the localization of epilepsy EEG data using various time-frequency data representation algorithms. Continuous wavelet transform (CWT), empirical Fourier decomposition (EFD), empirical mode decomposition (EMD), empirical wavelet transform (EWT), and variational mode decomposition (VMD) were exploited for the acquisition of 2D scalograms from 1D data. The research evaluates the effect of multiple factors, including noisy versus denoised scalograms, different optimizers, learning rates, single versus dual channels, model size, and computational time consumption. The benchmark Bern-Barcelona EEG dataset is used for testing purpose. Results obtained show that the combination of MobileNetV2, Continuous Wavelet Transform (CWT) and Adam optimizer at a learning rate of 10−4, coupled with dual-data channels, provides the best performance metrics. Specifically, these parameters result in optimal sensitivity, specificity, f1-score, and classification accuracy, with respective values of 96.06%, 96.15%, 96.08%, and 96.10%. To further corroborate the efficacy of opted pretrained models on exploited Signal Decomposition (SD) algorithms, the classifiers are also being simulated on Temple University database at pinnacle modeling composition. A similar pattern in the outcome readily validate the findings of our study and robustness of deep learning models on epilepsy EEG scalograms.The conclusions drawn emphasize the potential of pretrained CNN-based models to create a robust, automated system for diagnosing epileptiform. Furthermore, the study offers insights into the effectiveness of varying time-frequency techniques and classifier parameters for classifying epileptic EEG data.
Flexible and fully integrated 4-bit SAR ADC using metal-oxide TFTs
Authors: Chen Jun-Rong , Mei Xiang-Lin , Hu Yun-Feng , Zhou Lei , Xu Miao , Wang Lei , Wu Wei-Jing , Liu Yu-Rong , Peng Jun-Biao
Published: April 2024

This paper presents a flexible fully integrated 4-bit successive approximation register (SAR) analog-to-digital converter (ADC), which is fabricated by unipolar n-type indium-zinc-oxide thin-film transistors. A bootstrap switch and a comparator with a pre-amplifier are proposed and employed to realize the SAR ADC. The fabricated SAR ADC achieves a sampling rate of up to 20 kHz and a peak signal-to-noise and distortion ratio of 22.9 dB, corresponding to an effective-number-of-bits of 3.52 bits. The static performance of −0.58/+0.37 LSB DNL and −0.49/+0.39 LSB INL is achieved.
Atom-light interactions using optical nanofibres—a perspective
Authors: Li Wenfang , Brown Dylan , Vylegzhanin Alexey , Shahrabifarahani Zohreh , Raj Aswathy , Du Jinjin , Nic Chormaic Síle
Published: April 2024

Complete control of light-matter interactions at a single quantum level is critical for quantum science applications such as precision measurement and information processing. Nanophotonic devices, developed with recent advancements in nanofabrication techniques, can be used to tailor the interactions between single photons and atoms. One example of such a nanophotonic device is the optical nanofibre, which provides an excellent platform due to the strongly confined transverse light fields, long interaction length, low loss, and diverse optical modes. This facilitates a strong interaction between atoms and guided light, revealing chiral atom-light processes and the prospect of waveguide quantum electrodynamics. This paper highlights recent advances, experimental techniques, and future perspectives of the optical nanofibre-atom hybrid quantum platform.
A multi-modal microscope for integrated mapping of cellular forces and Brillouin scattering with high resolution
Authors: Meek Andrew T , Busse Franziska , Kronenberg Nils M , Dinh San Vinh , Berghaus Kim V , Booth Jonathan H , Scarcelli Giuliano , Gather Malte C
Published: April 2024

Mechanical forces and stiffness play key roles in the health and development of cells and tissue, but despite the physical connection between these quantities, they cannot be monitored in parallel in most cases. Here, we introduce a fully integrated microscope that combines a method for high-resolution cell force imaging (elastic resonator interference stress microscopy, ERISM) with non-contact mapping of the elastic properties of cells (via Brillouin microscopy). In order to integrate both techniques, we had to account for the strong back reflection on the surface of the microcavity used for ERISM measurements as well as the local destruction of the cavity under illumination for Brillouin microscopy measurements. Therefore, we developed an elastic optical microcavity with minimal absorption that can perform ERISM measurements without sustaining laser damage during Brillouin microscopy. Furthermore, an unequal-arm Michelson interferometer was designed to suppress the back reflection of the laser on the ERISM microcavity surface using division by amplitude interference to reduce the reflected light and enhance the Brillouin signal. We show the utility of our integrated microscope by simultaneously mapping cellular forces and Brillouin shifts in cultures of fibroblast cells.
Influence of compound layer on the corrosion resistance of low alloy steel in a 3.5% NaCl solution
Authors: Wang L
Published: April 2024

Samples of AISI 4140 low alloy steel were nitrided at different conditions by using plasma nitriding. The optical microscopy observation and x-ray diffraction analysis showed that a 3 ∼ 12 μm thick compound layer composed of ε-Fe2–3N and γ′-Fe4N was formed on the surface after nitriding treatments. The corrosion behavior was evaluated by measuring the anodic polarization curves in a 3.5% NaCl solution along with the observation of corroded surfaces and cross-sectional morphologies using optical and scanning electron microscope. The results indicated that the corrosion resistance of low alloy steel was significantly enhanced through the formation of compound layer. The thickness of compound layer was one important factor in determining its corrosion resistance.
Large area MoSe2 and MoSe2/Bi2Se3 films on sapphire (0001) for near-infrared photodetection
Authors: Kumar Rahul , Aggarwal Vishnu , Gautam Sudhanshu , Yadav Aditya , Singh Bheem , Ganesan Ramakrishnan , Gupta Govind , Kushvaha Sunil Singh
Published: April 2024

The fabrication of heterojunction-based photodetectors (PDs) is well known for the enhancement of PDs performances, tunable nature of photoconductivity, and broadband application. Herein, the PDs based on MoSe2 and MoSe2/Bi2Se3 heterojunction on sapphire (0001) substrates were deposited using a r.f. magnetron sputtering system. The high-resolution x-ray diffraction and Raman spectroscopy characterizations disclosed the growth of the 2-H phase of MoSe2 and the rhombohedral phase of Bi2Se3 thin films on sapphire (0001). The chemical and electronic states of deposited films were studied using x-ray photoelectron spectroscopy and revealed the stoichiometry growth of MoSe2. We have fabricated metal-semiconductor–metal type PD devices on MoSe2 and MoSe2/Bi2Se3 heterojunction and the photo-response measurements were performed at external voltages of 0.1–5 V under near-infrared (1064 nm) light illumination. The bare MoSe2 PD device shows positive photoconductivity behavior whereas MoSe2/Bi2Se3 heterojunction PD exhibits negative photoconductivity. It was found that the responsivity of MoSe2 and MoSe2/Bi2Se3 heterojunction PDs is ~ 1.39 A W−1 and ~ 5.7 A W−1, respectively. The enhancement of photoresponse of MoSe2/Bi2Se3 PD nearly four-fold compared to bare MoSe2 PD shows the importance of heterojunction structures for futuristics optoelectronic applications.
Effect of carbon dots supplementation in Chlorella vulgaris biomass production and its composition
Authors: Solis Flores Sergio , López-Pacheco Itzel Y , Villalba-Rodriguez Angel M , González-González Reyna Berenice , Parra-Saldívar Roberto , Iqbal Hafiz M N
Published: April 2024

Microalgae cultures have an excellent ability to capture CO2 and produce high, medium, and low valuable biocompounds such as proteins, carbohydrates, lipids, pigments, and polyhydroxyalkanoates; those compounds have shown excellent properties in the pharmaceutical, cosmetic, food, and medical industries. Recently, the supplementation of carbon dots (CDs) in autotrophic microalgae cultures has been explored as a new strategy to increase light capture and improve photoluminescence, which in turn enhances biomass growth and biocompounds production. In this work, we synthesized CDs through a simple carbonization method using orange juice as a natural precursor. The green synthesized CDs were analyzed in detail through characterization techniques such as Fourier-transform infrared spectroscopy (FTIR), UV–visible, fluorescence spectroscopy, and ζ potential analysis. Moreover, CDs were added to Chlorella vulgaris to analyze the response under different photoperiod cycles and CDs dosages. The optimal results were obtained with the addition of 0.5 mg l−1 of CDs under a photoperiod cycle of 16 h:8 h (light:dark). In these conditions, a maximum biomass production of 2.12 g l−1 was observed, which represents an enhancement of 112% and 17% in comparison to the control samples under the photoperiod of 12 h:12 h and 16 h:8 h (light/dark), respectively. Furthermore, the production of lipids, proteins, and carbohydrates was significantly increased to 249 mg g−1, 285 mg g−1, and 217 mg g−1 dry weight, respectively. These results suggest that the addition of CDs enhances cell growth and increases the production of lipids and proteins, being a strategy with great potential for the food and pharmaceutical industries.
Neurofilament Biophysics: From Structure to Biomechanics
Authors: Ding Erika A. , Kumar Sanjay
Published: April 2024

Neurofilaments (NFs) are multisubunit, neuron-specific intermediate filaments consisting of a 10-nm diameter filament “core” surrounded by a layer of long intrinsically disordered protein (IDP) “tails.” NFs are thought to regulate axonal caliber during development and then stabilize the mature axon, with NF subunit misregulation, mutation, and aggregation featuring prominently in multiple neurological diseases. The field’s understanding of NF structure, mechanics, and function has been deeply informed by a rich variety of biochemical, cell biological, and mouse genetic studies spanning more than four decades. These studies have contributed much to our collective understanding of NF function in axonal physiology and disease. In recent years, however, there has been a resurgence of interest in NF subunit proteins in two new contexts: as potential blood- and cerebrospinal fluid-based biomarkers of neuronal damage, and as model IDPs with intriguing properties. Here, we review established principles and more recent discoveries in NF structure and function. Where possible, we place these findings in the context of biophysics of NF assembly, interaction, and contributions to axonal mechanics.
Kinesin Regulation in the Proximal Axon is Essential for Dendrite-selective Transport
Authors: Mendoza Christina S. , Plowinske Cameron R. , Montgomery Andrew C. , Quinones Geraldine B. , Banker Gary , Bentley Marvin
Published: April 2024

Neurons are polarized and typically extend multiple dendrites and one axon. To maintain polarity, vesicles carrying dendritic proteins are arrested upon entering the axon. To determine whether kinesin regulation is required for terminating anterograde axonal transport, we overexpressed the dendrite-selective kinesin KIF13A. This caused mistargeting of dendrite-selective vesicles to the axon and a loss of dendritic polarity. Polarity was not disrupted if the kinase MARK2/Par1b was coexpressed. MARK2/Par1b is concentrated in the proximal axon, where it maintains dendritic polarity–likely by phosphorylating S1371 of KIF13A, which lies in a canonical 14-3-3 binding motif. We probed for interactions of KIF13A with 14-3-3 isoforms and found that 14-3-3β and 14-3-3ζ bound KIF13A. Disruption of MARK2 or 14-3-3 activity by small molecule inhibitors caused a loss of dendritic polarity. These data show that kinesin regulation is integral for dendrite-selective transport. We propose a new model in which KIF13A that moves dendrite-selective vesicles in the proximal axon is phosphorylated by MARK2. Phosphorylated KIF13A is then recognized by 14-3-3, which causes dissociation of KIF13A from the vesicle and termination of transport. These findings define a new paradigm for the regulation of vesicle transport by localized kinesin tail phosphorylation, to restrict dendrite-selective vesicles from entering the axon.
Antiparallel microtubule bundling supports KIF15-driven mitotic spindle assembly
Authors: Salazar Brittany M. , Ohi Ryoma
Published: April 2024

The spindle is a bipolar microtubule-based machine that is crucial for accurate chromosome segregation. Spindle bipolarity is generated by Eg5 (a kinesin-5), a conserved motor that drives spindle assembly by localizing to and sliding apart antiparallel microtubules. In the presence of Eg5 inhibitors (K5Is), KIF15 (a kinesin-12) can promote spindle assembly, resulting in K5I-resistant cells (KIRCs). However, KIF15 is a less potent motor than Eg5, suggesting that other factors may contribute to spindle formation in KIRCs. Protein Regulator of Cytokinesis 1 (PRC1) preferentially bundles antiparallel microtubules, and we previously showed that PRC1 promotes KIF15-microtubule binding, leading us to hypothesize that PRC1 may enhance KIF15 activity in KIRCs. Here, we demonstrate that: 1) loss of PRC1 in KIRCs decreases spindle bipolarity, 2) overexpression of PRC1 increases spindle formation efficiency in KIRCs, 3) overexpression of PRC1 protects K5I naïve cells against the K5I S-trityl-L-cysteine (STLC), and 4) PRC1 overexpression promotes the establishment of K5I resistance. These effects are not fully reproduced by a TPX2, a microtubule bundler with no known preference for microtubule orientation. These results suggest a model wherein PRC1-mediated bundling of microtubules creates a more favorable microtubule architecture for KIF15-driven mitotic spindle assembly in the context of Eg5 inhibition.
TGFβ overcomes FGF-induced transinhibition of EGFR in lens cells to enable fibrotic secondary cataract
Authors: VanSlyke Judy K. , Boswell Bruce A. , Musil Linda S.
Published: April 2024

To cause vision-disrupting fibrotic secondary cataract (PCO), lens epithelial cells that survive cataract surgery must migrate to the posterior of the lens capsule and differentiate into myofibroblasts. During this process, the cells become exposed to the FGF that diffuses out of the vitreous body. In normal development, such relatively high levels of FGF induce lens epithelial cells to differentiate into lens fiber cells. It has been a mystery as to how lens cells could instead undergo a mutually exclusive cell fate, namely epithelial to myofibroblast transition, in the FGF-rich environment of the posterior capsule. We and others have reported that the ability of TGFβ to induce lens cell fibrosis requires the activity of endogenous ErbBs. We show here that lens fiber-promoting levels of FGF induce desensitization of ErbB1 (EGFR) that involves its phosphorylation on threonine 669 mediated by both ERK and p38 activity. Transinhibition of ErbB1 by FGF is overcome by a time-dependent increase in ErbB1 levels induced by TGFβ, the activation of which is increased after cataract surgery. Our studies provide a rationale for why TGFβ upregulates ErbB1 in lens cells and further support the receptor as a therapeutic target for PCO.
N-terminal signals in the SNX-BAR paralogs Vps5 and Vin1 guide endosomal coat complex formation
Authors: Shortill Shawn P. , Frier Mia S. , Davey Michael , Conibear Elizabeth
Published: April 2024

Endosomal coats incorporate membrane-binding subunits such as sorting nexin (SNX) proteins. The Saccharomyces cerevisiae SNX–BAR paralogs Vin1 and Vps5 are respective subunits of the endosomal VINE and retromer complexes whose dimerizing BAR domains are required for complex assembly and membrane association. However, a degree of promiscuity is predicted for yeast BAR–BAR pairings, and recent work has implicated the unstructured N-terminal domains of Vin1 and Vps5 in coat formation. Here, we map N-terminal signals in both SNX–BAR paralogs that contribute to the assembly and function of two distinct endosomal coats in vivo. Whereas Vin1 leverages a polybasic region and adjacent hydrophobic motif to bind Vrl1 and form VINE, the N-terminus of Vps5 interacts with the retromer subunit Vps29 at two sites, including a conserved hydrophobic pocket in Vps29 that engages other accessory proteins in humans. We also examined the sole isoform of Vps5 from the milk yeast Kluyveromyces lactis and found that ancestral yeasts may have used a nested N-terminal signal to form both VINE and retromer. Our results suggest that the specific assembly of Vps5-family SNX–BAR coats depends on inputs from unique N-terminal sequence features in addition to BAR domain coupling, expanding our understanding of endosomal coat biology.
OpenAnnotateApi: Python and R packages to efficiently annotate and analyze chromatin accessibility of genomic regions
Authors: Gao Zijing , Jiang Rui , Chen Shengquan
Published: April 2024

Chromatin accessibility serves as a critical measurement of physical contact between nuclear macromolecules and DNA sequence, providing valuable insights into the comprehensive landscape of regulatory mechanisms, thus we previously developed the OpenAnnotate web server. However, as an increasing number of epigenomic analysis software tools emerged, web-based annotation often faced limitations and inconveniences when integrated into these software pipelines. To address these issues, we here develop two software packages named OpenAnnotatePy and OpenAnnotateR. In addition to web-based functionalities, these packages encompass supplementary features, including the capability for simultaneous annotation across multiple cell types, advanced searching of systems, tissues and cell types, and converting the result to the data structure of mainstream tools. Moreover, we applied the packages to various scenarios, including cell type revealing, regulatory element prediction, and integration into mainstream single-cell ATAC-seq analysis pipelines including EpiScanpy, Signac, and ArchR. We anticipate that OpenAnnotateApi will significantly facilitate the deciphering of gene regulatory mechanisms, and offer crucial assistance in the field of epigenomic studies.

Availability and implementation

OpenAnnotateApi for R is available at https://github.com/ZjGaothu/OpenAnnotateR and for Python is available at https://github.com/ZjGaothu/OpenAnnotatePy.
shinyseg: a web application for flexible cosegregation and sensitivity analysis
Authors: Carrizosa Christian , Undlien Dag E , Vigeland Magnus D
Published: April 2024

Motivation

Cosegregation analysis is a powerful tool for identifying pathogenic genetic variants, but its implementation remains challenging. Existing software is either limited in scope or too demanding for many end users. Moreover, current solutions lack methods for assessing the robustness of cosegregation evidence, which is important due to its reliance on uncertain estimates.

Results

We present shinyseg, a comprehensive web application for clinical cosegregation analysis. Our app streamlines penetrance specification based on either liability classes or epidemiological data such as risks, hazard ratios, and age of onset distribution. In addition, it incorporates sensitivity analyses to assess the robustness of cosegregation evidence, and offers support in clinical interpretation.

Availability and implementation

The shinyseg app is freely available at https://chrcarrizosa.shinyapps.io/shinyseg, with documentation and complete R source code on https://chrcarrizosa.github.io/shinyseg and https://github.com/chrcarrizosa/shinyseg.
Adenoma mimicking intraductal papillary neoplasm of the bile duct arising in an intrahepatic biliary duplication cyst
Authors: Tsuji Yuichi , Kotaro Shimada , Isoda Hiroyoshi , Ishii Takamichi , Takeuchi Yasuhide , Nakamoto Yuji
Published: April 2024

We report a case of a cystic liver tumour in a 47-year-old man with Peutz-Jeghers syndrome (PJS) who had undergone sclerotherapy at another hospital for a cyst in hepatic segment IV (S4) 7 years earlier. Based on the preoperative imaging findings, the patient was diagnosed with an intraductal papillary neoplasm of the bile duct. Percutaneous transhepatic portal vein embolization was performed to increase the residual liver volume, followed by resection of the three right hepatic lobes and the caudate lobe, biliary reconstruction, and portal vein reconstruction. Pathological examination revealed an adenoma arising in an intrahepatic biliary duplication cyst. Retrospectively, the preoperative diagnosis was difficult, but it aligned with previous reports of biliary duplication cysts due to its continuity with the bile duct. Additionally, intrahepatic biliary duplication cysts with tumour lesions or cases in which 18F-fluorodeoxyglucose positron emission tomography was performed have not been previously reported. Therefore, preoperatively listing this disease as a differential diagnosis was difficult. PJS and chronic inflammation associated with cyst sclerotherapy may have contributed to tumour development in the intrahepatic biliary duplication cyst.
Imaging of the brain–heart axis: prognostic value in a European setting
Authors: Mikail Nidaa , Sager Dominik F , Gebert Pimrapat , Haider Ahmed , Todorov Atanas , Bengs Susan , Sablonier Noemi , Glarner Isabelle , Vinzens Adriana , Sang Bastian Nastaran , Epprecht Gioia , Sütsch Claudia , Delcò Alessia , Fiechter Michael , Portmann Angela , Treyer Valerie , Wegener Susanne , Gräni Christoph , Pazhenkottil Aju , Gebhard Caroline E , Regitz-Zagrosek Vera , Tanner Felix C , Kaufmann Philipp A , Buechel Ronny R , Rossi Alexia , Gebhard Catherine
Published: April 2024

Background and Aims

Increasing data suggest that stress-related neural activity (SNA) is associated with subsequent major adverse cardiovascular events (MACE) and may represent a therapeutic target. Current evidence is exclusively based on populations from the U.S. and Asia where limited information about cardiovascular disease risk was available. This study sought to investigate whether SNA imaging has clinical value in a well-characterized cohort of cardiovascular patients in Europe.

Methods

In this single-centre study, a total of 963 patients (mean age 58.4 ± 16.1 years, 40.7% female) with known cardiovascular status, ranging from ‘at-risk’ to manifest disease, and without active cancer underwent 2-[18F]fluoro-2-deoxy-D-glucose positron emission tomography/computed tomography between 1 January 2005 and 31 August 2019. Stress-related neural activity was assessed with validated methods and relations between SNA and MACE (non-fatal stroke, non-fatal myocardial infarction, coronary revascularization, and cardiovascular death) or all-cause mortality by time-to-event analysis.

Results

Over a maximum follow-up of 17 years, 118 individuals (12.3%) experienced MACE, and 270 (28.0%) died. In univariate analyses, SNA significantly correlated with an increased risk of MACE (sub-distribution hazard ratio 1.52, 95% CI 1.05–2.19; P = .026) or death (hazard ratio 2.49, 95% CI 1.96–3.17; P < .001). In multivariable analyses, the association between SNA imaging and MACE was lost when details of the cardiovascular status were added to the models. Conversely, the relationship between SNA imaging and all-cause mortality persisted after multivariable adjustments.

Conclusions

In a European patient cohort where cardiovascular status is known, SNA imaging is a robust and independent predictor of all-cause mortality, but its prognostic value for MACE is less evident. Further studies should define specific patient populations that might profit from SNA imaging.
Fitting Assumed Distributions to Horizontal Point Sample Diameters
Authors: Van Deusen Paul C.
Published: April 2024

The theory is developed for fitting assumed distributions, such as the Weibull, to diameters which were derived from horizontal point samples. The method of maximum likelihood and the method of moments are discussed briefly as two ways of doing this. The results make it possible to fit assumed distributions to horizontal point data for such uses as providing growth and yield estimates by diameter class. Forest Sci. 32:146-148.
Effects of Laminated Root Rot on Relationships Between Stem Growth and Root-System Size, Morphology, and Spatial Distribution in Douglas-fir
Authors: Bloomberg W. J. , Hall A. A.
Published: April 2024

Root-system size (length, cross-sectional area, and volume) was measured in 30- to 40-year-old Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) in five stands. Mean root-system size varied widely among stands (length 2,485-5,316 cm; cross-sectional area 4,070-13,520 cm²; volume 72,760-251,020 cm³). Percentage of roots decayed by Phellinus weirii varied among stands and among root orders ranging 22-83 percent by length and 21-84 percent by volume. Root size distribution in P. weirii-infected trees was generally of the same magnitude and pattern as in healthy trees. Diameter at breast height (dbh) was highly correlated with total root-system size in all stands in all three root measures. Height was highly correlated with total root-system size in four stands. Diameter at breast height increment and dbh increment percent and height-dbh ratio were moderately correlated with root-system size in some stands and for some root measures. Height increment percent was poorly correlated with root-system size. Correlations of most stem variables with sizes or percent decay of roots stratified by root orders and by distance and depth zones were significantly stronger than correlations with total root-system size. Healthy and infected trees differed in the root orders and zones that were most strongly correlated with stem-growth variables. Diameter at breast height and height were mostly positively correlated with infected and healthy root sizes whereas increment variables were predominantly inversely correlated with infected root size. Stem radii measured vertically above junctions of infected roots with the stem base were smaller than those measured above junctions of healthy roots. Radial increments above infected roots producing adventitious branches were greater than those above other infected roots or above healthy roots. Forest Sci. 32:202-219.
Response of Three Conifer Species to Site Preparation and Shrub Control
Authors: Lanini W. T. , Radosevich S. R.
Published: April 2024

A 5-year field study was conducted to determine the effect of three methods of site preparation in combination with three levels of shrub suppression on subsequent microenvironmental, shrub and tree responses. Shrub canopy volume and survival, growth, and water potential of planted ponderosa pine (Pinus ponderosa Dougl. ex P. & C. Lawson.), sugar pine [Pinus lambertiana Dougl. (Strobus L. Mold.)], and white fir [Abies concolor (Gord. & Glend.) Lindl.] were measured. Ponderosa pine survived better than sugar pine or white fir regardless of shrub presence or absence. Shrub canopy volume did not influence tree survival; however, the presence of shrub debris from some treatments increased planting difficulty and resulted in increased tree mortality. Predawn and midday water potential, height, stem diameter, and canopy volume of conifers were highest when shrub canopy volumes were low. Forest Sci. 32:61-77.
Adaptive Variation in Pinus ponderosa from Intermountain Regions. I Snake and Salmon River Basins
Authors: Rehfeldt G. E.
Published: April 2024

Genetic differentiation of 64 populations from central Idaho was studied in field, greenhouse, and laboratory tests. Analyses of variables reflecting growth potential, phenology, morphology, cold hardiness, and periodicity of shoot elongation revealed population differentiation for a variety of traits. Regression models related as much as 61 percent of the variance among populations to the elevation and geographic location of the seed source. Clinal patterns of adaptive variation provide the basis for developing seed transfer guidelines that will control maladaptation in reforestation. In central Idaho, for example, seed transfer should be limited to within 180 m of the seed source. Forest Sci. 32:79-92.