bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial transcriptomics reveals alterations in perivascular macrophage lipid metabolism in the onset of Wooden Breast myopathy in broiler chickens
Authors: Wang Ziqing , Khondowe Paul , Brannick Erin , Abasht Behnam 
Published: February 2024

AbstractThis study aims to use spatial transcriptomics to characterize the cell-type-specific expression profile associated with the microscopic features observed in Wooden Breast myopathy. 1 cm3 muscle sample was dissected from the cranial part of the right pectoralis major muscle from three randomly sampled broiler chickens at 23 days post-hatch and processed with Visium Spatial Gene Expression kits (10X Genomics), followed by high-resolution imaging and sequencing on the Illumina Nextseq 2000 system. WB classification was based on histopathologic features identified. Sequence reads were aligned to the chicken reference genome (Galgal6) and mapped to histological images. Unsupervised K-means clustering and Seurat integrative analysis differentiated histologic features and their specific gene expression pattern, including lipid laden macrophages (LLM), unaffected myofibers, myositis and vasculature. In particular, LLM exhibited reprogramming of lipid metabolism with up-regulated lipid transporters and genes in peroxisome proliferator-activated receptors pathway, possibly through P. Moreover, overexpression of fatty acid binding protein 5 could enhance fatty acid uptake in adjacent veins. In myositis regions, increased expression of cathepsins may play a role in muscle homeostasis and repair by mediating lysosomal activity and apoptosis. A better knowledge of different cell-type interactions at early stages of WB is essential in developing a comprehensive understanding.
Post-COVID-19 patients suffer from chemosensory, trigeminal, and salivary dysfunctions
Authors: Rogn Åsmund , Jensen Janicke Liaaen , Iversen Per Ole , Singh Preet Bano 
Published: February 2024

AbstractRecent literature indicates that post-COVID-19 patients suffer from a plethora of complications, including chemosensory dysfunction. However, little attention has been given to understand the interactions between chemosensory, trigeminal, and salivary dysfunctions in these patients. The aims of this study were (1) to investigate the prevalence and combinations of chemosensory, trigeminal, and salivary dysfunctions, (2) to identify the odorants/tastants that are compromised, and (3) to explore possible associations between the four dysfunctions in post-COVID-19 patients. One hundred post-COVID-19 patients and 76 healthy controls (pre-COVID-19) were included in this cross-sectional, case-controlled study. Participants' smell, taste, trigeminal, and salivary functions were assessed. The patients had a significantly higher prevalence of parosmia (80.0%), hyposmia (42.0%), anosmia (53.0%), dysgeusia (34.0%), complete ageusia (3.0%), specific ageusia (27.0%), dysesthesia (11.0%) and dry mouth (18.0%) compared to controls (0.0% for all parameters, except 27.6% for hyposmia). Complete loss of bitter taste was the most prevalent specific ageusia (66.7%) and coffee was the most common distorted smell (56.4%). Seven different combinations of dysfunction were observed in the patients, the most common being a combination of olfactory and gustatory dysfunction (48.0%). These findings indicate that post-COVID-19 patients experience a range of chemosensory, trigeminal, and salivary disturbances, occurring in various combinations.
Crystal structures, phase transitions, thermodynamics, and molecular dynamics of organic–inorganic hybrid crystal [NH(CH3)3]2ZnCl4
Authors: Kim A Young , Na Changyub , Lim Ae Ran 
Published: February 2024

AbstractUnderstanding the physical properties of organic–inorganic hybrid [NH(CH3)3]2ZnCl4 is necessary for its potential application in batteries and fuel cells due to its environmentally-friendly, and highly stable character. Here, we determine its overall properties in detail, such as its orthorhombic crystal structure, and phase transition temperatures associated with five different phases. Structural geometry was studied by the chemical shifts caused by the local field around 1H. No changes were observed for the environment around 1H for CH3, whereas the 1H chemical shifts around NH in the cation were shown due to the change in the hydrogen bond N‒H···Cl. This is related to the change in Cl around Zn in the anion. In addition, the coordination geometry of 14N and 1H around 13C exhibited increased symmetry at high temperatures. Finally, we were able to understand its molecular dynamics by the significant change with temperature observed from the spin–lattice relaxation time T1ρ values, which represent the energy transfer for the 1H and 13C atoms of the cation. The activation energies obtained from the T1ρ results were 3–4 times large at phase I (> 348 K) than at phase V and IV (< 286 K). The relaxations show that the energy barriers in phases IV and V are related to the reorientation of methyl groups around the triple symmetry axis, while the reorientation of methyl groups of the cation in phase I is related to as a whole.
Assessing heatwave effects on disabled persons in South Korea
Authors: Kang Yeji , Baek Ingul , Park Jongchul 
Published: February 2024

AbstractThis study investigated the risk of heatwaves for people with disabilities and other socioeconomic attributes using Health Care Bigdata in South Korea. The Health Care Bigdata provides detailed information on heat-related illness (HRI) patients in 2011–2020 from seven major cities. We employed the Distributed Lag Nonlinear Model (DLNM) to measure heat waves' relative risk. Our findings are four-fold. First, the relative risk (RR) of disabled people was 5.075 (95% confidence interval 4.476–5.674), significantly surpassing that of non-disabled people, 3.296 (2.517–4.075). Second, among various personal characteristics studied, disability influenced RR the most, exceeding impacts from elderly (4.457: 3.748–5.166), low-income (3.909: 3.004–4.813), and outdoor (4.052: 2.940–5.164). Third, the disabled young group (5.305: 4.414–6.195) was more vulnerable than the non-disabled elderly group (4.287: 3.576–4.999). Lastly, no significant difference in relative risk was observed between the mild (4.413: 3.855–4.971) and severe disabled groups (4.013: 3.121–4.905).
A machine learning model to predict privacy fatigued users from social media personalized advertisements
Authors: Alwafi Ghadeer , Fakieh Bahjat 
Published: February 2024

AbstractThe increasing use of social media platforms as personalized advertising channels is a double-edged sword. A high level of personalization on these platforms increases users’ sense of losing control over personal data: This could trigger the privacy fatigue phenomenon manifested in emotional exhaustion and cynicism toward privacy, which leads to a lack of privacy-protective behavior. Machine learning has shown its effectiveness in the early prediction of people’s psychological state to avoid such consequences. Therefore, this study aims to classify users with low and medium-to-high levels of privacy fatigue, based on their information privacy awareness and big-five personality traits. A dataset was collected from 538 participants via an online questionnaire. The prediction models were built using the Support Vector Machine, Naïve Bayes, K-Nearest Neighbors, Decision Tree, and Random Forest classifiers, based on the literature. The results showed that awareness and conscientiousness trait have a significant relationship with privacy fatigue. Support Vector Machine and Naïve Bayes classifiers outperformed the other classifiers by attaining a classification accuracy of 78%, F1 of 87%, recall of 100% and 98%, and precision of 78% and 79% respectively, using five-fold cross-validation.
Structure–activity relationships for the G-quadruplex-targeting experimental drug QN-302 and two analogues probed with comparative transcriptome profiling and molecular modeling
Authors: Ahmed Ahmed Abdullah , Chen Shuang , Roman-Escorza Maria , Angell Richard , Oxenford Sally , McConville Matthew , Barton Naomi , Sunose Mihiro , Neidle Dan , Haider Shozeb , Arshad Tariq , Neidle Stephen 
Published: February 2024

AbstractThe tetrasubstituted naphthalene diimide compound QN-302 binds to G-quadruplex (G4) DNA structures. It shows high potency in pancreatic ductal adenocarcinoma (PDAC) cells and inhibits the transcription of cancer-related genes in these cells and in PDAC animal models. It is currently in Phase 1a clinical evaluation as an anticancer drug. A study of structure–activity relationships of QN-302 and two related analogues (CM03 and SOP1247) is reported here. These have been probed using comparisons of transcriptional profiles from whole-genome RNA-seq analyses, together with molecular modelling and molecular dynamics simulations. Compounds CM03 and SOP1247 differ by the presence of a methoxy substituent in the latter: these two compounds have closely similar transcriptional profiles. Whereas QN-302 (with an additional benzyl-pyrrolidine group), although also showing down-regulatory effects in the same cancer-related pathways, has effects on distinct genes, for example in the hedgehog pathway. This distinctive pattern of genes affected by QN-302 is hypothesized to contribute to its superior potency compared to CM03 and SOP1247. Its enhanced ability to stabilize G4 structures has been attributed to its benzyl-pyrrolidine substituent fitting into and filling most of the space in a G4 groove compared to the hydrogen atom in CM03 or the methoxy group substituent in SOP1247.
Stress and strain analysis and parameter optimization of pipe truss tower connection of super-large tower crane based on FEM
Authors: Zeng Guang , Chen Kun , Wang Yupeng , Liu Yuanpeng , Zhang Qian , Zhang Yalong 
Published: February 2024

AbstractClamping bushing structure is an internode connection mechanism designed for the standard section of tubular truss tower. In this paper, the clamping bushing structure of the connecting mechanism of super-large tower crane is taken as the research object, a three-dimensional model of clamping bushing structure is established and imported into ABAQUS, and its multi-body contact model is further constructed to study the contact and bearing relationship of the structure under multiple working conditions, and the accuracy of the calculation results of the model is verified by the experimental stress test under tensile working conditions. In addition, this study is based on the control variable method, and through the design of orthogonal test table, the influence degree of five variable parameters of clamping bushing on the bearing capacity of the structure is investigated. Finally, through the range analysis, the optimal horizontal combination of variables and parameters of clamping bushing structure is obtained, and the optimal matching relationship between the shape of the tower connecting mechanism and the bearing capacity is obtained. The results show that, compared with the original model, the stress concentration at the most dangerous section of the optimized joint and the bushing is obviously alleviated, in which the stress peaks of the upper and lower joints are kept below 500 MPa, and the stress peaks of the bushing groove are also reduced to between 573 and 722 MPa. Moreover, the designed and optimized lower joint can reduce the maximum equivalent plastic strain of the joint root circumference by 56.05% under the original maximum tensile condition, and the overall distribution trend of equivalent plastic strain is more uniform, and a more reliable structural design is obtained, which plays an important guiding role in the design, optimization and analysis of the connecting mechanism of the tower body of large tower crane.
Convergent evolution of BRCA2 reversion mutations under therapeutic pressure by PARP inhibition and platinum chemotherapy
Authors: Walmsley Charlotte S. , Jonsson Philip , Cheng Michael L. , McBride Sean , Kaeser Christopher , Vargas Herbert Alberto , Laudone Vincent , Taylor Barry S. , Kappagantula Rajya , Baez Priscilla , Richards Allison L. , Noronha Anne Marie , Perera Dilmi , Berger Michael , Solit David B. , Iacobuzio-Donahue Christine A. , Scher Howard I. , Donoghue Mark T. A. , Abida Wassim , Schram Alison M. 
Published: February 2024

AbstractReversion mutations that restore wild-type function of the BRCA gene have been described as a key mechanism of resistance to Poly(ADP-ribose) polymerase (PARP) inhibitor therapy in BRCA-associated cancers. Here, we report a case of a patient with metastatic castration-resistant prostate cancer (mCRPC) with a germline BRCA2 mutation who developed acquired resistance to PARP inhibition. Extensive genomic interrogation of cell-free DNA (cfDNA) and tissue at baseline, post-progression, and postmortem revealed ten unique BRCA2 reversion mutations across ten sites. While several of the reversion mutations were private to a specific site, nine out of ten tumors contained at least one mutation, suggesting a powerful clonal selection for reversion mutations in the presence of therapeutic pressure by PARP inhibition. Variable cfDNA shed was seen across tumor sites, emphasizing a potential shortcoming of cfDNA monitoring for PARPi resistance. This report provides a genomic portrait of the temporal and spatial heterogeneity of prostate cancer under the selective pressure of a PARP inhibition and exposes limitations in the current strategies for detection of reversion mutations.
Recreational mobility prior and during the COVID-19 pandemic
Authors: Ghadiri Zahra , Mashhadi Afra , Timme Marc , Ghanbarnejad Fakhteh 
Published: February 2024

AbstractThe COVID-19 pandemic and the resulting economic recession negatively affected many people’s physical, social, and psychological health and has been shown to change population-level mobility, but little attention has been given to park visitations as an indicator. Estimating the frequency of park visitations from aggregated mobility data of all the parks in Washington State (USA), we study trends in park use one year prior to and two years during the COVID-19 pandemic. Our findings indicate that the gravity model is a robust model for the park visitation behavior in different spatial resolutions of city level and state level and different socio-economical classes. Incorporating network structure, our detailed analysis highlights that high-income level residents changed their recreational behavior by visiting their local parks more and a broader recreational options outside of their local census area; whereas the low-income residents changed their visitation behavior by reducing their recreational choices.
Machine learning reveals features of spinon Fermi surface
Authors: Zhang Kevin , Feng Shi , Lensky Yuri D. , Trivedi Nandini , Kim Eun-Ah 
Published: February 2024

AbstractWith rapid progress in simulation of strongly interacting quantum Hamiltonians, the challenge in characterizing unknown phases becomes a bottleneck for scientific progress. We demonstrate that a Quantum-Classical hybrid approach (QuCl) of mining sampled projective snapshots with interpretable classical machine learning can unveil signatures of seemingly featureless quantum states. The Kitaev-Heisenberg model on a honeycomb lattice under external magnetic field presents an ideal system to test QuCl, where simulations have found an intermediate gapless phase (IGP) sandwiched between known phases, launching a debate over its elusive nature. We use the correlator convolutional neural network, trained on labeled projective snapshots, in conjunction with regularization path analysis to identify signatures of phases. We show that QuCl reproduces known features of established phases. Significantly, we also identify a signature of the IGP in the spin channel perpendicular to the field direction, which we interpret as a signature of Friedel oscillations of gapless spinons forming a Fermi surface. Our predictions can guide future experimental searches for spin liquids.
Exploring solar energy systems: A comparative study of optimization algorithms, MPPTs, and controllers
Authors: Güven Aykut Fatih 
Published: February 2024

AbstractThis study elucidates the use of optimization algorithms to identify the controller parameters employed in adjusting the current and voltage values of loads powered by solar energy systems and battery groups. Parameters for these controllers were independently derived using a combination of ant colony optimization with Levy flight, hybrid firefly‐particle swarm optimization, hybrid gravitation search algorithm‐particle swarm optimization, alongside the implementation of Jaya and whale optimization algorithms. The results from each method were juxtaposed for thorough analysis. In addition, three distinct Maximum Power Point Tracker (MPPT) algorithms were employed in the system: perturbation and observation, open circuit voltage, and incremental conductance (IC). To assess the system’s adaptability to real‐world conditions, it was tested against varying temperatures and sunlight levels. Moreover, potential changes in the loads were considered by varying the load. The efficacy of the controllers was examined by altering both the environment and load. The effectiveness of the controllers was examined by referring to the integral of time‐weighted absolute error value. The system was simulated using MATLAB/Simulink software. This study demonstrates that the fractional‐order PID controller achieves the most effective results, the Jaya algorithm provides the best controller parameters, and the IC technique exhibits the highest performance in MPPT.
Ab initio simulations of neutron stars’ oblique electrospheres with realistic neutron star parameters
Authors: Mottez F. 
Published: February 2024

Context. Electrospheres are environments with the same origin as pulsars; a highly magnetized rotating neutron star. In pulsars, a cascade of electron-positron pair creation enriches the plasma. The plasma surrounding an electrosphere consists only of particles that have escaped from the neutron star’s surface. Electrospheres with a magnetic axis aligned with the rotation axis have been well described for decades. Models of electrospheres with an oblique magnetic axis relative to the rotation axis have resisted most theoretical investigations. Some electrospheres and pulsars have been simulated using particle-in-cell codes, but the numerical constraints did not allow the use of realistic neutron star parameters.
Aims. We aimed to develop a numerical simulation code optimized for understanding the physics of electrospheres and pulsars, with realistic neutron star parameters. As a first step, presented in this paper, we focused on the simulation of oblique electrospheres with realistic physical parameters.
Methods. A specific code was developed for the computation of stationary solutions. The resolution of Maxwell’s equations was based on spectral methods. Particle motions included their finite inertia. No hypothesis was made in relation to the force-free behavior of the electrospheric plasma. The numerical code is called Pulsar ARoMa (pulsar asymmetric rotating magnetosphere).
Results. Various numerical simulations were conducted using realistic neutron star parameters. We find that oblique electrospheres possess the same global structure as aligned force-free electrospheres, with two domes of electrons and a torus of positively charged particles. The domes are not centered on the magnetic axis; nor are they symmetric. Yet, the solutions do not exhibit a force-free behavior.
Conclusions. The simulations performed with the Pulsar ARoMa code require modest resources and little computing time. This code will be upgraded for more ambitious investigations into pulsar physics.
The Astrochemistry Low-energy Electron Cross-Section (ALeCS) database
Authors: Gaches Brandt A. L. , Grassi Tommaso , Vogt-Geisse Stefan , Bovolenta Giulia M. , Vallance Claire , Heathcote David , Padovani Marco , Bovino Stefano , Gorai Prasanta 
Published: February 2024

Context. Electron–molecule interaction is a fundamental process in radiation-driven chemistry in space, from the interstellar medium to comets. Therefore, knowledge of interaction cross sections is key. There have been a plethora of both theoretical and experimental studies of total ionization cross sections spanning from diatomics to complex organics. However, the data are often spread over many sources or are not public or readily available.
Aims. We introduce the Astrochemistry Low-energy Electron cross-section (ALeCS) database. This is a public database for electron interaction cross sections and ionization rates for molecules of astrochemical interest. In particular, we present here the first data release, comprising total ionization cross sections and ionization rates for over 200 neutral molecules.
Methods. We include optimized geometries and molecular orbital energies at various levels of quantum chemistry theory. Furthermore, for a subset of the molecules, we have calculated ionization potentials. We computed the total ionization cross sections using the binary-encounter Bethe model and screening-corrected additivity rule, and we computed ionization rates and reaction network coefficients for molecular cloud environments.
Results. We present the cross sections and reaction rates for >200 neutral molecules ranging from diatomics to complex organics, with the largest being C14H10. We find that the screening-corrected additivity rule cross sections generally significantly overestimate experimental total ionization cross sections. We demonstrate that our binary-encounter Bethe cross sections agree well with experimental data. We show that the ionization rates scale roughly linearly with the number of constituent atoms in the molecule.
Conclusions. We introduce and describe the public ALeCS database. For the initial release, we include total ionization cross sections for >200 neutral molecules and several cations and anions calculated with different levels of quantum chemistry theory, the chemical reaction rates for the ionization, and network files in the formats of the two most popular astrochemical networks: the Kinetic Database for Astrochemistry, and UMIST. The database will be continuously updated for more molecules and interactions.