bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional genomics screens reveal a role for TBC1D24 and SV2B in antibody-dependent enhancement of dengue virus infection
Authors: Belmont Laura , Contreras Maya , Cartwright-Acar Catiana H. , Marceau Caleb D. , Agrawal Aditi , Levoir Lisa M. , Lubow Jay , Goo Leslie 
Published: October 2024

ABSTRACT

Under some conditions, dengue virus (DENV) can hijack IgG antibodies to facilitate its uptake into target cells expressing Fc gamma receptors (FcgR)—a process known as antibody-dependent enhancement (ADE) of infection. Beyond a requirement for FcgR, host dependency factors for this unusual IgG-mediated infection route remain unknown. To identify cellular factors exclusively required for ADE, here, we performed CRISPR knockout (KO) screens in an
in vitro
system poorly permissive to infection in the absence of IgG antibodies. Validating our approach, a top hit was FcgRIIa, which facilitates the binding and internalization of IgG-bound DENV but is not required for canonical infection. Additionally, we identified host factors with no previously described role in DENV infection, including TBC1D24 and SV2B, which have known functions in regulated secretion. Using genetic knockout and
trans
-complemented cells, we validated a functional requirement for these host factors in ADE assays performed with monoclonal antibodies and polyclonal sera in multiple cell lines and using all four DENV serotypes. We show that knockout of TBC1D24 or SV2B impaired the binding of IgG-DENV complexes to cells without affecting FcgRIIa expression levels. Thus, we identify cellular factors beyond FcgR that promote efficient ADE of DENV infection. Our findings represent a first step toward advancing fundamental knowledge behind the biology of a non-canonical infection route implicated in disease.

IMPORTANCE

Antibodies can paradoxically enhance rather than inhibit dengue virus (DENV) infection in some cases. To advance knowledge of the functional requirements of antibody-dependent enhancement (ADE) of infection beyond existing descriptive studies, we performed a genome-scale CRISPR knockout (KO) screen in an optimized
in vitro
system permissive to efficient DENV infection only in the presence of IgG. In addition to FcgRIIa, a known receptor that facilitates IgG-mediated uptake of IgG-bound, but not naked DENV particles, our screens identified TBC1D24 and SV2B, cellular factors with no known role in DENV infection. We validated a functional role for TBC1D24 and SV2B in mediating ADE of all four DENV serotypes in different cell lines and using various antibodies. Thus, we identify cellular factors beyond Fc gamma receptors that promote ADE mechanisms. This study represents a first step toward advancing fundamental knowledge beyond a poorly understood non-canonical viral entry mechanism.
Phosphorylation of Ser711 residue in the hypervariable region of zoonotic genotype 3 hepatitis E virus is important for virus replication
Authors: Wang Bo , Subramaniam Sakthivel , Tian Debin , Mahsoub Hassan M. , Heffron C. Lynn , Meng Xiang-Jin 
Published: October 2024

ABSTRACT

Hepatitis E virus (HEV) is distinct from other hepatotropic viruses because it is zoonotic. HEV-1 and HEV-2 exclusively infect humans, whereas HEV-3 and HEV-4 are zoonotic. However, the viral and/or host factors responsible for cross-species HEV transmission remain elusive. The hypervariable region (HVR) in HEV is extremely heterogenetic and is implicated in HEV adaptation. Here, we investigated the potential role of Serine phosphorylation in the HVR in HEV replication. We first analyzed HVR sequences across different HEV genotypes and identified a unique region at the N-terminus of the HVR, which is variable in the human-exclusive HEV genotypes but relatively conserved in zoonotic HEV genotypes. Using predictive tools, we identified four potential phosphorylation sites that are highly conserved in zoonotic HEV-3 and HEV-4 genomes but absent in human-exclusive HEV-1 strains. To explore the functional significance of these putative phosphorylation sites, we introduced mutations into the HEV-3 infectious clone and indicator replicon, replacing each Serine residue individually with alanine or aspartic acid, and assessed the impact of these substitutions on HEV-3 replication. We found that the phospho-blatant S711A mutant significantly reduced virus replication, whereas the phospho-mimetic S711D mutant modestly reduced virus replication. Conversely, mutations in the other three Serine residues did not significantly affect HEV-3 replication. Furthermore, we demonstrated that Ser711 phosphorylation did not alter host cell tropism of zoonotic HEV-3. In conclusion, our results showed that potential phosphorylation of the Ser711 residue significantly affects HEV-3 replication
in vitro
, providing new insights into the potential mechanisms of zoonotic HEV transmission.

IMPORTANCE

HEV is an important zoonotic pathogen, causing both acute and chronic hepatitis E and extrahepatic manifestation of diseases, such as neurological sequelae. The zoonotic HEV-3 is linked to chronic infection and neurological diseases. The specific viral and/or host factors facilitating cross-species HEV infection are unknown. The intrinsically disordered HVR in ORF1 is crucial for viral fitness and adaptation, both
in vitro
and
in vivo
. We hypothesized that phosphorylation of Serine residues in the HVR of zoonotic HEV by unknown host cellular kinases is associated with cross-species HEV transmission. In this study, we identified a conserved region within the HVR of zoonotic HEV strains but absent in the human-exclusive HEV-1 and HEV-2. We elucidated the important role of phosphorylation at the Ser711 residue in zoonotic HEV-3 replication, without altering the host cell tropism. These findings contribute to our understanding the mechanisms of cross-species HEV transmission.
Attenuated African swine fever viruses and the live vaccine candidates: a comprehensive review
Authors: Fan Jiaqi , Yu Haisheng , Miao Faming , Ke Junnan , Hu Rongliang 
Published: October 2024

ABSTRACT

The African swine fever virus (ASFV) is spreading worldwide and causing huge economic losses to the global pig industry. The ASFV genome is 170–193 kb in length, contains approximately 150 open reading frames, and encodes more than 200 proteins, most of which have unknown functions. Owing to the unique viral structure, replication strategy, large number of genes of unknown function, and complicated pathogenesis, vaccine development research is challenging. Several naturally attenuated ASFV isolates have been extensively investigated and many genetically manipulated, gene-deleted, and cell-adapted ASFVs have been reported. Currently, live attenuated viruses prepared from weakly virulent strains are an efficient method to provide effective protection in vaccinated pigs; however, these have seldom been widely approved for vaccine use, except in Vietnam. Herein, we summarize the attenuated isolates or vaccine candidates for live vaccines derived from different sources, including naturally mutated, attenuated, cell-adapted, and genetically modified recombinant ASFVs. This will help to understand the gene function and immunogenicity of attenuated live ASFV, as well as the shortcomings of these viruses as vaccine candidates, and provide clues to prepare live, efficient, and safe vaccines for African swine fever.

IMPORTANCE
Outbreaks of African swine fever (ASF) have caused devastating losses to the global pig industry. Pigs immunized with ASFV attenuated virus can resist the lethal challenge of a strongly virulent virus. Here, we summarize the virulence of naturally mutated, cell-adapted, and genetically recombinant ASFV for pigs, and the protective effect after facing an attack challenge. We also analyze the advantages and disadvantages of ASFV attenuated viruses as vaccine candidates to provide clues for the preparation of efficient and safe live African swine fever vaccines.
Inhaled argon dilates pulmonary vasculature in rat isolated lungs
Authors: Hees Josephine E. , Cleveland William J. , Balzer Claudius , Riess Matthias L. 
Published: October 2024

During cardiopulmonary resuscitation, pulmonary vasoconstriction due to hypoxia and hypercarbia restricts blood flow from the right to the left heart, resulting in reduced cardiac output that further inhibits adequate oxygenation and the ability to distribute oxygenated blood and medications. An inhaled pulmonary vasodilator could attenuate vasoconstriction and, therefore, increase cardiac output. We used rat isolated lungs to test if inhaled Argon leads to pulmonary vasodilation in phenylephrine-treated lungs. Lungs of 13 adult male Sprague–Dawley rats were isolated, ventilated, and perfused. Pulmonary artery and left atrium were cannulated and lungs perfused at constant flow with 4% albumin physiological saline solution. Controls ( n = 6) were ventilated with 65% N2, 5% CO2, 30% O2, and Argon lungs ( n = 7) with 65% Argon, 5% CO2, and 30% O2. Pulmonary mean arterial pressure (pMAP) and airway pressure (AWP) were recorded continuously, and pulmonary vascular resistance (PVR) was calculated. Following baseline readings, phenylephrine, a pulmonary vasoconstrictor, was perfused at increasing concentrations from 10−7 to 10−3 mol/L every 5 min. Statistics: Student’s t test, α = 0.05. Argon led to significantly lower pMAPs and PVRs, independent of AWP. Thus, it significantly dilated pre-constricted pulmonary vessels in an ex vivo lung model. When given during resuscitation, this might aid to increase cardiac output.
Barrow’s nonlinear charged anti-de Sitter black hole and stability
Authors: Du Yun-Zhi , Gu Qiang 
Published: October 2024

AbstractAs we know, the horizon area of a black hole will increase when it absorbs matter. Based on Barrow’s concept of a fractal black hole horizon, it has been proposed (Phys Lett B 831:137181, 2022) that for a spherically fractal structure, the minimum increase in the horizon area is the area of the smallest bubble sphere. The corresponding black hole entropy is of a logarithmic form, which is similar to that of Boltzmann entropy under a certain condition. Based on this, we re-derive the entropy of Barrow’s Einstein–power-Yang–Mills (EPYM) anti-de Sitter (AdS) black hole, and calculate its temperature and heat capacity. There exists an interesting phenomenon wherein the ratio between Barrow’s temperature and the Hawking temperature of the EPYM AdS black hole is fully consistent with that of other Schwarzschild-like black holes. The Barrow and Hawking temperatures within a certain range of $$\Lambda $$
Λ
are found to increase monotonically, and the corresponding heat capacities are all positive, which means that these black holes are thermodynamically stable. In addition, for Barrow’s EPYM AdS black hole, its heat capacity has a Schottky anomaly-like behavior, which may reflect the existence of a discrete energy level and microscopic degrees of freedom.
Anisotropic model observing pulsars from Neutron Star Interior Composition with modified Van der Waals equation of state
Authors: Mardan S. A. , Khalid A. , Manzoor Rubab , Riaz Muhammad Bilal 
Published: October 2024

AbstractThis paper is designed for heavy pulsars coming from the Neutron Star Interior Composition Explorer. The research model is describe by Einstein field equations for anisotropic fluid configuration with spherical symmetry. As per present perceptiveness, modified non-linear Van der Waals equation of state is used to relate physical variables. The continuity of inner and outer matter is obtained by comparing inner spacetime to outer Schwarzschild metric. The physical viability of this model is evaluated and further it is compared with observational data of pulsars PSR J0348+0432, PSR J0740+6620 and PSR J0030+0451. The model fulfils all physical and mathematical characteristics of the dense structure studies. It offers the factual proofs carried by evolution of celestial configurations. The working model presented here is physically viable and shows stable behaviour.
Secondary vertex reconstruction with MaskFormers
Authors: Van Stroud Samuel , Pond Nikita , Hart Max , Barr Jackson , Rettie Sébastien , Facini Gabriel , Scanlon Timothy 
Published: October 2024

AbstractIn high-energy particle collisions, the reconstruction of secondary vertices from heavy-flavour hadron decays is crucial for identifying and studying jets initiated by b- or c-quarks. Traditional methods, while effective, require extensive manual optimisation and struggle to perform consistently across wide regions of phase space. Meanwhile, recent advancements in machine learning have improved performance but are unable to fully reconstruct multiple vertices. In this work we propose a novel approach to secondary vertex reconstruction based on recent advancements in object detection and computer vision. Our method directly predicts the presence and properties of an arbitrary number of vertices in a single model. This approach overcomes the limitations of existing techniques. Applied to simulated proton-proton collision events, our approach demonstrates significant improvements in vertex finding efficiency, achieving a 10% improvement over an existing state-of-the-art method. Moreover, it enables vertex fitting, providing accurate estimates of key vertex properties such as transverse momentum, radial flight distance, and angular displacement from the jet axis. When integrated into a flavour tagging pipeline, our method yields a 50% improvement in light-jet rejection and a 15% improvement in c-jet rejection at a b-jet selection efficiency of 70%. These results demonstrate the potential of adapting advanced object detection techniques for particle physics, and pave the way for more powerful and flexible reconstruction tools in high-energy physics experiments.
Graviton reggeization and high energy gravitational scattering of scalar particles
Authors: Bondarenko S. 
Published: October 2024

AbstractIn this paper we consider a high energy scattering of free scalar particles through a gravitational field. The one particle t-channel amplitude of the scattering in this limit is governed by reggeized graviton. Therefore, we discuss an appearance of the reggeized gravitons in the framework of Einstein–Hilbert gravity and consider Lipatov’s effective action for the reggeized gravitons. We calculate the trajectory of the corresponding t-channel amplitude in the framework and thereafter define the leading order amplitude of scattering of two massive scalar particles. An impact factor of the interaction of scalar particle with the reggeized gravitons is also calculated and possible applications of the approach are discussed as well.
Potential Role of APC Mutations in the Prognosis and Targeted Therapy of Gastric Adenocarcinoma
Authors: Zhang Cao , Qin Jingjing , Zhou Wenjuan , Huang Zexuan , Ye Jingjing , He Yaqin 
Published: October 2024

Background: Adenomatous polyposis coli (APC) gene, an oncogene, has been implicated in stomach adenocarcinoma (STAD), which is a common type of gastric cancer (GC). Although the relationship between APC gene mutations and gastric adenocarcinoma has been comprehensively studied, the potential role of these mutations in the prognosis and targeted therapy remains known.Methods: We utilized The Cancer Genome Atlas (TCGA) database to obtain gene expression matrices, clinical information, and mutation data from patients with STAD. The mutation status of the APC gene was analyzed, and its correlation with tumor mutational burden (TMB), microsatellite instability (MSI), and clinical prognosis in STAD was investigated. Gene set enrichment analysis (GSEA) was conducted to explore the pathological role of APC gene mutations in STAD metabolic pathways. Drug sensitivity analysis was conducted to identify potential targeted antitumor drugs for patients with APC gene mutations in gastric adenocarcinoma.Results: The results revealed that 88% (46/52) of STAD samples had nonsynonymous mutations. The mutation group exhibited a significantly higher TMB than the wild‐type group (p < 0.001), and the percentage of high MSI (MSI‐H) was significantly higher in the mutation group than in the wild‐type group (p < 0.001). Patients with APC mutations had a worse prognosis than those with APC wild‐type (p = 0.009). The APC gene mutation group displayed significant enrichment in amino acids, RNA, and several pathways (|NES| > 1 and nominal p value < 0.01). Compared to the wild‐type group, the mutation group exhibited a higher infiltration proportion of natural killer (NK) cells resting and eosinophils, whereas a lower infiltration proportion of monocytes and resting mast cells (p value < 0.05). AZD5991 exhibited significant sensitivity in patients with STAD carrying APC mutations (p = 0.028).Conclusion: APC gene mutations play a crucial role in the prognosis, molecular characteristics, and potential therapeutic strategies for gastric adenocarcinoma.
An Ensemble Framework Augmenting Surveillance Cameras for Detecting Intruder Clusters as Potential Mobs
Authors: Esan Omobayo Ayokunle , Osunmakinde Isaac O. 
Published: October 2024

<p>Many developing nations around the world curtail crimes through video surveillance technology, but the crime rate is still high. This is compounded by short-staffed security operatives and a deficiency of security infrastructure to assist security operatives with knowledge-driven decision support systems in the low-resource constraint environment. In a public environment, it is challenging to detect intruder clusters accurately as potential mobs for early warning. Previous research investigated some classical techniques, but their recommendations were insufficient. This research develops a Machine Learning (ML) 3-tiers Ensemble framework, which integrates Gray Level Co-occurrence Matrices (GLCM) principles to enhance the capabilities of surveillance cameras and security operatives to effectively discern and respond to potential mob formations. The University of California San Diego (UCSD) pedestrian datasets that are publicly available were used for the experiments. With an improved overall average precision of 0.98, recall of 0.98, and accuracy of 98.52% on the UCSD dataset, the suggested framework outperforms the widely used methods for the detection of intruder clusters. The reduction in computational time on processors showcases the framework's significant advancements as a promising solution for robust real-time threat assessment applications.</p>
Strategies for motion- and respiration-robust estimation of fMRI intrinsic neural timescales
Authors: Goldberg Andrew , Rosario Isabella , Power Jonathan , Horga Guillermo , Wengler Kenneth 
Published: October 2024

Abstract
Intrinsic neural timescales (INT) reflect the time window of neural integration within a brain region and can be measured via resting-state functional magnetic resonance imaging (rs-fMRI). Despite the potential relevance of INT to cognition, brain organization, and neuropsychiatric illness, the influences of physiological artifacts on rs-fMRI INT have not been systematically considered. Two artifacts, head motion and respiration, pose serious issues in rs-fMRI studies. Here, we described their impact on INT estimation and tested the ability of two denoising strategies for mitigating these artifacts, high-motion frame censoring and global signal regression (GSR). We used a subset of the Human Connectome Project Young Adult (HCP-YA) dataset with runs annotated for breathing patterns (Lynch et al., 2020) and at least one “clean” (reference) run that had minimal head motion and no respiration artifacts; other runs from the same participants (n = 46) were labeled as “non-clean.” We found that non-clean runs exhibited brain-wide increases in INT compared with their respective clean runs and that the magnitude of error in INT between non-clean and clean runs correlated with the amount of head motion. Importantly, effect sizes were comparable with INT effects reported in the clinical literature. GSR and high-motion frame censoring improved the similarity between INT maps from non-clean runs and their respective clean run. Using a pseudo-random frame-censoring approach, we uncovered a relationship between the number of censored frames and both the mean INT and mean error, suggesting that frame censoring itself biases INT estimation. A group-level correction procedure reduced this bias and improved similarity between non-clean runs and their respective clean run. Based on our findings, we offer recommendations for rs-fMRI INT studies, which include implementing GSR and high-motion frame censoring with Lomb–Scargle interpolation of censored frames, and performing group-level correction of the bias introduced by frame censoring.
Accelerating the Digital Transition
Authors: Sona Federica 
Published: October 2024

Abstract
Investigating the potential compatibility between the ongoing shariʿa-compliant cyber reforms with the standards enshrined in the European Declaration on Digital Rights and Principles, the article regards the contemporary European digital agenda as a point of reference to examine the variegated Muslim responses to modern technologies, including virtual Islamic (e-)counseling. Comparing Western and Islamic attitudes toward the usage of robotics and a (human-centric) artificial intelligence, it becomes clear that these tools must support individuals, being Islamic scholars or Western legal professionals. While skillfully relying on different languages and transcending domestic borders, European Islamic bodies can also engage in synergetic collaborations with state institutions at inter/national levels by aligning themselves with the cyber reorientation of the digital public space.
Narrating Ecopolitics and the Poetics of Slow Violence in Imbolo Mbue’s How Beautiful We Were
Authors: Tournay-Theodotou Petra 
Published: October 2024

Abstract
In her second novel How Beautiful We Were (2021), the Cameroonian-American writer Imbolo Mbue addresses the devastating environmental and human consequences of Big Oil on a community in a fictional African setting. In this article I investigate the power of narratives to evoke environmental injustice and discuss the narrative strategies and dominant themes employed in this ‘oil novel’ to depict the violent disruptions experienced by the environment and the members of the community. While my reading is guided by insights gained from the work of a number of postcolonial environmental critics, several of the concepts proposed by Rob Nixon (2011) have proven especially useful. More precisely, in this article I explore issues such as the power of literary representation and narrative strategies, the impact of colonial legacies and post-independence conditions, neo-colonial realities of toxic imperialism, and their repercussions on cultural identity and environmental integrity.