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22 pages, 663 KB  
Article
Similarity Self/Ideal Index (SSI): A Feature-Based Approach to Modeling Psychological Well-Being
by Alejandro Sanfeliciano, Carlos Hurtado-Martínez, Luis Botella and Luis Angel Saúl
Mathematics 2025, 13(24), 3954; https://doi.org/10.3390/math13243954 - 11 Dec 2025
Viewed by 445
Abstract
This paper introduces a similarity index aimed at modeling psychological well-being through a set-theoretic formalization of self–ideal alignment. Inspired by Tversky’s feature-based model of similarity, the proposed index quantifies the degree of overlap and divergence between the current self-perception and the ideal self, [...] Read more.
This paper introduces a similarity index aimed at modeling psychological well-being through a set-theoretic formalization of self–ideal alignment. Inspired by Tversky’s feature-based model of similarity, the proposed index quantifies the degree of overlap and divergence between the current self-perception and the ideal self, each represented as a vector of signed attributes. The formulation extends traditional approaches in Personal Construct Psychology by incorporating directional and magnitude-based comparisons across constructs, and its mathematical properties can be expressed within a fuzzy similarity space that ensures boundedness and internal coherence. Unlike standard correlational methods commonly used in psychological assessment, this model provides an alternative framework that allows for asymmetric weighting of discrepancies and non-linear representations of similarity. Developed within the WimpGrid formalism—a graph-theoretical extension of constructivist assessment—the index offers potential applications in clinical modeling, idiographic measurement, and the mathematical analysis of dynamic self-concept systems. We discuss its relevance as a generalizable tool for quantitative psychology, and its potential for integration into computational models of personality and self-organization. Full article
(This article belongs to the Section E: Applied Mathematics)
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17 pages, 4561 KB  
Article
High-Throughput Molecular Characterization of the Microbiome in Breast Implant-Associated Anaplastic Large Cell Lymphoma and Peri-Implant Benign Seromas
by Evelina Rogges, Giorgio Bertolazzi, Davide Vacca, Marina Borro, Gianluca Lopez, Maurizio Simmaco, Anna Scattone, Guido Firmani, Michail Sorotos, Fabio Santanelli di Pompeo, Niccolò Noccioli, Emanuele Savino, Andrea Vecchione and Arianna Di Napoli
Cancers 2025, 17(23), 3839; https://doi.org/10.3390/cancers17233839 - 29 Nov 2025
Viewed by 496
Abstract
Background: Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is a mature T-cell lymphoma linked to textured breast implants. A leading hypothesis suggests that chronic inflammation, combined with immunological and genetic factors, drives its pathogenesis. Two previous studies investigating bacterial biofilms on breast [...] Read more.
Background: Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is a mature T-cell lymphoma linked to textured breast implants. A leading hypothesis suggests that chronic inflammation, combined with immunological and genetic factors, drives its pathogenesis. Two previous studies investigating bacterial biofilms on breast implant capsules have produced conflicting results, particularly regarding the enrichment of Ralstonia spp. Methods: We analyzed the microbiota profiles in seroma samples from 10 BIA-ALCL patients and 12 patients with non-neoplastic effusion, subclassified into acute-, mixed-, and chronic-type based on cellular composition. We used two metagenomic approaches: 16S rRNA gene sequencing and Nanopore sequencing with the “What’s in My Pot?” (WIMP) taxonomic classifier. Our analyses included alpha and beta diversity metrics, as well as comparisons of Gram status and oxygen requirements. Results: Both sequencing methods identified Staphylococcaceae, Propionibacteriaceae, and Bradyrhizobiaceae as the most prevalent bacterial families in both BIA-ALCL and benign seroma samples. Notably, the Burkholderiaceae family was more abundant in some of the benign seromas according to the 16S rRNA sequencing, but Ralstonia spp. were not detected. BIA-ALCL showed higher richness (based on Nanopore data) and higher evenness (based on 16S rRNA data) compared to acute-type seromas, indicating a more homogenous representation of the different taxa identified. BIA-ALCL seromas did not cluster together based on Nanopore data, but they did form a distinct cluster with 16S rRNA data. This cluster was differentiated from the other two clusters by a relatively balanced presence of multiple families without overt dominance. We observed no significant differences in Gram staining between BIA-ALCL and benign samples using either method. However, non-aerobic bacterial families were enriched in BIA-ALCL cases only when analyzed with the Nanopore pipeline. Conclusions: Overall, our findings did not identify a distinctive microbial signature specifically associated with BIA-ALCL. Full article
(This article belongs to the Special Issue Oncogenesis of Lymphoma)
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14 pages, 644 KB  
Review
Very-High-Energy Gamma-Ray Observations as a Probe to the Nature of Dark Matter and Prospects for MACE
by Mani Khurana, Krishna Kumar Singh, Atul Pathania, Pawan Kumar Netrakanti and Kuldeep Kumar Yadav
Galaxies 2025, 13(3), 53; https://doi.org/10.3390/galaxies13030053 - 2 May 2025
Cited by 1 | Viewed by 1386
Abstract
Searching for very-high-energy photons arising from dark matter interactions in selected astrophysical environments is a promising strategy to probe the existence and particle nature of dark matter. Among the many particle candidates, motivated by the extensions of the Standard Model, Weakly Interacting Massive [...] Read more.
Searching for very-high-energy photons arising from dark matter interactions in selected astrophysical environments is a promising strategy to probe the existence and particle nature of dark matter. Among the many particle candidates, motivated by the extensions of the Standard Model, Weakly Interacting Massive Particles (WIMPs) are considered the most compelling candidate for the elusive dark matter in the universe. In this contribution, we report an overview of the important developments in the field of indirect searching for dark matter through cosmic gamma-ray observations. We mainly focus on the role of atmospheric Cherenkov telescopes in probing the dark matter. Finally, we emphasize the opportunities for the Major Atmospheric Cherenkov Experiment (MACE) situated in Hanle, India, to explore WIMPs in the mass range of 200 GeV to 10 TeV for Segue1 and Draco dwarf–spheroidal galaxies. Full article
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27 pages, 1056 KB  
Article
Quantum Mechanical Numerical Model for Interaction of Dark Atom with Atomic Nucleus of Matter
by Timur Bikbaev, Maxim Khlopov and Andrey Mayorov
Physics 2025, 7(1), 8; https://doi.org/10.3390/physics7010008 - 7 Mar 2025
Viewed by 1913
Abstract
Within the framework of the XHe hypothesis, the positive results of the DAMA/NaI and DAMA/LIBRA experiments on the direct search for dark matter particles can be explained by the annual modulation of the radiative capture of dark atoms into low-energy bound states with [...] Read more.
Within the framework of the XHe hypothesis, the positive results of the DAMA/NaI and DAMA/LIBRA experiments on the direct search for dark matter particles can be explained by the annual modulation of the radiative capture of dark atoms into low-energy bound states with sodium nuclei. Since this effect is not observed in other underground WIMP (weakly interacting massive particle) search experiments, it is necessary to explain these results by investigating the possibility of the existence of low-energy bound states between dark atoms and the nuclei of matter. Numerical modeling is used to solve this problem, since the study of the XHe–nucleus system is a three-body problem and leaves no possibility of an analytical solution. To understand the key properties and patterns underlying the interaction of dark atoms with the nuclei of baryonic matter, we develop the quantum mechanical description of such an interaction. In the numerical quantum mechanical model presented, takes into account the effects of quantum physics, self-consistent electromagnetic interaction, and nuclear attraction. This approach allows us to obtain a numerical model of the interaction between the dark atom and the nucleus of matter and interpret the results of direct experiments on the underground search for dark matter, within the framework of the dark atom hypothesis. Thus, in this paper, for the first time, steps are taken towards a consistent quantum mechanical description of the interaction of dark atoms, with unshielded nuclear attraction, with the nuclei of atoms of matter. The total effective interaction potential of the OHe–Na system has therefore been restored, the shape of which allows for the preservation of the integrity and stability of the dark atom, which is an essential requirement for confirming the validity of the OHe hypothesis. Full article
(This article belongs to the Special Issue Beyond the Standard Models of Physics and Cosmology: 2nd Edition)
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21 pages, 419 KB  
Article
The Impact of Electric Currents on Majorana Dark Matter at Freeze Out
by Lukas Karoly and David C. Latimer
Universe 2025, 11(2), 66; https://doi.org/10.3390/universe11020066 - 14 Feb 2025
Viewed by 1096
Abstract
Thermal relics with masses in the GeV to TeV range remain possible candidates for the Universe’s dark matter (DM). These neutral particles are often assumed to have vanishing electric and magnetic dipole moments so that they do not interact with single real photons, [...] Read more.
Thermal relics with masses in the GeV to TeV range remain possible candidates for the Universe’s dark matter (DM). These neutral particles are often assumed to have vanishing electric and magnetic dipole moments so that they do not interact with single real photons, but the anapole moment, a static electromagnetic property whose features are akin to that of a classical toroidal solenoid, can still be non-zero, permitting interactions with single virtual photons. In some models, DM predominantly annihilates into charged standard model particles through a p-wave process mediated by the anapole moment. The anapole moment is also responsible for another interaction of interest. If a DM medium were subjected to an electric current, a DM particle whose anapole moment was aligned with the current would have lower energy than the state with an antialigned anapole moment. Given these interactions, if a collection of initially unpolarized DM particles were subjected to an electric current, then the DM medium would become partially polarized, according to the Boltzmann distribution. In such a polarized medium, DM annihilation into photons, a subdominant s-wave process realizable through higher order interactions, would be somewhat suppressed. If the local electric current existed during a time in which the DM begins to drop out of thermal equilibrium with the rest of the Universe, the suppressed annihilation could lead to a small local excess in the relic DM density relative to a current-free region. This mechanism by which the local DM density can be perturbed is novel. Using effective interactions to model a DM particle’s anapole moment and polarizabilities (responsible for s-wave annihilation into two photons), we compute the changes in the DM density produced by long- and short-lived currents around freeze out. If we employ the most stringent constraints on DM annihilation into two photons, we find that long-lived currents can result in a fractional change in the DM density on the order of 1017 for DM masses around 100 GeV; for short-lived currents, this fractional change in local DM density is on the order of 1023 for the same DM mass. Full article
(This article belongs to the Section High Energy Nuclear and Particle Physics)
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50 pages, 3558 KB  
Article
Dark Atoms of Nuclear Interacting Dark Matter
by Vitaly A. Beylin, Timur E. Bikbaev, Maxim Yu. Khlopov, Andrey G. Mayorov and Danila O. Sopin
Universe 2024, 10(9), 368; https://doi.org/10.3390/universe10090368 - 11 Sep 2024
Cited by 7 | Viewed by 2256
Abstract
The lack of positive evidence for Weakly Interacting Massive Particles (WIMPs) as well as the lack of discovery of supersymmetric (SUSY) particles at the LHC may appeal to a non-supersymmetric solution for the Standard Model problem of the Higgs boson mass divergence, the [...] Read more.
The lack of positive evidence for Weakly Interacting Massive Particles (WIMPs) as well as the lack of discovery of supersymmetric (SUSY) particles at the LHC may appeal to a non-supersymmetric solution for the Standard Model problem of the Higgs boson mass divergence, the origin of the electroweak energy scale and the physical nature of the cosmological dark matter in the approach of composite Higgs boson. If the Higgs boson consists of charged constituents, their binding can lead to stable particles with electroweak charges. Such particles can take part in sphaleron transitions in the early Universe, which balance their excess with baryon asymmetry. Constraints on exotic charged species leave only stable particles with charge 2n possible, which can bind with n nuclei of primordial helium in neutral dark atoms. The predicted ratio of densities of dark atoms and baryonic matter determines the condition for dark atoms to dominate in the cosmological dark matter. To satisfy this condition of the dark-atom nature of the observed dark matter, the mass of new stable 2n charged particles should be within reach of the LHC for their searches. We discuss the possibilities of dark-atom binding in multi-atom systems and present state-of-the-art quantum mechanical descriptions of dark-atom interactions with nuclei. Annual modulations in such interactions with nuclei of underground detectors can explain the positive results of DAMA/NaI and DAMA/LIBRA experiments and the negative results of the underground WIMP searches. Full article
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8 pages, 361 KB  
Article
Theoretical WIMP–Nucleus Scattering Rates for Isomeric Nuclei
by John D. Vergados and Dennis Bonatsos
Particles 2024, 7(3), 810-817; https://doi.org/10.3390/particles7030048 - 10 Sep 2024
Cited by 2 | Viewed by 1494
Abstract
The direct detection of dark matter constituents, particularly weakly interacting massive particles (WIMPs), is central to particle physics and cosmology. In this paper, we develop the formalism for WIMP–nucleus-induced transitions from isomeric nuclear states, with particular focus on the experimentally interesting target 180 [...] Read more.
The direct detection of dark matter constituents, particularly weakly interacting massive particles (WIMPs), is central to particle physics and cosmology. In this paper, we develop the formalism for WIMP–nucleus-induced transitions from isomeric nuclear states, with particular focus on the experimentally interesting target 180Ta. Full article
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8 pages, 588 KB  
Brief Report
Constraining the Inner Galactic DM Density Profile with H.E.S.S.
by Jaume Zuriaga-Puig
Astronomy 2024, 3(2), 114-121; https://doi.org/10.3390/astronomy3020008 - 11 Apr 2024
Viewed by 2051
Abstract
In this short review, corresponding to a talk given at the conference “Cosmology 2023 in Miramare”, we combine an analysis of five regions observed by H.E.S.S. in the Galactic Center, intending to constrain the Dark Matter (DM) density profile in a WIMP annihilation [...] Read more.
In this short review, corresponding to a talk given at the conference “Cosmology 2023 in Miramare”, we combine an analysis of five regions observed by H.E.S.S. in the Galactic Center, intending to constrain the Dark Matter (DM) density profile in a WIMP annihilation scenario. For the analysis, we include the state-of-the-art Galactic diffuse emission Gamma-optimized model computed with DRAGON and a wide range of DM density profiles from cored to cuspy profiles, including different kinds of DM spikes. Our results are able to constrain generalized NFW profiles with an inner slope γ1.3. When considering DM spikes, the adiabatic spike is completely ruled out. However, smoother spikes given by the interactions with the bulge stars are compatible if γ0.8, with an internal slope of γsp-stars=1.5. Full article
(This article belongs to the Special Issue Current Trends in Cosmology)
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12 pages, 2683 KB  
Article
A Simple Model of the Energy Threshold for Snowball Chambers
by Matthew Szydagis, Cecilia Levy, Aleksey E. Bolotnikov, Milind V. Diwan, George J. Homenides, Alvine C. Kamaha, Joshua Martin, Richard Rosero and Minfang Yeh
Universe 2024, 10(2), 81; https://doi.org/10.3390/universe10020081 - 8 Feb 2024
Viewed by 2307
Abstract
Cloud and bubble chambers have historically been used for particle detection, capitalizing on supersaturation and superheating, respectively. Here, we present new results from a prototype snowball chamber, in which an incoming particle triggers the crystallization of a purified, supercooled liquid. We demonstrate, for [...] Read more.
Cloud and bubble chambers have historically been used for particle detection, capitalizing on supersaturation and superheating, respectively. Here, we present new results from a prototype snowball chamber, in which an incoming particle triggers the crystallization of a purified, supercooled liquid. We demonstrate, for the first time, simulation agreement with our first results from 5 years ago: the higher temperature of the freezing of water and significantly shorter time spent supercooled compared to the control in the presence of a Cf-252 fission neutron source. This is accomplished by combining Geant4 modeling of neutron interactions with the Seitz nucleation model used in superheated bubble chambers, including those seeking dark matter. We explore the possible implications of using this new technology for GeV-scale WIMP searches, especially in terms of spin-dependent proton coupling, and report the first supercooling of WbLS (water-based liquid scintillator). Full article
(This article belongs to the Special Issue Recent Development and Prospects in Dark Matter Research)
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13 pages, 481 KB  
Article
Application of Host-Depleted Nanopore Metagenomic Sequencing in the Clinical Detection of Pathogens in Pigs and Cats
by Xu Han and Zhaofei Xia
Animals 2023, 13(24), 3838; https://doi.org/10.3390/ani13243838 - 13 Dec 2023
Cited by 5 | Viewed by 4866
Abstract
Metagenomic sequencing is a valuable tool for non-specifically detecting various microorganisms in samples, offering unique advantages for detecting emerging pathogens, fastidious or uncultivable pathogens, and mixed infections. It has recently been applied to clinically detect pathogenic microorganisms in animals; however, the high proportion [...] Read more.
Metagenomic sequencing is a valuable tool for non-specifically detecting various microorganisms in samples, offering unique advantages for detecting emerging pathogens, fastidious or uncultivable pathogens, and mixed infections. It has recently been applied to clinically detect pathogenic microorganisms in animals; however, the high proportion of host genes, expensive sequencing equipment, and the complexity of sequencing and data analysis methods have limited its clinical utility. In this study, a combination of tissue homogenization and nuclease digestion was employed to remove host genes from pig and cat samples; DNA and RNA were then extracted and subjected to nonselective PCR amplification to simultaneously detect DNA and RNA pathogen genomes using R9.4.1 or R10.4.1 flow cells on the MinION platform. Real-time pathogen detection was conducted using EPI2M WIMP, and viral genome assembly was performed using NanoFilt, minimap2, samtools, and ivar. Pathogens in five clinical samples (serum, nasopharyngeal swab, feces, or ascites) from cats and four clinical samples (lung or small intestine tissue) from pigs were examined by metagenomic sequencing, and the results were consistent with those obtained by PCR and bacterial culture. Additionally, we detected four viruses and three bacteria that may be associated with diseases. A comparison of results before and after host gene removal in three samples showed a 9–50% reduction in host genes. We also compared the assembly efficiency of six virus genomes and found that data volumes ranging from 3.3 to 98.3 MB were sufficient to assemble >90% of the viral genomes. In summary, this study utilized optimized nanopore metagenomic sequencing and analysis methods to reduce host genes, decrease the required data volume for sequencing analysis, and enable real-time detection to determine when to stop sequencing. The streamlined sequencing and analysis process overcomes barriers to the veterinary clinical application of metagenomic sequencing and provides a reference for clinical implementation. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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15 pages, 723 KB  
Article
Axionic Dark Matter in a Bi-Metric Universe
by Carlos Maldonado and Fernando Méndez
Universe 2023, 9(10), 429; https://doi.org/10.3390/universe9100429 - 27 Sep 2023
Cited by 2 | Viewed by 2275
Abstract
We study the evolution and production of axion dark matter in a universe model with two scale factors corresponding to different patches of the universe. The interaction between patches is described through a deformed Poisson bracket structure. The first part of the present [...] Read more.
We study the evolution and production of axion dark matter in a universe model with two scale factors corresponding to different patches of the universe. The interaction between patches is described through a deformed Poisson bracket structure. The first part of the present paper is devoted to a review of the results reported in previous works concerning the study of dark matter as WIMPs and FIMPs. The new results concerning axionic dark matter in this bi-metric scenario show that different values of the deformation parameter κ allow values of masses and misalignment angles forbidden in standard cosmology. The present model can also be considered a different type of nonstandard cosmology consistent with previously reported results. Full article
(This article belongs to the Section Cosmology)
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15 pages, 803 KB  
Article
Mitigating Technological Anxiety through the Application of Natural Interaction in Mixed Reality Systems
by Yiming Sun and Tatsuo Nakajima
Future Internet 2023, 15(6), 216; https://doi.org/10.3390/fi15060216 - 18 Jun 2023
Cited by 3 | Viewed by 2884
Abstract
Technology anxiety contributes to an increased cognitive load and reduces user adoption of novel technologies. An illustrative example of this phenomenon is observed in the field of smart homes.To address this issue, we have identified an interaction paradigm known as natural interaction, which [...] Read more.
Technology anxiety contributes to an increased cognitive load and reduces user adoption of novel technologies. An illustrative example of this phenomenon is observed in the field of smart homes.To address this issue, we have identified an interaction paradigm known as natural interaction, which enables humans to engage with technology in a way that closely resembles natural human behavior and communication. This approach offers more user-friendly interactions that users are already familiar with, potentially reducing their cognitive load. In this paper, we present a case study of a smart lock system where we implement natural interaction and deploy it on a mixed reality (MR) device. By leveraging advanced features offered by MR head-mounted displays, we recreate the experience of people opening locks in everyday life. We conduct a user study comparing this interaction with traditional WIMP interaction in a mixed-reality environment. Through the analysis of collected data and user feedback, we examine the advantages and limitations of our proposed system. Full article
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23 pages, 10215 KB  
Article
Estimation of Interaction Locations in Super Cryogenic Dark Matter Search Detectors Using Genetic Programming-Symbolic Regression Method
by Nikola Anđelić, Sandi Baressi Šegota, Matko Glučina and Zlatan Car
Appl. Sci. 2023, 13(4), 2059; https://doi.org/10.3390/app13042059 - 5 Feb 2023
Cited by 2 | Viewed by 2209
Abstract
The Super Cryogenic Dark Matter Search (SuperCDMS) experiment is used to search for Weakly Interacting Massive Particles (WIMPs)—candidates for dark matter particles. In this experiment, the WIMPs interact with nuclei in the detector; however, there are many other interactions (background interactions). To separate [...] Read more.
The Super Cryogenic Dark Matter Search (SuperCDMS) experiment is used to search for Weakly Interacting Massive Particles (WIMPs)—candidates for dark matter particles. In this experiment, the WIMPs interact with nuclei in the detector; however, there are many other interactions (background interactions). To separate background interactions from the signal, it is necessary to measure the interaction energy and to reconstruct the location of the interaction between WIMPs and the nuclei. In recent years, some research papers have been investigating the reconstruction of interaction locations using artificial intelligence (AI) methods. In this paper, a genetic programming-symbolic regression (GPSR), with randomly tuned hyperparameters cross-validated via a five-fold procedure, was applied to the SuperCDMS experiment to estimate the interaction locations with high accuracy. To measure the estimation accuracy of obtaining the SEs, the mean and standard deviation (σ) values of R2, the root-mean-squared error (RMSE), and finally, the mean absolute error (MAE) were used. The investigation showed that using GPSR, SEs can be obtained that estimatethe interaction locations with high accuracy. To improve the solution, the five best SEs were combined from the three best cases. The results demonstrated that a very high estimation accuracy can be achieved with the proposed methodology. Full article
(This article belongs to the Special Issue Evolutionary Computation: Theories, Techniques, and Applications)
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30 pages, 3503 KB  
Review
Dark Matter Searches with Top Quarks
by J. Katharina Behr and Alexander Grohsjean
Universe 2023, 9(1), 16; https://doi.org/10.3390/universe9010016 - 27 Dec 2022
Cited by 4 | Viewed by 3033
Abstract
Collider signatures with top quarks provide sensitive probes of dark matter (DM) production at the Large Hadron Collider (LHC). In this article, we review the results of DM searches in final states with top quarks conducted by the ATLAS and CMS Collaborations at [...] Read more.
Collider signatures with top quarks provide sensitive probes of dark matter (DM) production at the Large Hadron Collider (LHC). In this article, we review the results of DM searches in final states with top quarks conducted by the ATLAS and CMS Collaborations at the LHC, including the most recent results on the full LHC Run 2 dataset. We highlight the complementarity of DM searches in final states with top quarks with searches in other final states in the framework of various simplified models of DM. A reinterpretation of a DM search with top quarks in the context of an effective field theory description of scalar dark energy is also discussed. Finally, we give an outlook on the potential of DM searches with top quarks in LHC Run 3, at the high-luminosity LHC, and possible future colliders. In this context, we highlight new benchmark models that could be probed by existing and future searches as well as those that predict still-uncovered signatures of anomalous top-quark production and decays at the LHC. Full article
(This article belongs to the Special Issue Top Quark at the New Physics Frontier)
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26 pages, 1444 KB  
Article
Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
by Gaelle Esnault, Bernadette Earley, Paul Cormican, Sinead M. Waters, Ken Lemon, S. Louise Cosby, Paula Lagan, Thomas Barry, Kate Reddington and Matthew S. McCabe
Viruses 2022, 14(9), 1859; https://doi.org/10.3390/v14091859 - 24 Aug 2022
Cited by 11 | Viewed by 4572
Abstract
Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing [...] Read more.
Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software. Full article
(This article belongs to the Section Animal Viruses)
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