bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of the competition between Colletotrichum godetiae and C. nymphaeae, two pathogenic species in olive
Authors: Garcia-Lopez M. Teresa , Serrano M. Socorro , Camiletti Boris X. , Gordon Ana , Estudillo Cristina , Trapero Antonio , Diez Concepcion M. , Moral Juan 
Published: April 2023

AbstractOlive anthracnose, a critical olive fruit disease that adversely impacts oil quality, is caused by Colletotrichum species. A dominant Colletotrichum species and several secondary species have been identified in each olive-growing region. This study surveys the interspecific competition between C. godetiae, dominant in Spain, and C. nymphaeae, prevalent in Portugal, to shed light on the cause of this disparity. When Petri-dishes of Potato Dextrose Agar (PDA) and diluted PDA were co-inoculated with spore mixes produced by both species, C. godetiae displaced C. nymphaeae, even if the percentage of spores in the initial spore mix inoculation was just 5 and 95%, respectively. The C. godetiae and C. nymphaeae species showed similar fruit virulence in separate inoculations in both cultivars, the Portuguese cv. Galega Vulgar and the Spanish cv. Hojiblanca, and no cultivar specialization was observed. However, when olive fruits were co-inoculated, the C. godetiae species showed a higher competitive ability and partially displaced the C. nymphaeae species. Furthermore, both Colletotrichum species showed a similar leaf survival rate. Lastly, C. godetiae was more resistant to metallic copper than C. nymphaeae. The work developed here allows a deeper understanding of the competition between C. godetiae and C. nymphaeae, which could lead to developing strategies for more efficient disease risk assessment.
In silico study of HASDI (high-affinity selective DNA intercalator) as a new agent capable of highly selective recognition of the DNA sequence
Authors: Zaremba Andrii A. , Zaremba Polina Yu. , Zahorodnia Svitlana D. 
Published: April 2023

AbstractCancer as an acquired genetic disease is based on changes both in the genome itself and in transcription processes. Accordingly, it is at the DNA level that it makes sense to search for and design agents capable of effective and selective anticancer action. In this study, we used an iterative approach based on a molecular dynamics simulation to design a highly selective DNA-intercalating agent called HASDI. To confirm its selective affinity to DNA, we conducted two simulation experiments: HASDI in a complex with a DNA fragment of the EBNA1 gene (it targets 16 nucleotide pairs of this gene) and HASDI in a complex with a random DNA fragment of the KCNH2 gene. The molecular dynamics simulation was carried out in the GROMACS 2019 package. The binding energy was calculated by gmx_MMPBSA 1.5.2. The further analysis was performed using the built-in utilities of GROMACS, gmx_MMPBSA and also XMGRACE and Pymol 1.8. As a result, we determined that the EBNA1-50nt/HASDI complex was stable throughout the whole simulation trajectory. HASDI, due to the presence of a linker modified depending on a specific pair of nitrogenous bases, formed an average of 32 hydrogen bonds with a sequence of 16 nucleotide pairs. Phenazine rings were stably intercalated every 2 base pairs. The root-mean-square deviation of HASDI in such a complex fluctuated around the value of 6.5 Å and had no tendency to increase. The calculated value of the binding free energy was − 235.3 ± 7.77 kcal/mol. The KCNH2-50nt/HASDI complex, as an example of the intercalation of the designed structure into a random part of the human genome, maintained the stability of its position at a level comparable to the EBNA1-50nt/HASDI complex. The phenazine rings were constantly intercalated in their original positions, and the root-mean-square deviation fluctuated around one value, although it had a tendency to chaotic changes. At the same time, this complex was characterized by 17–19 hydrogen bonds, on average, and the binding free energy was − 193.47 ± 14.09 kcal/mol. Moreover, the DNA duplex had local single-nucleotide melting in the region of the 4th linker. According to a significant decrease in the number of hydrogen bonds, a decrease in energy gain, as well as a decrease in the stability of the DNA duplex characteristic of the KCNH2-50nt/HASDI complex compared to the target EBNA1-50nt/HASDI complex, the molecule we designed can be considered a potentially selective DNA polyintercalating agent capable of relatively accurate recognition of 16 base pairs.
Control of magnetic states and spin interactions in bilayer CrCl3 with strain and electric fields: an ab initio study
Authors: Ebrahimian Ali , Dyrdał Anna , Qaiumzadeh Alireza 
Published: April 2023

AbstractUsing ab initio density functional theory, we demonstrated the possibility of controlling the magnetic ground-state properties of bilayer CrCl$$_{3}$$

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by means of mechanical strains and electric fields. In principle, we investigated the influence of these two fields on parameters describing the spin Hamiltonian of the system. The obtained results show that biaxial strains change the magnetic ground state between ferromagnetic and antiferromagnetic phases. The mechanical strain also affects the direction and amplitude of the magnetic anisotropy energy (MAE). Importantly, the direction and amplitude of the Dzyaloshinskii–Moriya vectors are also highly tunable under external strain and electric fields. The competition between nearest-neighbor exchange interactions, MAE, and Dzyaloshinskii–Moriya interactions can lead to the stabilization of various exotic spin textures and novel magnetic excitations. The high tunability of magnetic properties by external fields makes bilayer CrCl$$_{3}$$

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a promising candidate for application in the emerging field of two-dimensional quantum spintronics and magnonics.
Long noncoding RNA SNHG6 silencing sensitized esophageal cancer cells to 5-FU via EZH2/STAT pathway
Authors: Tan Ran , Liu Jia , Wang Jiang , Zhang Wei , He Meng , Zhang Yueli 
Published: April 2023

AbstractChemotherapy was the main treatment method for esophageal cancer (EC) patients. However, chemotherapy resistance due to multiple factors is a major barrier to EC treatment. For investigating how small nucleolar RNA host gene 6 (SNHG6) affected the 5-fluorouracil (5-FU) resistance in EC as well as its possible molecular mechanism. This work conducted cell viability assay, clone formation, scratch assays together with cell apoptosis for evaluating the roles of SNHG6 and enhancer of zeste homolog 2 (EZH2, the histone-lysine N-methyltransferase). Relevant molecular mechanism was identified by RT-qPCR analysis together with Western-blot (WB) assays. Our data showed that SNHG6 expression increased in EC cells. SNHG6 promotes colony formation and migration, whereas suppresses EC cell apoptosis. SNHG6 silencing markedly promoted 5-FU-mediated suppression on KYSE150 and KYSE450 cells. Additional mechanism studies showed that SNHG6 modulating STAT3 and H3K27me3 via promoting EZH2 level. Similar to the function of SNHG6, abnormal expression of EZH2 promotes the malignancy of EC and intensifies its resistance to 5-FU. In addition, overexpression of EZH2 abolished the role of SNHG6 silencing in 5-FU sensitivity in EC cells. SNHG6 overexpression promoted malignancy of EC and increased EC cell resistance to 5-FU. Besides, further molecular mechanism studies provided a novel regulatory pathways that SNHG6 knockdown promoted EC cell sensitivity to 5-FU by modulating STAT3 and H3K27me3 via promoting EZH2 expression.
Hidden chamber discovery in the underground Hellenistic necropolis of Neapolis by muography
Authors: Tioukov Valeri , Morishima Kunihiro , Leggieri Carlo , Capriuoli Federico , Kitagawa Nobuko , Kuno Mitsuaki , Manabe Yuta , Nishio Akira , Alexandrov Andrey , Gentile Valerio , Iuliano Antonio , De Lellis Giovanni 
Published: April 2023

AbstractWe report in this paper the muography of an archaeological site located in the highly populated “Sanità” district in the center of Naples, ten meters below the current street level. Several detectors capable of detecting muons - high energy charged particles produced by cosmic rays in the upper layers of atmosphere - were installed underground at the depth of 18 m, to measure the muon flux over several weeks. By measuring the differential flux with our detectors in a wide angular range, we have produced a radiographic image of the upper layers. Despite the architectural complexity of the site, we have clearly observed the known structures as well as a few unknown ones. One of the observed new structures is compatible with the existence of a hidden, currently inaccessible, burial chamber.
Association of high proprotein convertase subtilisin/kexin type 9 antibody level with poor prognosis in patients with diabetes: a prospective study
Authors: Yamagata Hiroki , Hayashi Aiko , Yoshida Yoich , Koshizaka Masaya , Onishi Shunichiro , Yoshida Tomohiko , Hiwasa Takaki , Takemoto Minoru 
Published: April 2023

AbstractIn addition to pathogenic autoantibodies, polyclonal autoantibodies with unknown physiological roles and pathogenicity are produced in the body. Moreover, serum antibodies against the proprotein convertase subtilisin/kexin type 9 (PCSK9) protein, which is integral to cholesterol metabolism, have also been observed. PCSK9 was also reported to be associated with insulin secretion and diabetes mellitus (DM). Therefore, we aimed to examine the clinical significance of PCSK9 antibodies (PCSK9-Abs) levels. We measured blood PCSK9-Abs and PCSK9 protein levels in 109 healthy donors (HDs) and 274 patients with DM (type 2 DM: 89.8%) using an amplified luminescence proximity homogeneous assay-linked immunosorbent assay. Subsequently, patients with DM were followed up (mean: 4.93 years, standard deviation: 2.77 years, maximum: 9.58 years, minimum: 0.07 years) to examine associations between antibody titers and mortality, myocardial infarction, stroke onset, and cancer. The primary endpoint of this study was to examine whether PCSK9-Abs can be a prognostic marker for overall mortality among the patients with diabetes. The secondary endpoint was to examine the relationship between PCSK9-Abs and clinical parameters. Although both PCSK9-Abs and PCSK9 protein levels were significantly higher in the DM group than in the HD group (p < 0.008), PCSK9-Abs and PCSK9 protein levels showed no correlation in either group. Mortality was significantly associated with higher PCSK9-Ab levels, but unrelated to PCSK9 protein levels. After investigating for potential confounding factors, higher PCSK9-Ab levels were still associated with increased mortality among the patients with DM. PCSK9-Abs may be a novel prognostic marker for overall mortality in patients with diabetes, and further studies are warranted to verify its usefulness.
Sound source localization based on residual network and channel attention module
Authors: Hu Fucai , Song Xiaohui , He Ruhan , Yu Yongsheng 
Published: April 2023

AbstractThis paper presents a sound source localization (SSL) model based on residual network and channel attention mechanism. The method takes the combination of log-Mel spectrogram and generalized cross-correlation phase transform (GCC-PHAT) as the input features, and extracts the time–frequency information by using the residual structure and channel attention mechanism, thus obtaining a better localizing performance. The residual blocks are introduced to extract deeper features, which can stack more layers for high-level features and avoid gradient vanishing or exploding at the same time. The attention mechanism is taken into account for the feature extraction stage in the proposed SSL model, which can focus on the most important information on the input features. We use the signals collected by microphone array to explore the performance of the model under different features, and find the most suitable input features of the proposed method. We compare our method with other models on public dataset. Experience results show a quite substantial improvement of sound source localizing performance.
A database of heterogeneous faces for studying naturalistic expressions
Authors: Long Houqiu , Peluso Natalie , Baker Chris I. , Japee Shruti , Taubert Jessica 
Published: April 2023

AbstractFacial expressions are thought to be complex visual signals, critical for communication between social agents. Most prior work aimed at understanding how facial expressions are recognized has relied on stimulus databases featuring posed facial expressions, designed to represent putative emotional categories (such as ‘happy’ and ‘angry’). Here we use an alternative selection strategy to develop the Wild Faces Database (WFD); a set of one thousand images capturing a diverse range of ambient facial behaviors from outside of the laboratory. We characterized the perceived emotional content in these images using a standard categorization task in which participants were asked to classify the apparent facial expression in each image. In addition, participants were asked to indicate the intensity and genuineness of each expression. While modal scores indicate that the WFD captures a range of different emotional expressions, in comparing the WFD to images taken from other, more conventional databases, we found that participants responded more variably and less specifically to the wild-type faces, perhaps indicating that natural expressions are more multiplexed than a categorical model would predict. We argue that this variability can be employed to explore latent dimensions in our mental representation of facial expressions. Further, images in the WFD were rated as less intense and more genuine than images taken from other databases, suggesting a greater degree of authenticity among WFD images. The strong positive correlation between intensity and genuineness scores demonstrating that even the high arousal states captured in the WFD were perceived as authentic. Collectively, these findings highlight the potential utility of the WFD as a new resource for bridging the gap between the laboratory and real world in studies of expression recognition.
Clinical characteristics and risk factors of patients with eosinophilic fasciitis associated with pleural effusion
Authors: Chen Zhifeng , Wasti Binaya , Shang Yulin , Jia Aijun , Xiang Xudong , Ouyang Ruoyun 
Published: April 2023

AbstractTo investigate the risk factors of eosinophilic fasciitis (EF) associated with pleural effusion (PE). A retrospective analysis was performed on 22 patients with EF diagnosed by skin biopsy in our hospital, and they were divided into EF-PE and EF according to chest computed tomography examination. The clinical characteristics, clinical manifestations, comorbidities and laboratory test indicators of the two groups were collected and compared, and the risk factors for occurring PE in patients with EF were determined by multivariate logistic regression analysis. Among 22 patients with EF, 8 had PE. The age, course of disease, incidence of fever, weight loss, cough and shortness of breath, pulmonary infection, hypothyroidism, hydronephrosis and kidney stone, swelling rate of small vascular endothelial cells, consolidation shadows, C-reactive protein and thyroid stimulating hormone in EF-PE group were higher than those in EF group, while free triiodothyronine and thyroxine were lower than those in EF group. Age, fever, shortness of breath, C-reactive protein, ESR, thyroid stimulating hormone, pulmonary infection, hypothyroidism, hydronephrosis, kidney stones, swollen small vascular endothelial cells and chest CT consolidation shadows were identified as risk factors for happening PE in patients with EF, while free triiodothyronine and free thyroxine were identified as protective factors against PE in patients with EF. The incidence of EF-PE was 36.36% in this study. Advanced age, high C-reactive protein, ESR, thyroid stimulating hormone, incidence of fever, shortness of breath, pulmonary infection, hydronephrosis, kidney stones, swollen small vascular endothelial cells, chest CT consolidation shadows, and low free triiodothyronine and thyroxine suggest that patients with EF are significantly at increased risk of PE.
Modeling pressure drop values across ultra-thin nanofiber filters with various ranges of filtration parameters under an aerodynamic slip effect
Authors: Lee Songhui , Bui-Vinh Dai , Baek Minwoo , Kwak Dong-Bin , Lee Handol 
Published: April 2023

AbstractComputational fluid dynamics simulations of fibrous filters with 56 combinations of different fiber sizes, packing densities, face velocities, and thicknesses were conducted for developing models that predict pressure drops across nanofiber filters. The accuracy of the simulation method was confirmed by comparing the numerical pressure drops to the experimental data obtained for polyacrylonitrile electrospun nanofiber filters. In the simulations, an aerodynamic slip effect around the surface of the small nanofibers was considered. The results showed that, unlike in the case of conventional filtration theory, pressure drops across the thin layers of electrospun nanofiber filters are not proportional to the thickness. This might be a critical factor for obtaining precise pressure drops across the electrospun nanofiber filters with extremely thin layers. Finally, we derived the product of drag coefficient and Reynolds number as a function of packing density, Knudsen number, and ratio of thickness to fiber diameter to get the correlation equation for pressure drop prediction. The obtained equation predicted the pressure drops across the nanofiber filters with the maximum relative difference of less than 15%.
Absorption versus adsorption: high-throughput computation of impurities in 2D materials
Authors: Davidsson Joel , Bertoldo Fabian , Thygesen Kristian S. , Armiento Rickard 
Published: April 2023

AbstractDoping of a two-dimensional (2D) material by impurity atoms occurs via two distinct mechanisms: absorption of the dopants by the 2D crystal or adsorption on its surface. To distinguish the relevant mechanism, we systematically dope 53 experimentally synthesized 2D monolayers by 65 different chemical elements in both absorption and adsorption sites. The resulting 17,598 doped monolayer structures were generated using the newly developed ASE —a Python tool to set up point defects in 2D and bulk materials—and subsequently relaxed by an automated high-throughput density functional theory (DFT) workflow. We find that interstitial positions are preferred for small dopants with partially filled valence electrons in host materials with large lattice parameters. In contrast, adatoms are favored for dopants with a low number of valence electrons due to lower coordination of adsorption sites compared to interstitials. The relaxed structures, characterization parameters, defect formation energies, and magnetic moments (spins) are available in an open database to help advance our understanding of defects in 2D materials.
Covalent bonded bilayers from germanene and stanene with topological giant capacitance effects
Authors: Zhang Binglei , Grassano Davide , Pulci Olivia , Liu Yang , Luo Yi , Conte Adriano Mosca , Kusmartsev Fedor Vasilievich , Kusmartseva Anna 
Published: April 2023

AbstractThe discovery of twisted bilayer graphene with tunable superconductivity has diverted great focus at the world of twisted van der Waals heterostructures. Here we propose a paradigm for bilayer materials, where covalent bonding replaces the van der Waals interaction between the layers. On the example of germanene-stanene bilayer, we show that such systems demonstrate fascinating topological properties and manifest giant capacitance effects of the order of C = 102μ F as well as dipole-like charge densities of q = 1 − 2 × 10−4μ C cm−2, showing promise for 2D ferroelectricity. The observed unique behaviour is closely linked to transverse strain-induced buckling deformations at the bilayer/substrate interface. In alternative GeSn bilayer structures with low twist angles the strain distortions trigger rich topological defect physics. We propose that the GeSn bilayer topology may be switched locally by a substrate-strain-induced electric fields. We demonstrate an approach to fabricate covalent bilayer materials, holding vast possibilities to transform applications technologies across solar, energy and optoelectronic sectors.
Mechanistic insights into the deformation and degradation of a 2D metal organic framework
Authors: Sahabudeen Hafeesudeen , Zhang Qiang , Liu Yue , Heuchel Matthias , Machatschek Rainhard 
Published: April 2023

Abstract2D metal-organic frameworks (2D-MOFs) materials can be subjected to various modes of mechanical stresses and strains in a wide range of applications, for which their mechanical properties are critical to reach practical implementations. Despite the rapid developments focused on the preparation of ultrathin 2D-MOF materials, very little is known about their mechanical and degradation behavior. Here, we use the established 2D-MOF PdTCPP-Cu (NAFS-13) as model system, to introduce the Langmuir–Blodgett (LB) technique, combined with interfacial rheology, as a novel in situ method for direct determination of the in-plane Young’s modulus by simultaneously measuring the 2D shear and compression moduli of a 2D-MOF formed at the air-water interface. Furthermore, it can be used to evaluate mechanistic models describing the degradation kinetics of 2D MOFs. To provide a deeper understanding of the factors that determine the Young’s modulus observed in such a set up, we carried out nanoindentation measurements and molecular dynamics (MD) simulations based on classical force fields. This protocol allows us to gain mechanistic insights into the impact of structural defects, temperature, tensile and compression stress on the Young’s modulus of 2D MOFs.
Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor
Authors: Bose Sucharita , Steussy C. Nicklaus , López-Pérez Daneli , Schmidt Tim , Kulathunga Samadhi C. , Seleem Mohamed N. , Lipton Mark , Mesecar Andrew D. , Rodwell Victor W. , Stauffacher Cynthia V. 
Published: April 2023

AbstractHMG-CoA reductase (HMGR), a rate-limiting enzyme of the mevalonate pathway in Gram-positive pathogenic bacteria, is an attractive target for development of novel antibiotics. In this study, we report the crystal structures of HMGR from Enterococcus faecalis (efHMGR) in the apo and liganded forms, highlighting several unique features of this enzyme. Statins, which inhibit the human enzyme with nanomolar affinity, perform poorly against the bacterial HMGR homologs. We also report a potent competitive inhibitor (Chembridge2 ID 7828315 or compound 315) of the efHMGR enzyme identified by a high-throughput, in-vitro screening. The X-ray crystal structure of efHMGR in complex with 315 was determined to 1.27 Å resolution revealing that the inhibitor occupies the mevalonate-binding site and interacts with several key active site residues conserved among bacterial homologs. Importantly, 315 does not inhibit the human HMGR. Our identification of a selective, non-statin inhibitor of bacterial HMG-CoA reductases will be instrumental in lead optimization and development of novel antibacterial drug candidates.