bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis
Authors: Mazurel Danuta , Carda-Diéguez Miguel , Langenburg Thomas , Žiemytė Miglė , Johnston William , Martínez Carlos Palazón , Albalat Fernando , Llena Carmen , Al-Hebshi Nezar , Culshaw Shauna , Mira Alex , Rosier Bob T. 
Published: June 2023

AbstractA few studies indicate that nitrate can reduce dysbiosis from a periodontitis point of view. However, these experiments were performed on samples from healthy individuals, and it is unknown if nitrate will be effective in periodontal patients, where the presence of nitrate-reducing bacteria is clearly reduced. The aim of this study was to test the effect of nitrate and a nitrate-reducing R. aeria (Ra9) on subgingival biofilms of patients with periodontitis. For this, subgingival plaque was incubated with 5 mM nitrate for 7 h (n = 20) or 50 mM nitrate for 12 h (n = 10), achieving a ~50% of nitrate reduction in each case. Additionally, Ra9 was combined with 5 mM nitrate (n = 11), increasing the nitrate reduced and nitrite produced (both p < 0.05). The addition of nitrate to periodontitis communities decreased biofilm mass (50 mM > 5 mM, both p < 0.05). Five millimolar nitrate, 50 mM nitrate and 5 mM nitrate + Ra9 led to 3, 28 and 20 significant changes in species abundance, respectively, which were mostly decreases in periodontitis-associated species. These changes led to a respective 15%, 63% (both p < 0.05) and 6% (not significant) decrease in the dysbiosis index. Using a 10-species biofilm model, decreases in periodontitis-associated species in the presence of nitrate were confirmed by qPCR (all p < 0.05). In conclusion, nitrate metabolism can reduce dysbiosis and biofilm growth of periodontitis communities. Five millimolar nitrate (which can be found in saliva after vegetable intake) was sufficient, while increasing this concentration to 50 mM (which could be achieved by topical applications such as a periodontal gel) increased the positive effects. Ra9 increased the nitrate metabolism of periodontitis communities and should be tested in vivo.
Machine learning molecular dynamics simulation identifying weakly negative effect of polyanion rotation on Li-ion migration
Authors: Xu Zhenming , Duan Huiyu , Dou Zhi , Zheng Mingbo , Lin Yixi , Xia Yinghui , Zhao Haitao , Xia Yongyao 
Published: June 2023

AbstractUnderstanding the physical picture of Li ion transport in the current ionic conductors is quite essential to further develop lithium superionic conductors for solid-state batteries. The traditional practice of directly extrapolating room temperature ion diffusion properties from the high-temperature (>600 K) ab initio molecular dynamics simulations (AIMD) simulations by the Arrhenius assumption unavoidably cause some deviations. Fortunately, the ultralong-time molecular dynamics simulation based on the machine-learning interatomic potentials (MLMD) is a more suitable tool to probe into ion diffusion events at low temperatures and simultaneously keeps the accuracy at the density functional theory level. Herein, by the low-temperature MLMD simulations, the non-linear Arrhenius behavior of Li ion was found for Li3ErCl6, which is the main reason for the traditional AIMD simulation overestimating its ionic conductivity. The 1μs MLMD simulations capture polyanion rotation events in Li7P3S11 at room temperature, in which four [PS4]3− tetrahedra belonging to a part of the longer-chain [P2S7]4− group are noticed with remarkable rotational motions, while the isolated group [PS4]3− does not rotate. However, no polyanion rotation is observed in Li10GeP2S12, β-Li3PS4, Li3ErCl6, and Li3YBr6 at 300 K during 1μs simulation time. Additionally, the ultralong-time MLMD simulations demonstrate that not only there is no paddle-wheel effect in the crystalline Li7P3S11 at room temperature, but also the rotational [PS4]3− polyanion groups have weakly negative impacts on the overall Li ion diffusion. The ultralong-time MLMD simulations deepen our understanding of the relationship between the polyanion rotation and cation diffusion in ionic conductors at room environments.
Alteration of medieval stained glass windows in atmospheric medium: review and simplified alteration model
Authors: Verney-Carron Aurélie , Sessegolo Loryelle , Chabas Anne , Lombardo Tiziana , Rossano Stéphanie , Perez Anne , Valbi Valentina , Boutillez Chloé , Muller Camille , Vaulot Cyril , Trichereau Barbara , Loisel Claudine 
Published: June 2023

AbstractStained glass windows are a precious heritage to pass on to future generations. However, medieval stained glass windows are particularly altered due to their chemical composition and the effects of climatic (mainly water and temperature), environmental (pollution) and biological factors. In this review, we present the alteration patterns observed on ancient Si-K-Ca stained glass windows. To better understand their formation mechanisms and determine the alteration rates, different exposure campaigns to the current atmosphere in a position sheltered from rain or not and laboratory experiments in aqueous medium or in gaseous phase have been conducted. Either model glass or ancient stained glass windows were studied. Isotopic tracers (D,18O,29Si) have been used as they constitute a powerful tool to elucidate the involved processes and to measure their kinetics. Thanks to all of these data, an alteration scenario of medieval stained glass alteration is proposed. Besides, the extrapolation of kinetic data based on several hypotheses over seven centuries gives very consistent results compared to the ancient stained glass samples.
Probing resonating valence bonds on a programmable germanium quantum simulator
Authors: Wang Chien-An , Déprez Corentin , Tidjani Hanifa , Lawrie William I. L. , Hendrickx Nico W. , Sammak Amir , Scappucci Giordano , Veldhorst Menno 
Published: June 2023

AbstractSimulations using highly tunable quantum systems may enable investigations of condensed matter systems beyond the capabilities of classical computers. Quantum dots and donors in semiconductor technology define a natural approach to implement quantum simulation. Several material platforms have been used to study interacting charge states, while gallium arsenide has also been used to investigate spin evolution. However, decoherence remains a key challenge in simulating coherent quantum dynamics. Here, we introduce quantum simulation using hole spins in germanium quantum dots. We demonstrate extensive and coherent control enabling the tuning of multi-spin states in isolated, paired, and fully coupled quantum dots. We then focus on the simulation of resonating valence bonds and measure the evolution between singlet product states which remains coherent over many periods. Finally, we realize four-spin states with s-wave and d-wave symmetry. These results provide means to perform non-trivial and coherent simulations of correlated electron systems.
A chromosome-level genome assembly of tomato pinworm, Tuta absoluta
Authors: Liu Ying , Chen Xi , Yin Yanqiong , Li Xiaowei , He Kang , Zhao Xueqing , Li Xiangyong , Luo Xiyan , Mei Yang , Wang Zuoqi , Shu Runguo , Cheng Ziqi , Gebretsadik Kifle Gebreegziabiher , Luo Chen , Wang Ran , Lv Yaobin , Chen Aidong , Li Fei 
Published: June 2023

AbstractThe tomato pinworm, Tuta absoluta, or Phthorimaea absouta, is native to South America, but quickly spread to other regions of world, including Europe, Africa, and Asia, devastating to global tomato production. However, a lack of high-quality genome resources makes it difficult to understand its high invasiveness and ecological adaptation. Here, we sequenced the genome of the tomato pinworm using Nanopore platforms, yielding a genome assembly of 564.5 Mb with contig N50 of 3.33 Mb. BUSCO analysis demonstrated that this genome assembly has a high-level completeness of 98.0% gene coverage. In total, 310 Mb are repeating sequences accounting for 54.8% of genome assembly, and 21,979 protein-coding genes are annotated. Next, we used the Hi-C technique to anchor 295 contigs to 29 chromosomes, yielding a chromosome-level genome assembly with a scaffold N50 of 20.7 Mb. In sum, the high-quality genome assembly of the tomato pinworm is a useful gene resource that contributes to a better understanding of the biological characteristics of its invasiveness and will help in developing an efficient control policy.
Increased red blood cell deformation in children and adolescents after SARS-CoV-2 infection
Authors: Eder Julian , Schumm Leonie , Armann Jakob P. , Puhan Milo A. , Beuschlein Felix , Kirschbaum Clemens , Berner Reinhard , Toepfner Nicole 
Published: June 2023

AbstractSevere coronavirus disease 2019 (COVID-19) is associated with hyperinflammation, hypercoagulability and hypoxia. Red blood cells (RBCs) play a key role in microcirculation and hypoxemia and are therefore of special interest in COVID-19 pathophysiology. While this novel disease has claimed the lives of many older patients, it often goes unnoticed or with mild symptoms in children. This study aimed to investigate morphological and mechanical characteristics of RBCs after SARS-CoV-2 infection in children and adolescents by real-time deformability-cytometry (RT-DC), to investigate the relationship between alterations of RBCs and clinical course of COVID-19. Full blood of 121 students from secondary schools in Saxony, Germany, was analyzed. SARS-CoV-2-serostatus was acquired at the same time. Median RBC deformation was significantly increased in SARS-CoV-2-seropositive compared to seronegative children and adolescents, but no difference could be detected when the infection dated back more than 6 months. Median RBC area was the same in seropositive and seronegative adolescents. Our findings of increased median RBC deformation in SARS-CoV-2 seropositive children and adolescents until 6 months post COVID-19 could potentially serve as a progression parameter in the clinical course of the disease with an increased RBC deformation pointing towards a mild course of COVID-19.
Identification of molecular mechanisms causing skin lesions of cutaneous leishmaniasis using weighted gene coexpression network analysis (WGCNA)
Authors: Momeni Kavoos , Ghorbian Saeid , Ahmadpour Ehsan , Sharifi Rasoul 
Published: June 2023

AbstractLeishmaniasis is an infectious disease, caused by a protozoan parasite. Its most common form is cutaneous leishmaniasis, which leaves scars on exposed body parts from bites by infected female phlebotomine sandflies. Approximately 50% of cases of cutaneous leishmaniasis fail to respond to standard treatments, creating slow-healing wounds which cause permanent scars on the skin. We performed a joint bioinformatics analysis to identify differentially expressed genes (DEGs) in healthy skin biopsies and Leishmania cutaneous wounds. DEGs and WGCNA modules were analyzed based on the Gene Ontology function, and the Cytoscape software. Among almost 16,600 genes that had significant expression changes on the skin surrounding Leishmania wounds, WGCNA determined that one of the modules, with 456 genes, has the strongest correlation with the size of the wounds. Functional enrichment analysis indicated that this module includes three gene groups with significant expression changes. These produce tissue-damaging cytokines or disrupt the production and activation of collagen, fibrin proteins, and the extracellular matrix, causing skin wounds or preventing them from healing. The hub genes of these groups areOAS1, SERPINH1,andFBLN1respectively. This information can provide new ways to deal with unwanted and harmful effects of cutaneous leishmaniasis.
Optimal quantum network decongestion strategies
Authors: Perju Verzotti Luca , Ciobanu Bogdan-Călin , Popescu Pantelimon George 
Published: June 2023

AbstractThis study clarifies the problem of decongestion in quantum networks, with a specific focus on the crucial task of entanglement distribution. Entangled particles are a valuable resource in quantum networks, as they are used for most quantum protocols. As such, ensuring that nodes in quantum networks are supplied with entanglement efficiently is mandatory. Many times, parts of a quantum network are contested by multiple entanglement resupply processes and the distribution of entanglement becomes a challenge. The most common network intersection topology, the star-shape and it’s various generalizations, are analyzed, and effective decongestion strategies, in order to achieve optimal entanglement distribution, are proposed. The analysis is comprehensive and relies on rigorous mathematical calculations which aids in selecting the most appropriate strategy for different scenarios optimally.
Stability analysis and control technology of the sump-surrounding rock under a 1200-m-deep goaf: a case study
Authors: Xie Shengrong , Li Hui , Chen Dongdong , Jiang Zaisheng , Cui Junqi , Liu Ruipeng 
Published: June 2023

AbstractIn this study, a sump in the Xingdong coal mine (buried at a depth of over 1200 m) was used to analyze the surrounding rock's stability and control technology. Under the combined influences of various complex conditions, such as the burial depth of over 1200 m, ultra-high ground stress, and location under the goaf, the sump support became extremely difficult, severely restricting the efficient production of the mine. The overall pressure-relief mechanisms and degree of the sump surrounding the rock environment under the goaf were studied, and the rationality of the sump location was verified through numerical simulations and field tests. A more effective support scheme was proposed based on the deformation characteristics and failure mechanisms of the temporary sump-surrounding rock under the supporting conditions. The combined control technology employed the lengthened strong anchor bolts (cables), full-section concrete-filled steel tubular supports, and pouring full-section reinforced concrete and full-section long-hole grouting reinforcement. The field test results showed that after adopting the new support scheme, the sump-surrounding rock tended to be stable after three months. The sump roof subsidence amount, floor heave amount, and convergence of the two sidewalls of the sump were 17.2–19.2 mm, 13.9–16.5 mm, and 23.2–27.9 mm, respectively, thus satisfying the application requirements. This study provides an essential reference for deep-mine roadway support under a complex high-ground-stress environment.
Emergence of a novel sublineage, MYMBD21 under SA-2018 lineage of Foot-and-Mouth Disease Virus serotype O in Bangladesh
Authors: Hossain Kazi Alamgir , Anjume Humaira , Alam K. M. Mazharul , Yeamin Ashabul , Akter Salma , Hossain M. Anwar , Sultana Munawar 
Published: June 2023

AbstractFoot-and-Mouth Disease (FMD) hinders the growth of the livestock industry in endemic countries like Bangladesh. The management and prevention of FMD are severely impacted by the high mutation rate and subsequent frequent generation of newer genotypes of the causative agent, Foot-and-Mouth Disease Virus (FMDV). The current study was conducted in nine districts of Bangladesh during 2019–21 to characterize the circulating FMDV strains based on the VP1 sequence analysis, the major antigenic recognition site providing serotype specificity and high variability of FMDV. This study detected the first emergence of the SA-2018 lineage in Bangladesh along with the predominance of Ind-2001e (or Ind-2001BD1) sublineage of ME-SA topotype under serotype O during 2019–21. The mutational spectrum, evolutionary divergence analysis and multidimensional plotting confirmed the isolates collected from Mymensingh districts, designated as MYMBD21 as a novel sublineage under the SA-2018 lineage. Analysis of the amino acid sequence revealed several changes in the G-H loop, B-C loop and C-terminal region of VP1, revealing a 12–13% divergence from the existing vaccine strains and a 95% VP1 protein homology, with most of the mutations potentially considerable as vaccine escape mutations, evidenced by three-dimensional structural analysis. This is the first report on the emergence of the SA-2018 lineage of ME-SA topotype of FMDV serotype O in Bangladesh, as well as a possible mutational trend towards the emergence of a distinct sublineage under SA-2018 lineage, which calls for in-depth genome-wide analysis and monitoring of the FMD situation in the country to implement a strategic vaccination and effective FMD control program.
Ready vascular permeability of a near-infrared fluorescent agent ASP5354 for intraoperative ureteral identification enables imaging of carcinoma tissues
Authors: Teranishi Katsunori 
Published: June 2023

AbstractThis study investigates the ability of a near-infrared fluorescence (NIRF) imaging agent, ASP5354, for in vivo fluorescence imaging of esophageal squamous cell carcinoma (ESCC) tissues. The ability of ASP5354 was evaluated using a single dose of ASP5354 or indocyanine green (ICG), which was intravenously administered to a KYSE850 human ESCC xenograft mouse model. Subsequently, in vivo NIRF images of the mouse were obtained using a clinically available camera system. ASP5354-specific NIRF signals were strongly detectable in KYSE850 carcinoma tissues immediately (30 s) following ASP5354 administration compared with normal tissues. Meanwhile, ICG could not distinguish between normal and carcinomatous tissues. To elucidate the associated imaging mechanisms, the vascular permeability of ASP5354 and ICG was investigated in rat back dermis treated with saline or histamine, which enhances vascular permeability, using in vivo NIRF imaging. ASP5354 exhibited higher vascular permeability in histamine-treated skin than in normal skin. KYSE850 carcinoma tissues can be distinguished from normal tissues based on the measurement of ASP5354-specific NIRF signals, and the mechanism that enables imaging relies on the specific and rapid leakage of ASP5354 from the capillaries into the stroma of carcinoma tissues.
A novel combined intelligent algorithm prediction model for the tunnel surface settlement
Authors: Wang You , Dai Fang , Jia Ruxue , Wang Rui , Sharifi Habibullah , Wang Zhenyu 
Published: June 2023

AbstractTo ensure the safety and stability of the shield tunnel construction process, the ground settlement induced by the shield construction needs to be effectively predicted. In this paper, a prediction method combining empirical mode decomposition (EMD), chaotic adaptive sparrow search algorithm (CASSA), and extreme learning machine (ELM) is proposed. First, the EMD is used to decompose the settlement sequence into trend vectors and fluctuation vectors to fully extract the effective information of the sequence; Second, the sparrow search algorithm is improved by introducing Cubic chaotic mapping to initialize the population and adaptive factor to optimize the searcher’s position formula, and the chaotic adaptive sparrow search algorithm is proposed; Finally, the CASSA-ELM prediction model is constructed by using CASSA to find the optimal values of weights and thresholds in the extreme learning machine. The fluctuation components and trend components decomposed by EMD are predicted one by one, and the prediction results are superimposed and reconstructed to obtain the predicted final settlement. Taking a shield interval in Jiangsu, China as an example, the meta-heuristic algorithm-optimized ELM model improves the prediction accuracy by 10.70% compared with the traditional ELM model. The combined EMD-CASSA-ELM prediction model can greatly improve the accuracy and speed of surface settlement prediction, and provide a new means for safety monitoring in shield tunnel construction. Intelligent prediction methods can predict surface subsidence more automatically and quickly, becoming a new development trend.
Modified stochastic medium prediction model for the deformation response of concealed underground stations under existing pipelines
Authors: Zhang Junru , Pan Tong , Ma Kaimeng , Xu Qiang , Kong Chao 
Published: June 2023

AbstractThe underground pipeline network in the city is so intertwined that the concealed excavation of a metro station inevitably leads to a series of underground pipelines, causing settlement deformation and further risk of leakage. The existing theoretical methods for analysing settlement deformation are mostly for circular chambers, whereas metro stations have a nearly square cross-sectional form and different construction methods are very different, which have a greater impact on the deformation of the overlying pipelines. In this paper, based on the random medium theory and Peck's formula, the improved random medium model for predicting ground deformation is modified, the correction coefficients λ and η for the influence of different construction methods are proposed, the prediction model of underground pipeline deformation under different construction methods is obtained, and the numerical models of four work methods commonly used in urban tunnel construction: pillar hole method, side hole method, middle hole method and Pile-Beam-Arch (PBA) method are constructed through simulation, and the mathematical analysis software was used to fit the results to the model and obtain the range of correction coefficients λ and η for each of the four methods, and the accuracy and applicability of the theoretical model was verified by combining with actual engineering cases. The influence on the overlying pipes is in descending order: side hole method, pillar hole method, middle hole method and PBA method. The theoretical model provided in this paper for predicting the deformation of pipes in any overlying strata of the tunnel is well suited to the actual project and has a high degree of correlation with the measured results.
Variational quantum non-orthogonal optimization
Authors: Bermejo Pablo , Orús Román 
Published: June 2023

AbstractCurrent universal quantum computers have a limited number of noisy qubits. Because of this, it is difficult to use them to solve large-scale complex optimization problems. In this paper we tackle this issue by proposing a quantum optimization scheme where discrete classical variables are encoded in non-orthogonal states of the quantum system. We develop the case of non-orthogonal qubit states, with individual qubits on the quantum computer handling more than one bit classical variable. Combining this idea with Variational Quantum Eigensolvers (VQE) and quantum state tomography, we show that it is possible to significantly reduce the number of qubits required by quantum hardware to solve complex optimization problems. We benchmark our algorithm by successfully optimizing a polynomial of degree 8 and 15 variables using only 15 qubits. Our proposal opens the path towards solving real-life useful optimization problems in today’s limited quantum hardware.