bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generative hypergraph models and spectral embedding
Authors: Gong Xue , Higham Desmond J. , Zygalakis Konstantinos 
Published: January 2023

AbstractMany complex systems involve interactions between more than two agents. Hypergraphs capture these higher-order interactions through hyperedges that may link more than two nodes. We consider the problem of embedding a hypergraph into low-dimensional Euclidean space so that most interactions are short-range. This embedding is relevant to many follow-on tasks, such as node reordering, clustering, and visualization. We focus on two spectral embedding algorithms customized to hypergraphs which recover linear and periodic structures respectively. In the periodic case, nodes are positioned on the unit circle. We show that the two spectral hypergraph embedding algorithms are associated with a new class of generative hypergraph models. These models generate hyperedges according to node positions in the embedded space and encourage short-range connections. They allow us to quantify the relative presence of periodic and linear structures in the data through maximum likelihood. They also improve the interpretability of node embedding and provide a metric for hyperedge prediction. We demonstrate the hypergraph embedding and follow-on tasks—including quantifying relative strength of structures, clustering and hyperedge prediction—on synthetic and real-world hypergraphs. We find that the hypergraph approach can outperform clustering algorithms that use only dyadic edges. We also compare several triadic edge prediction methods on high school and primary school contact hypergraphs where our algorithm improves upon benchmark methods when the amount of training data is limited.
A new method for identifying industrial clustering using the standard deviational ellipse
Authors: Zhao Ziwei , Zhao Zuoquan , Zhang Pei 
Published: January 2023

AbstractIndustrial agglomeration has attracted extensive attention from economists and geographers, yet it is still a challenge to identify the multi-agglomeration spatial structure and degree of industrial agglomeration in continuous space—there is still a lack of a more targeted industrial clustering method. The clustering method and the standard deviational ellipse (simply, ellipse) model have advantages in identifying the spatial structure and representing spatial information respectively. On this basis, we propose an ellipse-based approach to identifying industrial clusters. Our ellipse-based approach rests upon group nearest neighbor using the group-based nearest neighbor (GNN) ordering and spatial compactness matrix, where a number of point sequences with varying lengths, generated under the GNN ordering, are characterized by an ellipse and the elliptical parameters of these point sequences formulate the values and structure of the compactness matrix. Clustering is reformulated to identify ellipses with a specified parameter among a number of potential candidate ellipses, with significant changes (especially in the area) used as the cutoff criterion for determining the clusters’ border point. Our approach is illustrated in the location pattern of firms in Shanghai City, China in comparison with four well-known clustering methods. With the combination of elliptical parameters and spatial compactness, our approach may bring a new analytical ground for future industrial clustering research.
Semiconductor–metal transition in Bi2Se3 caused by impurity doping
Authors: Uchiyama Takaki , Goto Hidenori , Uesugi Eri , Takai Akihisa , Zhi Lei , Miura Akari , Hamao Shino , Eguchi Ritsuko , Ota Hiromi , Sugimoto Kunihisa , Fujiwara Akihiko , Matsui Fumihiko , Kimura Koji , Hayashi Kouichi , Ueno Teppei , Kobayashi Kaya , Akimitsu Jun , Kubozono Yoshihiro 
Published: January 2023

AbstractDoping a typical topological insulator, Bi2Se3, with Ag impurity causes a semiconductor–metal (S-M) transition at 35 K. To deepen the understanding of this phenomenon, structural and transport properties of Ag-doped Bi2Se3 were studied. Single-crystal X-ray diffraction (SC-XRD) showed no structural transitions but slight shrinkage of the lattice, indicating no structural origin of the transition. To better understand electronic properties of Ag-doped Bi2Se3, extended analyses of Hall effect and electric-field effect were carried out. Hall effect measurements revealed that the reduction of resistance was accompanied by increases in not only carrier density but carrier mobility. The field-effect mobility is different for positive and negative gate voltages, indicating that the EF is located at around the bottom of the bulk conduction band (BCB) and that the carrier mobility in the bulk is larger than that at the bottom surface at all temperatures. The pinning of the EF at the BCB is found to be a key issue to induce the S-M transition, because the transition can be caused by depinning of the EF or the crossover between the bulk and the top surface transport.
Predicting efficacy of drug-carrier nanoparticle designs for cancer treatment: a machine learning-based solution
Authors: Kibria Md Raisul , Akbar Refo Ilmiya , Nidadavolu Poonam , Havryliuk Oksana , Lafond Sébastien , Azimi Sepinoud 
Published: January 2023

AbstractMolecular Dynamic (MD) simulations are very effective in the discovery of nanomedicines for treating cancer, but these are computationally expensive and time-consuming. Existing studies integrating machine learning (ML) into MD simulation to enhance the process and enable efficient analysis cannot provide direct insights without the complete simulation. In this study, we present an ML-based approach for predicting the solvent accessible surface area (SASA) of a nanoparticle (NP), denoting its efficacy, from a fraction of the MD simulations data. The proposed framework uses a time series model for simulating the MD, resulting in an intermediate state, and a second model to calculate the SASA in that state. Empirically, the solution can predict the SASA value 260 timesteps ahead 7.5 times faster with a very low average error of 1956.93. We also introduce the use of an explainability technique to validate the predictions. This work can reduce the computational expense of both processing and data size greatly while providing reliable solutions for the nanomedicine design process.
Effect of type 2 diabetes on liver images of GD-EOB-DTPA-enhanced MRI during the hepatobiliary phase
Authors: Zhang Wen-Yu , Sun Hao-Yang , Zhang Wen-Long , Feng Rui 
Published: January 2023

AbstractTo analyze alterations of the liver appearance during the hepatobiliary phase of individuals with type 2 diabetes who are receiving gadolinium ethoxybenzyl diethylenetriamine pentaacetic acid (Gd-EOB-DTPA) enhanced magnetic resonance imaging (MRI). Fifty-seven individuals who received Gd-EOB-DTPA-enhanced MRI and had normal liver and renal function but did not have (control group) or have type 2 diabetes (observation group) were retrospectively included in this study. The liver enhancement ratio (LER) and contrast between liver parenchyma and portal vein (LPC) were calculated from hepatobiliary phase images. Utilizing liver to kidney signal intensity, signs of the biliary system, and signs of the portal vein, a functional liver imaging score (FLIS) was calculated. Wilcoxon rank-sum test was used to assess the between-group differences in LER, LPC, and FLIS. FLIS constituent ratios between the two groups were tested using the χ2 test. The effectiveness of LER, LPC, and FLIS for identifying type 2 diabetes was assessed by receiver operating characteristic curves (ROCs). The interobserver consistency of FLIS was evaluated using the intraclass correlation coefficients. The observation group’s LER and LPC were lower than the control group. The constituent ratio of the FLIS score (liver to kidney signal intensity, p = 0.011) showed a significant between-group difference. According to ROCs, LER and LPC were associated with the identification of type 2 diabetes. LER = 0.54 and LPC = 1.46 were the optimal cutoff for identifying type 2 diabetes, respectively. FLIS demonstrated excellent inter-reader agreement. The relative signal intensity of the liver during the hepatobiliary phase is decreased in patients with type 2 diabetes. This should be considered when individuals with type 2 diabetes undergo Gd-EOB-DTPA-enhanced MRI to avoid misdiagnoses, such as small hepatocellular carcinoma or abnormal liver function.
Postmenopausal hormone therapy and mortality before and after the Women’s Health Initiative study
Authors: Johansen Laura Løkkegaard , Thinggaard Mikael , Hallas Jesper , Osler Merete , Christensen Kaare 
Published: January 2023

AbstractWeighing risks and benefits of postmenopausal hormone therapy (HT) has proven a balancing act. We aimed to investigate the association between HT and mortality before and after the 2002 publication from the Women’s Health Initiative (WHI) study. This publication found that the risk of using HT outweighted the benefits, and thus it caused a marked reduction in systemic HT user prevalence. The 2002 WHI publication may also have caused a change in the subsequent HT user profile, as HT is no longer recommended in the prevention of chronic diseases. This cohort study included two populations followed from 1995: A 5% random sample of female singletons from the Danish general population (n = 52,388) and a sample of Danish female twins (n = 15,261). HT use was evaluated in 1995, 2000, 2005, and 2010. The association between HT, education, and mortality was investigated and controlled for potential unobserved familial confounding in a within-pair analysis. Singletons aged 56–75 using systemic HT in 2000 had a lower mortality compared to non-users (hazard ratio (HR) 0.83, 95% confidence interval (CI) 0.78–0.89). In 2005, the mortality was like that of the background population for this age group (HR 1.02, 95% CI 0.94–1.11). Recently postmenopausal twins showed a similar tendency. Systemic HT users, who had switched to local HT by 2005, had a substantially lower mortality than non-users (HR ranging from 0.42 to 0.67 depending on age group). In conclusion, we found that the prevalence of systemic HT use declined after 2002, and systemic HT users’ mortality changed from lower before 2002 to similar to that of the background population after 2002. This indicates that the healthiest users decided to either drop systemic HT or switcted to local HT, as recommendations changed following the WHI publication.
Predator-mediated diversity of stream fish assemblages in a boreal river basin, China
Authors: Zhang Jinrui , Yang Haitao , Ma Mengdi , Pu Tongxiao , Yin Xuwang 
Published: January 2023

AbstractPredator–prey interactions are critical for understanding species composition and community assembly; however, there is still limited research on whether and how the prey species composition or community assembly in natural communities are mediated by predators. To address this question, we performed a field investigation to examine the influence of the presence of Lutra lutra on the diversity of fish communities of the Hunchun River Basin, Jilin Province, China. Our results indicate that L. lutra, as a potential umbrella species and generalist predator in the stream ecosystem, promotes the coexistence of a vast variety of fish taxa, which emphasizes the importance of top-down control in the ecological community. We suggest that L. lutra regulates the fish community assembly likely through the stochastic process. Although this was a pilot study regarding predator–prey interactions, the results highlight the effects of predators on the prey community assembly, and emphasize the role of predators on the maintenance of biodiversity and ecosystem function. Future conservation decisions involving ecosystem biodiversity should require the inclusion of predation intensity. The inclusion of scientific research and protection of umbrella species would thus constitute an additional and important step in biodiversity conservation.
Cell types and synchronous-activity patterns of inspiratory neurons in the preBötzinger complex of mouse medullary slices during early postnatal development
Authors: Oke Yoshihiko , Miwakeichi Fumikazu , Oku Yoshitaka , Hirrlinger Johannes , Hülsmann Swen 
Published: January 2023

AbstractTo examine whether and how the inspiratory neuronal network in the preBötzinger complex (preBötC) develops during the early postnatal period, we quantified the composition of the population of inspiratory neurons between postnatal day 1 (p1) and p10 by applying calcium imaging to medullary transverse slices in double-transgenic mice expressing fluorescent marker proteins. We found that putative excitatory and glycinergic neurons formed a majority of the population of inspiratory neurons, and the composition rates of these two inspiratory neurons inverted at p5–6. We also found that the activity patterns of these two types of inspiratory neurons became significantly well-synchronized with the inspiratory rhythmic bursting pattern in the preBötC within the first postnatal week. GABAergic and GABA-glycine cotransmitting inspiratory neurons formed only a small population just after birth, which almost disappeared until p10. In conclusion, the inspiratory neuronal network in the preBötC matures at the level of both neuronal population and neuronal activities during early postnatal development.
Evolution of the strength characteristics of briquette and raw coal containing fluid
Authors: Zhang Feiyan , Niu Chen , Han Ying 
Published: January 2023

AbstractThe mechanical properties of coal containing fluid are an important factor affecting the safe mining of soft coal seams. In particular, for class III–V coal, coal and gas outbursts and other dynamic phenomena are prone to occur due to the influences of gas pressure and groundwater, which seriously threaten the safety and lives of field workers. However, briquette samples are usually used in place of raw coal in laboratory tests conducted on class III–V coal samples. Whether the research conclusions for briquette and raw coal are consistent and whether briquette coal can replace raw coal in research on strength characteristics need to be further verified. In this paper, the evolution of the strength characteristics of fluid-bearing briquette coal and raw coal is studied. The strength characteristics, instability failure characteristics, and acoustic emission characteristics of raw coal and briquette coal under uniaxial and triaxial compression are analyzed in detail. In addition, the influence of the water content and pore pressure on the strength characteristics of class III–V raw coal and briquette coal is further studied. The results show that the failure characteristic of raw coal is overall brittle failure, mainly axial splitting failure, whereas that of briquette is overall ductile failure, mainly cone-shaped continuous spalling. The strength parameters of the raw coal and briquette coal improve under confining pressure, but the internal difference in the raw coal is significantly reduced. The cohesion of the raw coal sample initially increases and then decreases with increasing water content, and the internal friction angle increases with increasing water content. In addition, it is verified that the strength, cohesion, elastic modulus, and deformation modulus of the briquette decrease with increasing pore pressure under different pore pressures, but the strength difference of the class III–V coal decreases under increasing pore pressure. Based on the abovementioned results, the strength parameters of a coal body are estimated using the Hoek–Brown (H–B) criterion. Based on a comparison of the strength parameters of the coal sample and coal body, the estimated strength parameters of the coal body are closer to the actual values on site.
Spatiotemporal biocontrol and rhizosphere microbiome analysis of Fusarium wilt of banana
Authors: Zhu Zhiyan , Wu Guiyun , Deng Rufang , Hu Xiaoying , Tan Haibo , Chen Yaping , Tian Zhihong , Li Jianxiong 
Published: January 2023

AbstractThe soil-borne fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes Fusarium wilt of banana (FWB), which devastates banana production worldwide. Biocontrol is considered to be the most efficient approach to reducing FWB. Here we introduce an approach that spatiotemporally applies Piriformospore indica and Streptomyces morookaensis strains according to their respective strength to increase biocontrol efficacy of FWB. P. indica successfully colonizes banana roots, promotes lateral root formation, inhibits Foc TR4 growth inside the banana plants and reduces FWB. S. morookaensis strain Sm4-1986 secretes different secondary compounds, of which xerucitrinin A (XcA) and 6-pentyl-α-pyrone (6-PP) show the strongest anti-Foc TR4 activity. XcA chelates iron, an essential nutrient in pathogen-plant interaction that determines the output of FWB. 6-PP, a volatile organic compound, inhibits Foc TR4 germination and promotes banana growth. Biocontrol trials in the field demonstrated that application of S. morookaensis lead to improvement of soil properties and increase of rhizosphere-associated microbes that are beneficial to banana growth, which significantly reduces disease incidence of FWB. Our study suggests that optimal utilization of the two biocontrol strains increases efficacy of biocontrol and that regulating iron accessibility in the rhizosphere is a promising strategy to control FWB.
A binary interaction map between turnip mosaic virus and Arabidopsis thaliana proteomes
Authors: Martínez Fernando , Carrasco José L. , Toft Christina , Hillung Julia , Giménez-Santamarina Silvia , Yenush Lynne , Rodrigo Guillermo , Elena Santiago F. 
Published: January 2023

AbstractViruses are obligate intracellular parasites that have co-evolved with their hosts to establish an intricate network of protein–protein interactions. Here, we followed a high-throughput yeast two-hybrid screening to identify 378 novel protein–protein interactions between turnip mosaic virus (TuMV) and its natural hostArabidopsis thaliana. We identified the RNA-dependent RNA polymerase NIb as the viral protein with the largest number of contacts, including key salicylic acid-dependent transcription regulators. We verified a subset of 25 interactionsin plantaby bimolecular fluorescence complementation assays. We then constructed and analyzed a network comprising 399 TuMV-A. thalianainteractions together with intravirus and intrahost connections. In particular, we found that the host proteins targeted by TuMV are enriched in different aspects of plant responses to infections, are more connected and have an increased capacity to spread information throughout the cell proteome, display higher expression levels, and have been subject to stronger purifying selection than expected by chance. The proviral or antiviral role of ten host proteins was validated by characterizing the infection dynamics in the corresponding mutant plants, supporting a proviral role for the transcriptional regulator TGA1. Comparison with similar studies with animal viruses, highlights shared fundamental features in their mode of action.
Cylinder aeroacoustics: experimental study of the influence of cross-section shape on spanwise coherence length
Authors: Margnat Florent , Gonçalves da Silva Pinto Wagner J. , Noûs Camille 
Published: January 2023

New data and review of the spanwise coherence length is provided for flows over cylinders of different cross-sections: circular of diameter d, and rectangular of sectional aspect ratios (breadth (b) to height (d) ratio AR = b/d) of 1, 2 and 3. In the present measurements, the body has both d and spanwise length of 70d fixed, and the Reynolds number (based on d) range 6000–27,000 is covered. Two-point data are obtained from two hot-wire probes, one fixed in the symmetry plane and the other moving on the corresponding spanwise axis. Their position in a cross plane are deduced from preliminary measurement of the mean flow with a single probe, allowing fair comparisons between the different geometries and the introduction of uncertainty bars on coherence length values. At all tested regimes, a very good agreement is noticed between velocity-based and pressure-based coherence experimental data. Coherence length definitions are revisited, and the aeroacoustically consistent, integral length definition is selected, allowing fair synthesis of literature data into a single chart and empirical functions. Definitions for coherence decay models (e.g. Gaussian or Laplacian) are also adapted so that coherence length and coherence integral shall be equivalent. This preliminary work on coherence data and its spanwise integration enables transparent regressions and model selection. Generally, the Gaussian model is relevant for the lift peak, while the coherence exhibits a Laplacian decay at harmonics. On average, at peak Strouhal number, the coherence length for the circular and square cylinders is of 5d while it is of the order of 15d for the rectangular sections. It is concluded that the flow over those latter geometries is still a two-dimensional dynamics at the tone frequency. These values are almost preserved over the tested Reynolds number range. Coherence length value at harmonics is extensively documented. Spanwise coherence length is also discussed as an ingredient of acoustic efficiency.
Stroke and Myocardial Infarction in Patients with Abdominal Aortic Aneurysm and New-Onset Atrial Fibrillation
Authors: Nicolajsen Chalotte W. , Nielsen Peter B. , Jensen Martin , Eldrup Nikolaj , Larsen Torben B. , Lip Gregory Y. H. , Goldhaber Samuel Z. , Søgaard Mette 
Published: January 2023

Objective We investigated the association between new-onset atrial fibrillation (AF) and risk of stroke and myocardial infarction (MI) in patients with abdominal aortic aneurysmal (AAA) disease.
Methods Observational crossover study using Danish nationwide data, including patients with AAA and incident AF between 1997 and 2018. We estimated the 1-year risk of stroke and MI and the within-individual odds ratios (ORs) of ischemic events before and after an AF diagnosis, stratified by year of AF diagnosis (1997–2010 and 2011–2018), and supplemented with analyses on changes in use of antithrombotic therapy.
Results A total of 3,035 AAA patients were included: 1,040 diagnosed during 1997 to 2010, and 1,995 during 2011 to 2018 (22.2% females, median age 78 years; median CHA2DS2-VASc score 4; interquartile range: 3–5). One-year risk of ischemic events after AF was 5.9% (confidence interval [CI] 95%: 4.6–7.5%) and 4.5% (CI 95%: 3.7–5.5%) for stroke and 5.4% (CI 95%: 4.2–6.9%) and 4.0% (CI 95%: 3.2–4.9%) for MI during 1997 to 2010 and 2011 to 2018, respectively. The OR of ischemic stroke before and after incident AF was 2.8 (CI 95%: 1.6–5.2) during 1997 to 2010; and 2.4 (CI 95%: 1.5 to 3.9) during 2011 to 2018, and 3.5 (CI 95%: 1.7–7.5) and 1.5 (CI 95%: 0.9–2.4) for MI. One-year proportion of prescription claims for oral anticoagulants after AF changed from 66.1% in 1997 to 2010 to 82.6% in 2011 to 2018, while antiplatelet prescription claims changed from 80.8 to 60.9%.
Conclusion Cardiovascular prognosis has improved in patients with prevalent AAA disease and new-onset AF in concordance with optimization of antithrombotic therapy over time. A diagnosis of AF conferred residual risk of stroke and MI.