bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism and deterioration pattern of sandstone surrounding rock voiding at bottom of heavy-haul railway tunnel
Authors: Li Zi-qiang , Yang Shi-jian , Feng Jian-wen , Zhang Hang , Huang Wei-wei , Li Zheng 
Published: May 2024

AbstractThis study combines laboratory experiments and discrete element simulation methods to analyze the mechanism and deterioration patterns of sandstone surrounding rock voiding the bottom of a heavy-haul railway tunnel. It is based on previously acquired measurement data from optical fiber grating sensors installed in the Taihangshan Mountain Tunnel of the Wari Railway. By incorporating rock particle wastage rate results, a method for calculating the peak strength and elastic modulus attenuation of surrounding rock is proposed. Research indicates that the operation of heavy-haul trains leads to an instantaneous increase in the dynamic water pressure on the bottom rock ranging 144.4–390.0%, resulting in high-speed water flow eroding the rock. After 1–2 years of operation, the bottom water and soil pressures increase by 526.5% and 390.0%, respectively. Focusing on sandstone surrounding rock with high observability, laboratory experiments were conducted to monitor the degradation stages of infiltration, particle loss, and voiding of rock under the action of dynamic water flow. The impact of water flow on the “cone-shaped” bottom rock deformation was also clarified. The extent of rock deterioration and voiding was determined using miniature water and soil pressure sensors in conjunction with discrete element numerical simulations. The measured rock particle loss was used as a criterion. Finally, a fitting approach is derived to calculate the peak strength and elastic modulus attenuation of surrounding rock, gaining insight into and providing a reference for the maintenance and disposal measures for the bottom operation of heavy-haul railway tunnels.
Optical coherence tomography choroidal enhancement using generative deep learning
Authors: Bellemo Valentina , Kumar Das Ankit , Sreng Syna , Chua Jacqueline , Wong Damon , Shah Janika , Jonas Rahul , Tan Bingyao , Liu Xinyu , Xu Xinxing , Tan Gavin Siew Wei , Agrawal Rupesh , Ting Daniel Shu Wei , Yong Liu , Schmetterer Leopold 
Published: May 2024

Abstract
Spectral-domain optical coherence tomography (SDOCT) is the gold standard of imaging the eye in clinics. Penetration depth with such devices is, however, limited and visualization of the choroid, which is essential for diagnosing chorioretinal disease, remains limited. Whereas swept-source OCT (SSOCT) devices allow for visualization of the choroid these instruments are expensive and availability in praxis is limited. We present an artificial intelligence (AI)-based solution to enhance the visualization of the choroid in OCT scans and allow for quantitative measurements of choroidal metrics using generative deep learning (DL). Synthetically enhanced SDOCT B-scans with improved choroidal visibility were generated, leveraging matching images to learn deep anatomical features during the training. Using a single-center tertiary eye care institution cohort comprising a total of 362 SDOCT-SSOCT paired subjects, we trained our model with 150,784 images from 410 healthy, 192 glaucoma, and 133 diabetic retinopathy eyes. An independent external test dataset of 37,376 images from 146 eyes was deployed to assess the authenticity and quality of the synthetically enhanced SDOCT images. Experts’ ability to differentiate real versus synthetic images was poor (47.5% accuracy). Measurements of choroidal thickness, area, volume, and vascularity index, from the reference SSOCT and synthetically enhanced SDOCT, showed high Pearson’s correlations of 0.97 [95% CI: 0.96–0.98], 0.97 [0.95–0.98], 0.95 [0.92–0.98], and 0.87 [0.83–0.91], with intra-class correlation values of 0.99 [0.98–0.99], 0.98 [0.98–0.99], and 0.95 [0.96–0.98], 0.93 [0.91–0.95], respectively. Thus, our DL generative model successfully generated realistic enhanced SDOCT data that is indistinguishable from SSOCT images providing improved visualization of the choroid. This technology enabled accurate measurements of choroidal metrics previously limited by the imaging depth constraints of SDOCT. The findings open new possibilities for utilizing affordable SDOCT devices in studying the choroid in both healthy and pathological conditions.
The implications of APOBEC3-mediated C-to-U RNA editing for human disease
Authors: Van Norden Melissa , Falls Zackary , Mandloi Sapan , Segal Brahm H. , Baysal Bora E. , Samudrala Ram , Elkin Peter L. 
Published: May 2024

AbstractIntra-organism biodiversity is thought to arise from epigenetic modification of constituent genes and post-translational modifications of translated proteins. Here, we show that post-transcriptional modifications, like RNA editing, may also contribute. RNA editing enzymes APOBEC3A and APOBEC3G catalyze the deamination of cytosine to uracil. RNAsee (RNA site editing evaluation) is a computational tool developed to predict the cytosines edited by these enzymes. We find that 4.5% of non-synonymous DNA single nucleotide polymorphisms that result in cytosine to uracil changes in RNA are probable sites for APOBEC3A/G RNA editing; the variant proteins created by such polymorphisms may also result from transient RNA editing. These polymorphisms are associated with over 20% of Medical Subject Headings across ten categories of disease, including nutritional and metabolic, neoplastic, cardiovascular, and nervous system diseases. Because RNA editing is transient and not organism-wide, future work is necessary to confirm the extent and effects of such editing in humans.
Infection-induced cascading failures – impact and mitigation
Authors: Li Bo , Saad David 
Published: May 2024

AbstractIn the context of epidemic spreading, many intricate dynamical patterns can emerge due to the cooperation of different types of pathogens or the interaction between the disease spread and other failure propagation mechanism. To unravel such patterns, simulation frameworks are usually adopted, but they are computationally demanding on big networks and subject to large statistical uncertainty. Here, we study the two-layer spreading processes on unidirectionally dependent networks, where the spreading infection of diseases or malware in one layer can trigger cascading failures in another layer and lead to secondary disasters, e.g., disrupting public services, supply chains, or power distribution. We utilize a dynamic message-passing method to devise efficient algorithms for inferring the system states, which allows one to investigate systematically the nature of complex intertwined spreading processes and evaluate their impact. Based on such dynamic message-passing framework and optimal control, we further develop an effective optimization algorithm for mitigating network failures.
In‐field comparison between G.652 and G.655 optical fibres for polarisation‐based quantum key distribution
Authors: Agnesi Costantino , Giacomin Massimo , Sartorato Daniele , Artuso Silvia , Vallone Giuseppe , Villoresi Paolo 
Published: May 2024

AbstractIntegration of Quantum Key Distribution (QKD) in existing telecommunication infrastructure is crucial for the widespread adoption of this quantum technology that offers the distillation of unconditionally secure keys between users. The authors report a field trial between the Points of Presence placed in Treviso and in Venezia—Mestre, Italy, exploiting the QuKy commercial polarisation‐based QKD platforms developed by ThinkQuantum S.r.l. and two different standards of single‐mode optical fibres, that is, G.652 and G.655 as a quantum channel. In this field trial, several configurations were tested, including the co‐existence of classical and quantum signals over the same fibre, providing a direct comparison between the performances of the G.652 and G.655 fibre standards for QKD applications.
Exploring measurement estimation strategies through concept cartoons designed with Realistic Mathematics Education
Authors: Çilingir Altiner Emel 
Published: May 2024

AbstractConcept cartoons, in relationship with Realistic Mathematics Education (RME), not only serve as a dynamic platform for problem-solving but also intricately weave mathematical concepts into the fabric of real-world scenarios, creating a harmonious fusion of theory and practical application. By using relatable characters and presenting ideas through engaging narratives, students are encouraged to tackle problems within the given context. The aim of this study was to investigate the measurement estimation strategies used by students when exposed to concept cartoons specifically designed for RME. A qualitative research methodology was followed, involving 46 fourth-grade students from a primary school. The data collection instrument utilized was “RME-Supported Concept Cartoons.” Descriptive analysis was employed to analyze the collected data. The concept cartoon activities incorporated measurement estimation strategies such as prior knowledge, unit iteration/separation, segmentation/chunking, and comparison, which students could potentially prefer. However, it was observed that students predominantly utilized division into unit iteration/separation and segmentation/chunking strategies over other estimation strategies. Furthermore, the frequency of strategy use did not exhibit significant variations based on gender. When examining the strategies developed by the students, it is noteworthy that the presence of “another solution-oriented option” and “irrelevant answers” was prominent.
Utilizing rare earth titanates to improve performance of solid-state electrochromic device
Authors: Nain Ritu , Bansal Love , Sagdeo P R , Kumar Rajesh 
Published: May 2024

Abstract
Exploring new materials and synthesis recipes are required to enhance the electrochromic performance especially, when used in solid-state devices. Here, polycrystalline gadolinium titanate (Gd2TiO5 or GTO), synthesized using a simple solid-state reaction method, has been used for this purpose by combining it with polythiophene (P3HT). The electrochemical investigation of the Gd2TiO5 doped P3HT electrode has been carried out using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS), which reveals the dominance of diffusion-controlled mechanism over charge storage on the electrode surface as compared to the P3HT electrode. The Gd2TiO5 doped P3HT solid-state electrochromic device shows color modulation at 515 nm and 670 nm wavelengths with a color contrast of as high as 79% and 42%, respectively, under an external bias of as low as ±1.4 V. The prepared device switches between maroon to a transparent state in less than a second under the external bias (±1.4 V) with a high coloration efficiency of 346 cm2/C. The device shows improved cycle life over 100 switching cycles at both the wavelengths, which makes it more suitable for real-life applications.
Culture, Cooperation, and Communication: The Co-evolution of Hominin Cognition, Sociality, and Musicality
Authors: Killin Anton 
Published: May 2024

Abstract
Music is a deeply entrenched human phenomenon. In this article, I argue that its evolutionary origins are intrinsically intertwined with the incremental anatomical, cognitive, social, and technological evolution of the hominin lineage. I propose an account of the evolution of Plio-Pleistocene hominins, focusing on traits that would be later implicated in music making. Such traits can be conceived as comprising the musicality mosaic or the multifaceted foundations of musicality. I then articulate and defend an account of protomusical behaviour, drawing theoretical licence from the social brain framework of Robin Dunbar and colleagues, as well as the evolutionary framework for human culture and cooperation developed by Kim Sterelny. The role of gene-culture co-evolution and niche construction is brought to the fore in articulating the evolutionary account. Finally, I defend the view that music subsequently developed via processes of social learning and cumulative culture.
Comparison of colorimetric methods for the analysis of total polyphenols in green tea extracts
Authors: Matsushita Kokoro , Honda Chihiro , Nakamura Yoriyuki , Kumazawa Shigenori 
Published: May 2024

ABSTRACT
Two colorimetric methods are used to determine the total polyphenol contents of tea, namely, “the Folin-Ciocalteu method,” defined by the International Organization for Standardization, and the “iron tartrate method,” specified in the Standard Tables of Food Composition in Japan. In this study, we compared the Folin-Ciocalteu and iron tartrate methods using green tea extracts. When comparing the 2 methods, the sum of the 4 major catechins measured using high-performance liquid chromatography (HPLC) was regarded as the standard value. The total polyphenol contents obtained using the Folin-Ciocalteu method were closer to the HPLC value than those obtained using the iron tartrate method. However, the iron tartrate method is adequate if the current official method is improved, that is, our results suggest that the coefficients appropriate for common green tea varieties, as well as the degree and duration of cover cultivation, in the official iron tartrate method must be considered.
methscore: a comprehensive R function for DNA methylation-based health predictors
Authors: Xu Zongli , Niu Liang , Kresovich Jacob K , Taylor Jack A 
Published: May 2024

Abstract

Motivation
DNA methylation-based predictors of various biological metrics have been widely published and are becoming valuable tools in epidemiologic studies of epigenetics and personalized medicine. However, generating these predictors from original source software and web servers is complex and time consuming. Furthermore, different predictors were often derived based on data from different types of arrays, where array differences and batch effects can make predictors difficult to compare across studies.

Results
We integrate these published methods into a single R function to produce 158 previously published predictors for chronological age, biological age, exposures, lifestyle traits and serum protein levels using both classical and principal component-based methods. To mitigate batch and array differences, we also provide a modified RCP method (ref-RCP) that normalize input DNA methylation data to reference data prior to estimation. Evaluations in real datasets show that this approach improves estimate precision and comparability across studies.

Availability and implementation
The function was included in software package ENmix, and is freely available from Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html).
Psilocybin reduces alcohol self-administration via selective left nucleus accumbens activation in rats
Authors: Jeanblanc Jérôme , Bordy Romain , Fouquet Grégory , Jeanblanc Virginie , Naassila Mickaël 
Published: May 2024

Abstract
The use of psilocybin to treat alcohol use disorder is very promising, but its mechanisms of action remain poorly understood. We combined behavioural, pharmacological and gene expression analyses to decipher the mechanisms of action of psilocybin, for the first time, when injected into the brain.
Male Long Evans rats underwent chronic operant ethanol self-administration before testing the effect of intraperitoneal psilocybin or directly within the nucleus accumbens core or the ventral tegmental area. Transcripts from the dopaminergic system were quantified in the nucleus accumbens and prefrontal cortex.
Psilocybin significantly reduced (by 50%) ethanol self-administration when injected 4 h before the session either intraperitoneally (1 mg/kg) or directly within the left nucleus accumbens (0.15 μg) but not the right nucleus accumbens or the left ventral tegmental area. The effect of intraperitoneal injection of psilocybin was prevented by intra-left nucleus accumbens injection of 0.3 μg of the 5-HT2A receptor antagonist ketanserin. In rats that self-administered ethanol but not in those self-administering saccharin, dopamine D2 receptor (D2R) mRNA was increased in both the nucleus accumbens and the prefrontal cortex by psilocybin, while dopamine D1 receptor mRNA was increased only in the prefrontal cortex.
As in humans, psilocybin reduced ethanol self-administration in rats through the 5-HT2A receptor within the left nucleus accumbens, possibly through increased D2R expression. Our results open unexpected perspectives regarding the hemispheric lateralization of psychedelic effects.
Use of waste plastic oil as a fuel in reactivity-controlled compression ignition engines: a bibliometric investigation from 2017–23
Authors: Kanchan Sumit , Singh Sandhu Sarbjot 
Published: May 2024

Abstract
Waste plastic oil, generated through the pyrolysis of plastic without oxygen, known as plastic-to-fuel conversion, stands as a promising alternative fuel. This research employs bibliometric analysis, a quantitative method, to comprehensively assess publications in the domain of waste plastic oil integration within reactivity-controlled compression ignition engines. Utilizing Scopus as the primary repository post-2017, the study categorizes information into pivotal aspects, including influential journals, countries, authors, affiliations, document types, thematic areas, sponsors and keywords. The analysis reveals significant contributions from diverse nations, prominently India, China, Turkey and Malaysia. Noteworthy is the prevalence of Energy, Engineering and Chemical Engineering as thematic focal points, with the journal Fuel leading the count followed by the journal Energy emerging as a prominent conduit. Institutional contributions are prolific, led by Gandhi Institute of Technology and Management University and Vellore Institute of Technology. Renowned authors ‘Gugulothu S.K’ and ‘He Z’ play a pivotal role in shaping the discourse. The National Natural Science Foundation of China stands out as a primary patron. This bibliometric analysis provides a structured understanding of waste plastic oil integration in reactivity-controlled compression ignition engines, laying the groundwork for future research avenues. The study identifies potential research platforms beyond Scopus, including Web of Science, CrossRef, Science Direct and Google Scholar, as valuable repositories for further exploration. Moreover, after careful observation of the research articles published by the top 10 authors as found in the study, it was found that the authors share a few common characteristics that helped them in advancing the understanding and application of waste plastic oil in reactivity-controlled compression ignition engines. These are also summarized in the present study with supporting data.
Elevated type-17 cytokines are present in axial spondyloarthritis stool
Authors: Brough India , Thompson Kelsey , Latore Ciara , Penkava Frank , Regan Chelsea , Pearson Claire , Shi Hui , Ridley Anna , Simone Davide , Lam Lilian , Bullers Samuel , Moussa Caroline , Feeney Rachel ,   Inflammatory Arthritis Microbiome Consortium (IAMC) Investigators Group, Al-Mossawi Mohammed H , Powrie Fiona , Young Stephen , Huttenhower Curtis , Bowness Paul 
Published: May 2024

Summary
Axial spondyloarthritis (axSpA) is characterized by type-17 immune-driven joint inflammation, and intestinal inflammation is present in around 70% of patients. In this study, we asked whether axSpA stool contained Th17-associated cytokines and whether this related to systemic Th17 activation. We measured stool cytokine and calprotectin levels by ELISA and found that patients with axSpA have increased stool IL-17A, IL-23, GM-CSF, and calprotectin. We further identified increased levels of circulating IL-17A+ and IL-17F+ T-helper cell lymphocytes in patients with axSpA compared to healthy donors. We finally assessed stool metabolites by unbiased nuclear magnetic resonance spectroscopy and found that multiple stool amino acids were negatively correlated with stool IL-23 concentrations. These data provide evidence of type-17 immunity in the intestinal lumen, and suggest its association with microbial metabolism in the intestine.
Inhibition profile of three biological nitrification inhibitors and their response to soil pH modification in two contrasting soils
Authors: Rojas-Pinzon Paula A , Prommer Judith , Sedlacek Christopher J , Sandén Taru , Spiegel Heide , Pjevac Petra , Fuchslueger Lucia , Giguere Andrew T 
Published: May 2024

Abstract
Up to 70% of the nitrogen (N) fertilizer applied to agricultural soils is lost through microbially mediated processes, such as nitrification. This can be counteracted by synthetic and biological compounds that inhibit nitrification. However, for many biological nitrification inhibitors (BNIs), the interaction with soil properties, nitrifier specificity, and effective concentrations are unclear. Here, we investigated three synthetic nitrification inhibitors (SNIs) (DCD, DMPP, and nitrapyrin) and three BNIs [methyl 3(4-hydroxyphenyl) propionate (MHPP), methyl 3(4-hydroxyphenyl) acrylate (MHPA), and limonene] in two agricultural soils differing in pH and nitrifier communities. The efficacies of SNIs and BNIs were resilient to short-term pH changes in the neutral pH soil, whereas the efficacy of some BNIs increased by neutralizing the alkaline soil. Among the BNIs, MHPA showed the highest inhibition and was, together with MHPP, identified as a putative AOB/comammox-selective inhibitor. Additionally, MHPA and limonene effectively inhibited nitrification at concentrations comparable to those used for DCD. Moreover, we identified the effective concentrations at which 50% and 80% of inhibition is observed (EC50 and EC80) for the BNIs, and similar EC80 values were observed in both soils. Overall, our results show that these BNIs could potentially serve as effective alternatives to SNIs currently used.
Light over mechanics: microbial community structure and activity in simulated migrating bedforms are controlled by oscillating light rather than by mechanical forces
Authors: Oprei Anna , Schreckinger José , Franzmann Insa , Lee Hayoung , Mutz Michael , Risse-Buhl Ute 
Published: May 2024

Abstract
Sandy sediments of lowland streams are transported as migrating ripples. Benthic microorganisms colonizing sandy grains are exposed to frequent moving–resting cycles and are believed to be shaped by two dominant environmental factors: mechanical stress during the moving phase causing biofilm abrasion, and alternating light–dark cycles during the resting phase. Our study consisted of two laboratory experiments and aimed to decipher which environmental factor causes the previously observed hampered sediment-associated microbial activity and altered community structure during ripple migration. The first experiment tested the effect of three different migration velocities under comparable light conditions. The second experiment compared migrating and stationary sediments under either constant light exposure or light oscillation. We hypothesized that microbial activity and community structure would be more strongly affected by (1) higher compared to lower migration velocities, and by (2) light oscillation compared to mechanical stress. Combining the results from both experiments, we observed lower microbial activity and an altered community structure in sediments exposed to light oscillation, whereas migration velocity had less impact on community activity and structure. Our findings indicate that light oscillation is the predominating environmental factor acting during ripple migration, resulting in an increased vulnerability of light-dependent photoautotrophs and a possible shift toward heterotrophy.