bluuebunny/crossref_metadata_2025 huggingface dataset:
Gurson-Tvergraad-Needleman model-based damage analyses of stainless steel springs at high temperature
Authors: Hou Lanxin , Hu Yifeng
Published: August 2023

In this paper, the Gurson-Tvergraad-Needleman (GTN) model is used to study the damage of stainless steel springs at high temperatures. The basic material and GTN damage parameters are determined from the stress-strain curves of tensile tests. Then the damage evolution of springs at 300 °C to 900 °C is analyzed based on finite element simulations. The results show that below 600 °C, the change of volume fraction of holes in the spring, along with the increase of load, has an obvious low growth stage, followed by a rapid growth stage. But above 600 °C, there is only a stable and rapid growth stage. The fracture positions predicted by finite element damage analyses agree with the experiments for round bars.
Study on low cycle fatigue of ferritic-martensitic steel at high temperature
Authors: Feng Zhao , Hu Yifeng , Cheng Pengming , Liu Xiao , Wang Hui
Published: August 2023

In 2011, a serious nuclear accident occurred in Fukushima, Japan, and one of the major causes was the destruction of the cladding material mainly made of Zr alloy due to a violent chemical reaction with high-temperature water vapor. Since then, scholars in various countries have been trying to find a better nuclear fuel cladding material. Because of its high temperature strength, ferritic/martensitic(F/M) steel is used in thermal power units. Over the past hundred years, the high temperature performance of ferritic/martensitic steel has developed simultaneously with the operating temperature of thermal power system. F/M steel is widely used in nuclear power system as well as thermal power, The fatigue life of nuclear fuel cladding material is an important parameter to study its service life, due to the special shape of the cladding material, especially for the pipe with a thickness of less than 0.5mm, it is difficult to directly measure its mechanical properties, this paper through special experimental materials and fixtures F/M pipe steel at room temperature and high temperature tensile test, as well as low cycle fatigue performance test, and its fracture port, surface crack analysis. Through the analysis and processing of experimental data, typical stress-cycle life curves, total strain amplitude-life curves, elastic strain amplitude-life curves, hysteresis curves with different strain amplitudes, and fatigue life prediction curves were obtained.
Surface energy calculation of brookite TiO2 using Inverse Wulff Construction
Authors: Lai Fuming , Zhao Min , Tong Shengfu
Published: August 2023

The Wulff construction methodology proves to be a highly useful approach in predicting the morphologies of nanoparticles. However, this approach requires the precise determination of surface energies for all orientations, which can be a challenging task due to the inherent complexity of measuring surface-free energies. In this work, the inverse Wulff construction is employed to effectively predicted surface energies from brookite TiO2 particle morphologies. This method can provide guidance for researchers to understand how to control the brookite TiO2 crystal morphology according to the synthetic method used.
The Safety Effect of Advanced Consolidation Grouted Rock under Blasting Shock Wave
Authors: Deng Ke , Zhang Man , Yang Kuoyu , Zhang Li , Xia Yunchi
Published: August 2023

Strong blasting disturbance leading to damage or even destruction of weak and fractured rock masses is a crucial problem to be solved during the construction process of underground engineering. For the blasting construction problem of advanced consolidation grouted rock near the excavation contour, the safety effect of blasting shock waves on grouted rock is investigated using a theoretical analysis method. The interaction process between blasting shock waves and grouted rock was studied based on the propagation characteristics of shock waves and the strain rate effect of rock strength. Considering the critical failure state, a safe vibration velocity model was established to analyze the effects of proportional distance, age, and grouting material. Results show that the first transmission and reflection effect creates the most dangerous state for grouted rock. SVV of super rapid strengthening cement is larger than that of ordinary cement. Choosing a suitable grouting material is essential to the following blasting design.
Synthesis of Highly Efficient CsPbBr3@Pb-MOF Photocatalyst at the Water-Oil Interface by Ultrasonication
Authors: Hou Yangwen , Sun Chunyi , Su Zhongming
Published: August 2023

In recent years, all inorganic perovskites have proven to be excellent photocatalytic materials. However, its poor stability and severe recombination of photogenerated electrons and holes have hindered its wide application. Herein, we employed a convenient and rapid one-pot sonochemical method to incorporate CsPbBr3 into Pb-MOF, aiming to enhance the stability and efficiency of photogenerated electron transfer. The CsPbBr3@Pb-MOF shows good photocatalytic efficiency, and 70% tetracycline hydrochloride (TCH) water solution is decomposed at 60 min visible light (λ>420 nm) irradiation. Meanwhile, CsPbBr3@Pb-MOF exhibits excellent photocatalytic stability.
Airborne Measurement of Earth Gravity by Comparing Three Kinds of Gravimeters
Authors: Cai Shaokun , Cao Juliang , Yu Ruihang , Xiong Zhiming
Published: August 2023

NUDT (National University of Defense Technology) has developed a strapdown gravimeter based on the SINS/GPS named SGA-WZ01. From April to May 2012, an airborne gravimetry flight test was carried out in the South China Sea. In this flight test, except SGA-WZ01, a 3-axis inertial platform gravimeter, GT-1A, and a damped 2-axis platform gravimeter, TAGS, were installed to obtain the gravity information. This was the first time that such a flight campaign was undertaken in China. The flight test contains one repeated line flight and four gridded line flights. The evaluation of the repeatability is based on repeated surveying lines, and the evaluation of the internal accuracy is based on all gridded lines. The results show that both GT-1A and TAGS have systematic biases about several mGal for repeated lines along west-east and northwest-southeast repeated lines, and the repeatability of SGA-WZ01 is consistent along repeated lines in different directions. The accuracy of gridded lines without crossover adjustment of GT-1A is about 1.73 mGal, while the crossover accuracy is 2.76 mGal and 2.08 mGal for TAGS and SGA-WZ01, respectively. The outcomes show that the performance of the SGA-WZ01 is comparable to that of foreign gravimeters.
The jitter frequency domain of long-span railway cable-stayed bridges considering the influence of pneumatic admittance
Authors: Liu Yanming , Yang Yongyi
Published: August 2023

The long-span bridge is highly sensitive to wind loads, and their random vibration response under static wind deformation and fluctuating wind load are relatively complex. The analysis of jitter response has become a key issue in the design. Taking the Hanjiatuo Yangtze River Bridge in the chongqing-lichuan railway as the engineering background, the influence of different aerodynamic admittance functions on the main girder jitter response is studied through frequency domain analysis. The results show that aerodynamic admittance has a great influence on the jitter response. Considering that the jitter displacement response of the aerodynamic admittance function is obviously smaller than the calculated results, the influence of aerodynamic admittance should be considered in the calculation and analysis.
Numerical analysis of fatigue strength for ultra-large ships considering springing
Authors: Chen Ling , Meng Qiao , Lu Chibo
Published: August 2023

Due to the low stiffness of ultra-large ships, the effect of springing becomes more obvious. The traditional quasi-static spectral method (QSM) ignores the coupling effect of hydrodynamic load and hull elastic characteristics, so it is unable to solve the problem of fatigue strength considering springing. To solve the problem and investigate the impact of springing response on fatigue, the stress mode superposition spectral method (SSM) suitable for ultra-large ships is proposed. The numerical analysis is performed on a real ship as an example. The results show that: Fatigue stress response generates new peaks at the high-frequency regions when considering the effect of springing, and fatigue damage is greatly increased. The degree of influence of springing response on fatigue strength is related to wave incident angles and sea conditions. This method has reference significance for the evaluation of fatigue strength of ultra-large ships considering springing effects.
A self-supporting Cu2S/CP lithium-ion battery anode
Authors: Chu Ruixia , Huang Wanyou , Yang Jun , Zhang Kesong , Qiu Fangyuan , Tan Shiwei , Zhu Peidong , Liu Dongying
Published: August 2023

Lithium-ion (Li-ion) batteries have been widely used in portable electronic devices and new energy vehicles in recent years. Although commercial graphite anode has good safety and low cost, its low theoretical capacity cannot better meet the demand for higher-capacity of power batteries. As an excellent electrode material, copper sulfide (Cu2S) has the advantages of high capacity and stability. Herein, Cu2S deposited on carbon paper (Cu2S@CP) was prepared by simple copper electrodeposition on carbon paper and sulphidation, which can be used to the anode of Li-ion batteries directly. Based on the three-dimensional structure of carbon paper and the high capacity of copper sulfide, the composite anode shows good lithium storage performance, which provides a new possibility for commercial power lithium-ion battery anode materials.
Zeolite Imidazolate Framework-Derived N-Doped Carbon-Supported Ultra-Low Platinum Catalyst for Enhancing Methanol Oxidation Reactions
Authors: Chen Yuting , Liu Zhongsu , Liu Chunyu , Zhang Shenhang , Li Haotian , Chen Hong , Dong Xingzheng , Chen Qianqian , Shi Xiaohua , Ren Guohong
Published: August 2023

Direct methanol fuel cells (DMFCs) have a broad application market due to their merits of high power density, wide source of raw materials, and convenient storage and transportation. At present, the common platinum (Pt) catalysts have some problems, such as low reserves, and expensive and poor reaction kinetics. Therefore, a zeolite imidazolate framework (ZIF) derived N-doped carbon-supported ultra-low platinum catalysts (Pt-Co@ZCN) are prepared using ZIF-67@ZIF-8 as the support. The effects of heating rate on the morphology and electrocatalytic performance of the synthesized materials are investigated. The characterization results reveal that the morphology and structure of Pt-Co@ZCN-900-2 are superior to other samples. The mass activity and stability toward methanol oxidation of the synthesized samples are also better than those of commercial Pt/C catalysts.
Modifying SiO @ C as High-performance Anode of Lithium-ion Batteries
Authors: Liu Tao , Zhang Ling , Wu Borong
Published: August 2023

SiO is a widely prospected anode material, which is an excellent substitute for pure silicon for lithium-ion batteries in the future, with the reason of lower expansion degree. However, the conductivity of SiO is also poor and has a side reaction with electrolytes. Here, we choose melamine as a nitrogen source to modify the carbon layer-coated SiO materials. This study shows that nitrogen and carbon shells lead to forming stable SEI, and improve the conductivity of the anodes. Consequently, at 0.1 C, the modified SiO materials in the anode achieve an excellent specific capacity (1711.5 mAh g-1), in addition, the decay rate of the capacity is 0.6% per cycle in the next 100 cycles. This method makes a new direction for the product of SiO materials.
Surface Modification of Micro-Silicon Anode for High-performance Lithium-Ion Batteries
Authors: Chen Tongren , Yan Wengang , Yu Dong , Ma Siyuan , Ma Liang , Huang Qing , Li Ning
Published: August 2023

Advanced lithium-ion batteries are urgently needed in consumer electronic products, electric vehicles, and energy storage, while the traditional carbonaceous anode materials with relatively low specific capacity gradually become difficult to meet the practical requirements in the market. Silicon-based anodes are considered one of the most promising alternatives in LIBs with high specific energy due to their considerable theoretical specific capacities. However, the large volume variation and severe surface parasitic reactions still limit the practical application of silicon anode. In this work, to suppress the surface side reactions and great volume changes, the electrochemical inert Li3PO4 is proposed to be coated as the physical barrier between the silicon and electrolyte. The as-coated micro-silicon has been successfully prepared via a facile spray drying method with a low-temperature thermal treatment. Li3PO4 coating layer with high shear modules can not only passivate the surface but also enable to suppression of the severe volumetric expansion and shrinkage of the silicon particle, thus enhancing the initial columbic efficiency and structural integrity of the silicon materials during long-term cycling. The optimized silicon anode with the proper amount of Li3PO4 displays a superior initial columbic efficiency higher than 90% and a highly reversible capacity of 1394 mAh g-1 after charging and discharging 200 times. It is hoped this work should shed light on the modification of high-capacity anode materials.
Investigation of the impact of annealing temperature on characteristics of porous SiOCH films
Authors: Zeng Min , Zhang Jing , Wang Yanrong
Published: August 2023

Porous SiOCH films with different porosity and low dielectric constant (k) were prepared by sol-gel and spin coating using methyltrimethoxy-silane (MTMS) and 1, 2-bis (trimethoxysilyl) ethane (BTMSE) as precursors and cetyltrimethylammonium chloride (CTAC) as porogen. The impact of different annealing temperatures on the chemical composition, hydrophobicity, pore arrangement, and dielectric constant of porous SiOCH films was investigated. The experimental results show that the SiOCH films with MTMS and BTMSE as precursors contain -C-C-bond and terminal methyl (Si-CH3). After annealing at 400 °C, the chemical composition of the films is stable. The water contact angle (WCA) is larger than 90°, and the films have good hydrophobicity.
Effects of selected retarders on workability window and other properties of cement-based sprayed mortars
Authors: Krivánková E , Kubátová D , Boháč M , Krejčí Kotlánová M , Rybová A , Zezulová A
Published: August 2023

Setting reducing agents were studied with respect to rheological properties of sprayed mortars based on fast-setting cement binder. The aim was to slightly delay the fast-setting effect caused mainly by tricalcium aluminate presence in order to adjust the workability window resulting in improved pumpability. Main experiments were performed using rotational rheometer and powder X-ray diffractometer. Additionally, 7day, 14day and 28day strength tests were done. The results show that chosen chemicals work as retarders, but not in required extent. Moreover, apart from the usual slower development of the strength due to the presence of retarder, at applied amounts, some of them can even have undesirable side effects such as causing weaker overall structure of the cured specimens.
Effect of siliceous sand volume fraction on the properties of alkali-activated slag mortars
Authors: Hajzler J , Bílek Jr V , Kejík M , Kucharczyková B
Published: August 2023

One of the critical factors affecting the performance of alkali-activated slag (AAS) is the nature and dose of alkali activator. The activator type can play a significant role during the transition from pastes to mortars or concretes. Therefore, three basic sodium activators (water glass, carbonate, and hydroxide) of the same molarity of 4M Na+ were used to prepare AAS-based mortars with different volume fractions of siliceous sand. These were compared by means of workability, mechanical strength, and long-term shrinkage under autogenous conditions. The results were compared to those obtained on pastes with similar workability. Increasing the content of the sand tended rather to decrease the mechanical properties, while greatly decreased autogenous shrinkage. Nevertheless, the most remarkable differences for different activators were observed when comparing the mortars with pastes. The transition from pastes to mortars resulted in the highest reduction in both compressive and flexural strength for sodium hydroxide. The flexural strength of the mortars with sodium water glass and sodium carbonate even increased considerably in presence of sand.
Future prospects in mRNA vaccine development
Authors: Mbatha Londiwe Simphiwe , Akinyelu Jude , Maiyo Fiona , Kudanga Tukayi
Published: August 2023

The recent advancements in messenger ribonucleic acid (mRNA) vaccine development have vastly enhanced their use as alternatives to conventional vaccines in the prevention of various infectious diseases and treatment of several types of cancers. This is mainly due to their remarkable ability to stimulate specific immune responses with minimal clinical side effects. This review gives a detailed overview of mRNA vaccines currently in use or at various stages of development, the recent advancements in mRNA vaccine development, and the challenges encountered in their development. Future perspectives on this technology are also discussed.
Recent legislation in the United States: consequences for the US and global energy and climate innovation systems
Authors: Hart David M
Published: August 2023

This Perspective sketches how recent legislation in the United States may impact the domestic and global energy and climate innovation systems, drawing on systems concepts articulated by Arnulf Grubler. It also sets out risks and gaps that could lead to less favorable outcomes.
Electrochemical and optical-based systems for SARS-COV-2 and various pathogens assessment
Authors: Ahmed Shahzad , Ansari Arshiya , Siddiqui Moin Ali , Imran Mohd , Kumari Beauty , Khan Afzal , Ranjan Pranay
Published: August 2023

A critical step in the process for preventing and identifying emergencies relating to health, safety, and welfare is the testing and quick diagnosis of microbial pathogens. Due to the fast spread of waterborne and food borne infections in society and the high costs associated with them, pathogen identification has emerged as one of the most difficult parts of the water and food sectors. Since the turn of the century, pathogens have demonstrated enormous epidemiological and pandemic potential. The emergence and dissemination of a novel virus with pandemic potential endanger the livelihoods and well-being of individuals worldwide. The severe acute respiratory syndrome-coronavirus-2 (SARS-COV-2) coronavirus pandemic has propagated to almost every country on Earth and has had a considerable negative influence on economies and communities. Despite improvements in identification techniques for viral diseases, all nations must now execute biosensing in a speedy, sensitive, focused, and consistent manner in order to address pressing global issues. Hence, in this review, we have critically summarised the recent advancement of electrochemical as well as optical biosensors for the monitoring of SARS-COV-2 and various pathogens. Then, we began by providing a technical overview of cutting-edge strategies utilised to combat diseases and emergencies for it, including the utilisation of point-of-care technology (POCT), artificial intelligence (AI), and the internet of medical things (IoMT). This review article explores the integration of POC, IoMT, and AI technologies in the context of personal healthcare, focusing on their potential to expedite the diagnosis and treatment of medical conditions, ultimately leading to improved patient outcomes. Subsequently, the notion and execution of multiplex testing are presented to enhance the comprehension of detecting multiple analytes. Finally, conclusions and future directions have been presented.
A green synthesis of CuInS2/MIL-101(Cr) nanocomposite with efficient visible light induced photocatalytic activity
Authors: Nguyen Hong Van T , Nguyen Manh B , Doan Huan V , Pham Xuan Nui
Published: August 2023

This study demonstrates the sustainable synthesis of multifunctional CIS@MIL-101(Cr) composites for water treatment applications. The composites were prepared via hybridization of CuInS2with MIL-101(Cr) resulting in the formation of CIS nanoplates incorporated into MIL-101(Cr). The composites exhibited enhanced visible light photocatalytic activity due to their low bandgap energy and were tested for tetracycline photodegradation achieving a degradation efficiency of 98.8%. The material showed high stability after four cycles, and the effects of reactive species on photodegradation were investigated. The kinetics and mechanism of the photocatalytic process were studied, and LC-MS analysis was conducted to identify intermediate products. These results demonstrate the potential of using waste PET to create new semiconductors for water pollution control, promoting a circular material pathway.
Decoding auditory-evoked response in affective states using wearable around-ear EEG system
Authors: Choi Jaehoon , Kaongoen Netiwit , Choi HyoSeon , Kim Minuk , Kim Byung Hyung , Jo Sungho
Published: August 2023

Objective. In this paper, an around-ear EEG system is investigated as an alternative methodology to conventional scalp-EEG-based systems in classifying human affective states in the arousal-valence domain evoked in response to auditory stimuli. Approach. EEG recorded from around the ears is compared to EEG collected according to the international 10–20 system in terms of efficacy in an affective state classification task. A wearable device with eight dry EEG channels is designed for ear-EEG acquisition in this study. Twenty-one subjects participated in an experiment consisting of six sessions over three days using both ear and scalp-EEG acquisition methods. Experimental tasks consisted of listening to an auditory stimulus and self-reporting the elicited emotion in response to the said stimulus. Various features were used in tandem with asymmetry methods to evaluate binary classification performances of arousal and valence states using ear-EEG signals in comparison to scalp-EEG. Main results. We achieve an average accuracy of 67.09% ± 6.14 for arousal and 66.61% ± 6.14 for valence after training a multi-layer extreme learning machine with ear-EEG signals in a subject-dependent context in comparison to scalp-EEG approach which achieves an average accuracy of 68.59% ± 6.26 for arousal and 67.10% ± 4.99 for valence. In a subject-independent context, the ear-EEG approach achieves 63.74% ± 3.84 for arousal and 64.32% ± 6.38 for valence while the scalp-EEG approach achieves 64.67% ± 6.91 for arousal and 64.86% ± 5.95 for valence. The best results show no significant differences between ear-EEG and scalp-EEG signals for classifications of affective states. Significance. To the best of our knowledge, this paper is the first work to explore the use of around-ear EEG signals in emotion monitoring. Our results demonstrate the potential use of around-ear EEG systems for the development of emotional monitoring setups that are more suitable for use in daily affective life log systems compared to conventional scalp-EEG setups.
Graphical structures for design and verification of quantum error correction
Authors: Chancellor Nicholas , Kissinger Aleks , Zohren Stefan , Roffe Joschka , Horsman Dominic
Published: August 2023

We introduce a high-level graphical framework for designing and analysing quantum error correcting codes, centred on what we term the coherent parity check (CPC). The graphical formulation is based on the diagrammatic tools of the ZX-calculus of quantum observables. The resulting framework leads to a construction for stabilizer codes that allows us to design and verify a broad range of quantum codes based on classical ones, and that gives a means of discovering large classes of codes using both analytical and numerical methods. We focus in particular on the smaller codes that will be the first used by near-term devices. We show how CSS codes form a subset of CPC codes and, more generally, how to compute stabilizers for a CPC code. As an explicit example of this framework, we give a method for turning almost any pair of classical

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CPC code. Further, we give a simple technique for machine search which yields thousands of potential codes, and demonstrate its operation for distance 3 and 5 codes. Finally, we use the graphical tools to demonstrate how Clifford computation can be performed within CPC codes. As our framework gives a new tool for constructing small- to medium-sized codes with relatively high code rates, it provides a new source for codes that could be suitable for emerging devices, while its ZX-calculus foundations enable natural integration of error correction with graphical compiler toolchains. It also provides a powerful framework for reasoning about all stabilizer quantum error correction codes of any size.
Contact–separation mode triboelectric nanogenerator utilizing carbon-fiber composite structure for harvesting mechanical energy
Authors: Lee Seonghwan , Park Young-Bin
Published: August 2023

The rapid depletion and adverse environmental impacts of fossil fuels necessitate the development of alternative sources of sustainable and ecofriendly energy to address the increasing energy demand due to population growth and technological advancement. Energy harvesting is a major strategy for the generation of sustainable and clean energy. It involves the scavenging and subsequent conversion of the energy from the surroundings into usable electrical energy. In this study, the conversion of the mechanical energy externally applied to a carbon-fiber-reinforced plastic (CFRP)-based structure into electrical energy using a triboelectric nanogenerator (TENG) was demonstrated. CFRPs are ultralight composites with high strength and stiffness, and they are primarily utilized in aircraft and automobiles. CFRP was the primary component of the CFRP-based TENG (CFRP-TENG) developed in this study. The carbon fibers of the CFRP acted as an electrode. Polyamide 6, which corresponded to the matrix of the CFRP, and polytetrafluoroethylene, which was attached to the surface of the CFRP, acted as friction pairs. The CFRP-TENG generated a voltage, short-circuit current, and power of up to 62 V, 7.76 μA, and 400 mW m−2, respectively, with an optimal external resistance of 20 MΩ. A structural CFRP was successfully applied as a TENG in this study; thus, the possibility of transforming a CFRP-based structure into a self-powering structure was demonstrated. The technique used in this study is expected to serve as a novel approach for energy generation in cyber-physical systems. This will facilitate the attachment of self-supporting energy systems such as sensors, power management systems, and actuators to the human body without additional batteries.
Associations between long-term exposure to fine particulate matter and osteoporotic fracture risks in South Korea
Authors: Heo Seulkee , Byun Garam , Kim Sera , Lee Whanhee , Lee Jong-Tae , Bell Michelle L
Published: August 2023

The prevalence of osteoporotic fracture is increasing globally due to rapid population growth and aging. Current evidence suggests adverse impacts of air pollution on bone mineral density loss and osteoporosis, but population-based evidence for the associations between fine particulate matter (particulate matter no larger than 2.5 μm in diameter [PM2.5]) and osteoporotic fracture is limited due to the small number of studies. This longitudinal study assessed the associations between long-term exposure to PM2.5 and osteoporotic fracture incidence in adults aged ⩾40 years, who enrolled in the National Health Insurance Service-National Sample Cohort data in 2002–2019 in South Korea. A time-varying moving window of past exposures of PM2.5 up to ten past years was estimated for participants’ residential addresses using modeled PM2.5. We used Cox proportional hazard models to estimate hazard ratios (HRs) of time-variant moving concentrations of PM2.5 exposure and osteoporotic fracture. The Cox models calculated HRs for an interquartile range (IQR) increase in PM2.5 exposure, adjusting for age, sex, body mass index, health behaviors, medications, disease history, income, and urbanicity. We assessed 161 831 participants over 993 104 person-year of follow-up. Results suggested linear and positive exposure-response associations for past PM2.5 exposure in the prior four years or more. The IQR increase in 5-year moving average PM2.5 was significantly associated with increased osteoporotic risk (HR = 1.079, 95% CI: 1.001, 1.164). The HRs were significant in women (1.102, 95% CI: 1.011, 1.200) and the subset of women aged 50–74 years (1.105, 95% CI: 1.005, 1.214) but not in men overall or by age groups. The association was not significantly different by income, physical activities, urbanicity, or diet. Overall, long-term PM2.5 exposure was associated with increased osteoporotic fracture risks in Korean adults, especially women.
KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations
Authors: Wu Jinyang , Ning Zhiwei , Ding Yidong , Wang Ying , Peng Qinke , Fu Laiyi
Published: August 2023

Recent studies have demonstrated the significant role that circRNA plays in the progression of human diseases. Identifying circRNA-disease associations (CDA) in an efficient manner can offer crucial insights into disease diagnosis. While traditional biological experiments can be time-consuming and labor-intensive, computational methods have emerged as a viable alternative in recent years. However, these methods are often limited by data sparsity and their inability to explore high-order information. In this paper, we introduce a novel method named Knowledge Graph Encoder from Transformer for predicting CDA (KGETCDA). Specifically, KGETCDA first integrates more than 10 databases to construct a large heterogeneous non-coding RNA dataset, which contains multiple relationships between circRNA, miRNA, lncRNA and disease. Then, a biological knowledge graph is created based on this dataset and Transformer-based knowledge representation learning and attentive propagation layers are applied to obtain high-quality embeddings with accurately captured high-order interaction information. Finally, multilayer perceptron is utilized to predict the matching scores of CDA based on their embeddings. Our empirical results demonstrate that KGETCDA significantly outperforms other state-of-the-art models. To enhance user experience, we have developed an interactive web-based platform named HNRBase that allows users to visualize, download data and make predictions using KGETCDA with ease. The code and datasets are publicly available at https://github.com/jinyangwu/KGETCDA.
NCAE: data-driven representations using a deep network-coherent DNA methylation autoencoder identify robust disease and risk factor signatures
Authors: Martínez-Enguita David , Dwivedi Sanjiv K , Jörnsten Rebecka , Gustafsson Mika
Published: August 2023

Precision medicine relies on the identification of robust disease and risk factor signatures from omics data. However, current knowledge-driven approaches may overlook novel or unexpected phenomena due to the inherent biases in biological knowledge. In this study, we present a data-driven signature discovery workflow for DNA methylation analysis utilizing network-coherent autoencoders (NCAEs) with biologically relevant latent embeddings. First, we explored the architecture space of autoencoders trained on a large-scale pan-tissue compendium (n = 75 272) of human epigenome-wide association studies. We observed the emergence of co-localized patterns in the deep autoencoder latent space representations that corresponded to biological network modules. We determined the NCAE configuration with the strongest co-localization and centrality signals in the human protein interactome. Leveraging the NCAE embeddings, we then trained interpretable deep neural networks for risk factor (aging, smoking) and disease (systemic lupus erythematosus) prediction and classification tasks. Remarkably, our NCAE embedding-based models outperformed existing predictors, revealing novel DNA methylation signatures enriched in gene sets and pathways associated with the studied condition in each case. Our data-driven biomarker discovery workflow provides a generally applicable pipeline to capture relevant risk factor and disease information. By surpassing the limitations of knowledge-driven methods, our approach enhances the understanding of complex epigenetic processes, facilitating the development of more effective diagnostic and therapeutic strategies.
Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches
Authors: Yi Dohun , Nam Jin-Wu , Jeong Hyobin
Published: August 2023

Structural variants (SVs) are genomic rearrangements that can take many different forms such as copy number alterations, inversions and translocations. During cell development and aging, somatic SVs accumulate in the genome with potentially neutral, deleterious or pathological effects. Generation of somatic SVs is a key mutational process in cancer development and progression. Despite their importance, the detection of somatic SVs is challenging, making them less studied than somatic single-nucleotide variants. In this review, we summarize recent advances in whole-genome sequencing (WGS)-based approaches for detecting somatic SVs at the tissue and single-cell levels and discuss their advantages and limitations. First, we describe the state-of-the-art computational algorithms for somatic SV calling using bulk WGS data and compare the performance of somatic SV detectors in the presence or absence of a matched-normal control. We then discuss the unique features of cutting-edge single-cell-based techniques for analyzing somatic SVs. The advantages and disadvantages of bulk and single-cell approaches are highlighted, along with a discussion of their sensitivity to copy-neutral SVs, usefulness for functional inferences and experimental and computational costs. Finally, computational approaches for linking somatic SVs to their functional readouts, such as those obtained from single-cell transcriptome and epigenome analyses, are illustrated, with a discussion of the promise of these approaches in health and diseases.
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation
Authors: Davidson Russell B , Coletti Mark , Gao Mu , Piatkowski Bryan , Sreedasyam Avinash , Quadir Farhan , Weston David J , Schmutz Jeremy , Cheng Jianlin , Skolnick Jeffrey , Parks Jerry M , Sedova Ada
Published: August 2023

Motivation

Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction.

Results

We present the predicted structural proteome (25 134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.

Availability and implementation

All data and code are available in public repositories, detailed at https://github.com/BSDExabio/SAFA. The structural models of the S. divinum proteome have been deposited in the ModelArchive repository at https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv.
Predicting insect body masses based on linear measurements: a phylogenetic case study on geometrid moths
Authors: Araújo Foerster Stênio Ítalo , Javoiš Juhan , Holm Sille , Tammaru Toomas
Published: August 2023

Dry body mass (DBM) is perhaps the most biologically informative variable describing body size in invertebrates. Unfortunately, obtaining species-specific indices of DBM is problematic because body mass inevitably changes during the course of the life of an individual. Here, we present a phylogenetically informed analysis of allometric relationships between body size and various linear measurements in the moth family Geometridae, which relies on DBM recorded at a fixed time point of adult life. We demonstrate that all measurements of wing size predict DBM with reasonable accuracy, with the distance between the most distal ends of the two forewings in traditionally mounted moths showing the best performance. Abdomen width provides independent morphometric information and can be used as a proxy of body plan, i.e. a measurement of shape that is not dependent on size. Incorporating abdomen width into the regression models considerably increases their predictive ability. We also show that the allometric relationships are reasonably consistent between the two sexes, between monophyletic clades of Geometridae and between the two geographical regions involved in the study (northern Europe and equatorial Africa). The derived equations thus appear to be general enough to be applied in various studies, from comparative phylogenetic analyses to applied projects monitoring insect biomass.
Dual roles of cellular communication network factor 6 (CCN6) in the invasion and metastasis of oral cancer cells to bone via binding to BMP2 and RANKL
Authors: Hochi Hiroaki , Kubota Satoshi , Takigawa Masaharu , Nishida Takashi
Published: August 2023

The acquisition of motility via epithelial–mesenchymal transition (EMT) and osteoclast induction are essential for the invasion and metastasis of oral squamous cell carcinoma (OSCC) to bone. However, the molecule suppressing both EMT and osteoclastogenesis is still unknown. In this study, we found that cellular communication network factor 6 (CCN6) was less produced in a human OSCC cell line, HSC-3 with mesenchymal phenotype, than in HSC-2 cells without it. Notably, CCN6 interacted with bone morphogenetic protein 2 (BMP2) and suppressed the cell migration of HSC-3 cells stimulated by BMP2. Moreover, knockdown of CCN6 in HSC-2 cells led to the promotion of EMT and enhanced the effect of transforming growth factor-β (TGF-β) on the promotion of EMT. Furthermore, CCN6 combined with BMP2 suppressed EMT. These results suggest that CCN6 strongly suppresses EMT in cooperation with BMP2 and TGF-β. Interestingly, CCN6 combined with BMP2 increased the gene expression of receptor activator of nuclear factor-κB ligand (RANKL) in HSC-2 and HSC-3 cells. Additionally, CCN6 interacted with RANKL, and CCN6 combined with RANKL suppressed RANKL-induced osteoclast formation. In metastatic lesions, increasing BMP2 due to the bone destruction led to interference with binding of CCN6 to RANKL, which results in the promotion of bone metastasis of OSCC cells due to continuous osteoclastogenesis. These findings suggest that CCN6 plays dual roles in the suppression of EMT and in the promotion of bone destruction of OSCC in primary and metastatic lesions, respectively, through cooperation with BMP2 and interference with RANKL.
IL-38 alleviates airway remodeling in chronic asthma via blocking the profibrotic effect of IL-36γ
Authors: Zhang Min , Zhou Jian-Xia , Huang Chu-Qin , Feng Kang-Ni , Zou Xiao-Ling , Cen Jie-Mei , Meng Ping , Li Hong-Tao , Zhang Tian-Tuo
Published: August 2023

Airway remodeling is a major feature of asthma. Interleukin (IL)-36γ is significantly upregulated and promotes airway hyper-responsiveness (AHR) in asthma, but its role in airway remodeling is unknown. Here, we aimed to investigate the role of IL-36γ in airway remodeling, and whether IL-38 can alleviate airway remodeling in chronic asthma by blocking the effects of IL-36γ. IL-36γ was quantified in mice inhaled with house dust mite (HDM). Extracellular matrix (ECM) deposition in lung tissues and AHR were assessed following IL-36γ administration to mice. Airway inflammation, AHR, and remodeling were evaluated after IL-38 or blocking IL-36 receptor (IL-36R) treatment in asthmatic mice. The effects of lung fibroblasts stimulated with IL-36γ and IL-38 were quantified in vitro. Increased expression of IL-36γ was detected in lung tissues of HDM-induced asthmatic mice. The intratracheal instillation of IL-36γ to mice significantly enhanced the ECM deposition, AHR, and the number of activated lung fibroblasts around the airways. IL-38 or blocking IL-36R treated asthmatic mice showed a significant alleviation in the airway inflammation, AHR, airway remodeling, and number of activated fibroblasts around airways as compared with the HDM group. In vitro, IL-36γ promoted the activation and migration of human lung fibroblasts (HFL-1). The administration of IL-38 can counteract these biological processes induced by IL-36γ in HFL-1cells. The results indicated that IL-38 can mitigate airway remodeling by blocking the profibrotic effects of IL-36γ in chronic asthma. IL-36γ may be a new therapeutic target, and IL-38 is a potential candidate agent for inhibiting airway remodeling in asthma.
Low CD4 Count or Being Out of Care Increases the Risk for Mpox Hospitalization Among People With Human Immunodeficiency Virus and Mpox
Authors: Philpott David C , Bonacci Robert A , Weidle Paul J , Curran Kathryn G , Brooks John T , Khalil George , Feldpausch Amanda , Pavlick Jessica , Wortley Pascale , O’Shea Jesse G
Published: August 2023

Human immunodeficiency virus (HIV)–associated immunosuppression may increase the risk of hospitalization with mpox. Among persons diagnosed with mpox in the state of Georgia, we characterized the association between hospitalization with mpox and HIV status. People with HIV and a CD4 count <350 cells/mm3 or who were not engaged in HIV care had an increased risk of hospitalization.
Time series DNA barcoding provides insight into factors influencing wood-boring and bark-feeding insect communities in Scots pine, Sitka spruce, and Noble fir stands
Authors: de Becquevort Sophie , Mckeown Niall J , Blake Max , Shaw Paul W
Published: August 2023

Bark-feeding and wood-boring insect pests can have significant negative impacts on conifers and wood production. The damage they cause is expected to increase in the future due to climate change and the growth of international trade. This study employed DNA barcoding of beetle juveniles (Coleoptera) sampled from standing trap trees and cut log piles at regular intervals over a 2-yr period to monitor the beetle community dynamics and associated environmental factors. Tree species was found to have a major influence on beetle communities, most strikingly at the start of early decay stages. Lower species diversity was reported from standing trap tree samples compared to log pile samples, likely due to higher residual defences in dying and recently dead trees. While the species identified from standing trap trees are more likely to be a threat to the forestry sector, the species found in the log piles are more likely to be beneficial due to their high abundance and their ability to compete with pests for breeding substrate. The analysis of beetles collected inside trees revealed additional information on ontogenetic niches and host preferences beyond that acquired solely from flight interception trap data. Our results offer insights on community composition and dynamics of bark-feeding and wood-boring insect species in Welsh conifer forests and provide resources for monitoring and management of potential pest species.
Inflammation in acute myocardial infarction: the good, the bad and the ugly
Authors: Matter Michael A , Paneni Francesco , Libby Peter , Frantz Stefan , Stähli Barbara E , Templin Christian , Mengozzi Alessandro , Wang Yu-Jen , Kündig Thomas M , Räber Lorenz , Ruschitzka Frank , Matter Christian M
Published: August 2023

Convergent experimental and clinical evidence have established the pathophysiological importance of pro-inflammatory pathways in coronary artery disease. Notably, the interest in treating inflammation in patients suffering acute myocardial infarction (AMI) is now expanding from its chronic aspects to the acute setting. Few large outcome trials have proven the benefits of anti-inflammatory therapies on cardiovascular outcomes by targeting the residual inflammatory risk (RIR), i.e. the smouldering ember of low-grade inflammation persisting in the late phase after AMI. However, these studies have also taught us about potential risks of anti-inflammatory therapy after AMI, particularly related to impaired host defence. Recently, numerous smaller-scale trials have addressed the concept of targeting a deleterious flare of excessive inflammation in the early phase after AMI. Targeting different pathways and implementing various treatment regimens, those trials have met with varied degrees of success. Promising results have come from those studies intervening early on the interleukin-1 and -6 pathways. Taking lessons from such past research may inform an optimized approach to target post-AMI inflammation, tailored to spare ‘The Good’ (repair and defence) while treating ‘The Bad’ (smouldering RIR) and capturing ‘The Ugly’ (flaming early burst of excess inflammation in the acute phase). Key constituents of such a strategy may read as follows: select patients with large pro-inflammatory burden (i.e. large AMI); initiate treatment early (e.g. ≤12 h post-AMI); implement a precisely targeted anti-inflammatory agent; follow through with a tapering treatment regimen. This approach warrants testing in rigorous clinical trials.
The patient experience of in-hospital telemetry monitoring: a qualitative analysis
Authors: Holm Marianne Sætrang , Fålun Nina , Bendz Bjørn , Fridlund Bengt , Langørgen Jørund , Pettersen Trond R , Sandau Kristin E , Norekvål Tone M
Published: August 2023

Aims

In-hospital telemetry monitoring has been an integrated part of arrhythmia monitoring for decades. A substantial proportion of patients require arrhythmia monitoring during stays in non-intensive care units. However, studies exploring patients’ experiences of telemetry monitoring are scarce. Therefore, the aim was to explore and describe patients’ experiences of in-hospital telemetry monitoring in a non-intensive care setting.

Methods and results

Twenty face-to-face, semi-structured interviews were conducted. Interviews were conducted before discharge at two university hospitals in Norway. The patients were purposively sampled, resulting in a well-balanced population comprising 11 men and nine women, mean age 62 years (range 25–83). Average monitoring time was 9 days (range 3–14). Data were audiotaped, transcribed verbatim, and coded using NVivo software. Qualitative content analysis using an inductive approach was performed. Patients expressed a need for individualized information during telemetry monitoring. Their feelings of safety were related to responses from nurses from the central monitoring station when alarms from the telemetry were triggered. Despite perceived physical restrictions and psychological limitations associated with telemetry monitoring, they found monitoring to be beneficial because it facilitated the diagnosis of arrhythmia. Moreover, they expressed a need for improvements in wearable monitoring equipment. Patients expressed ambivalent feelings about discontinuing the telemetry and their readiness for discharge.

Conclusion

Patients need individualized information about the results of their telemetry monitoring in order to better understand the arrhythmia management and to increase their experience of safety after discharge. The limitations patients experienced should be taken into consideration in further upgrades of telemetry monitoring equipment.