bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly of respiratory syncytial virus matrix protein lattice and its coordination with fusion glycoprotein trimers
Authors: Sibert Bryan S. , Kim Joseph Y. , Yang Jie E. , Ke Zunlong , Stobart Christopher C. , Moore Martin L. , Wright Elizabeth R. 
Published: July 2024

AbstractRespiratory syncytial virus (RSV) is an enveloped, filamentous, negative-strand RNA virus that causes significant respiratory illness worldwide. RSV vaccines are available, however there is still significant need for research to support the development of vaccines and therapeutics against RSV and related Mononegavirales viruses. Individual virions vary in size, with an average diameter of ~130 nm and ranging from ~500 nm to over 10 µm in length. Though the general arrangement of structural proteins in virions is known, we use cryo-electron tomography and sub-tomogram averaging to determine the molecular organization of RSV structural proteins. We show that the peripheral membrane-associated RSV matrix (M) protein is arranged in a packed helical-like lattice of M-dimers. We report that RSV F glycoprotein is frequently observed as pairs of trimers oriented in an anti-parallel conformation to support potential interactions between trimers. Our sub-tomogram averages indicate the positioning of F-trimer pairs is correlated with the underlying M lattice. These results provide insight into RSV virion organization and may aid in the development of RSV vaccines and anti-viral targets.
Unraveling the molecular architecture of autoimmune thyroid diseases at spatial resolution
Authors: Martínez-Hernández Rebeca , Sánchez de la Blanca Nuria , Sacristán-Gómez Pablo , Serrano-Somavilla Ana , Muñoz De Nova José Luis , Sánchez Cabo Fátima , Heyn Holger , Sampedro-Núñez Miguel , Marazuela Mónica 
Published: July 2024

AbstractAutoimmune thyroid diseases (AITD) such as Graves’ disease (GD) or Hashimoto’s thyroiditis (HT) are organ-specific diseases that involve complex interactions between distinct components of thyroid tissue. Here, we use spatial transcriptomics to explore the molecular architecture, heterogeneity and location of different cells present in the thyroid tissue, including thyroid follicular cells (TFCs), stromal cells such as fibroblasts, endothelial cells, and thyroid infiltrating lymphocytes. We identify damaged antigen-presenting TFCs with upregulated CD74 and MIF expression in thyroid samples from AITD patients. Furthermore, we discern two main fibroblast subpopulations in the connective tissue including ADIRF+ myofibroblasts, mainly enriched in GD, and inflammatory fibroblasts, enriched in HT patients. We also demonstrate an increase of fenestrated PLVAP+ vessels in AITD, especially in GD. Our data unveil stromal and thyroid epithelial cell subpopulations that could play a role in the pathogenesis of AITD.
Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau
Authors: Kang Luyao , Song Yutong , Mackelprang Rachel , Zhang Dianye , Qin Shuqi , Chen Leiyi , Wu Linwei , Peng Yunfeng , Yang Yuanhe 
Published: July 2024

AbstractPermafrost, characterized by its frozen soil, serves as a unique habitat for diverse microorganisms. Understanding these microbial communities is crucial for predicting the response of permafrost ecosystems to climate change. However, large-scale evidence regarding stratigraphic variations in microbial profiles remains limited. Here, we analyze microbial community structure and functional potential based on 16S rRNA gene amplicon sequencing and metagenomic data obtained from an ∼1000 km permafrost transect on the Tibetan Plateau. We find that microbial alpha diversity declines but beta diversity increases down the soil profile. Microbial assemblages are primarily governed by dispersal limitation and drift, with the importance of drift decreasing but that of dispersal limitation increasing with soil depth. Moreover, genes related to reduction reactions (e.g., ferric iron reduction, dissimilatory nitrate reduction, and denitrification) are enriched in the subsurface and permafrost layers. In addition, microbial groups involved in alternative electron accepting processes are more diverse and contribute highly to community-level metabolic profiles in the subsurface and permafrost layers, likely reflecting the lower redox potential and more complicated trophic strategies for microorganisms in deeper soils. Overall, these findings provide comprehensive insights into large-scale stratigraphic profiles of microbial community structure and functional potentials in permafrost regions.
Substantial differences in source contributions to carbon emissions and health damage necessitate balanced synergistic control plans in China
Authors: Chen Yilin , Shen Huizhong , Shen Guofeng , Ma Jianmin , Cheng Yafang , Russell Armistead G. , Zhao Shunliu , Hakami Amir , Tao Shu 
Published: July 2024

AbstractChina’s strategy to concurrently address climate change and air pollution mitigation is hindered by a lack of comprehensive information on source contributions to health damage and carbon emissions. Here we show notable discrepancies between source contributions to CO2 emissions and fine particulate matter (PM2.5)-related mortality by using adjoint emission sensitivity modeling to attribute premature mortality in 2017 to 53 sector and fuel/process combinations with high spatial resolution. Our findings reveal that monetized PM2.5 health damage exceeds climate impacts in over half of the analyzed subsectors. In addition to coal-fired energy generators and industrial boilers, the combined health and climate costs from energy-intensive processes, diesel-powered vehicles, domestic coal combustion, and agricultural activities exceed 100 billion US dollars, with health-related costs predominating. This research highlights the critical need to integrate the social costs of health damage with climate impacts to develop more balanced mitigation strategies toward these dual goals, particularly during fuel transition and industrial structure upgrading.
Design of polar boundaries enhancing negative electrocaloric performance by antiferroelectric phase-field simulations
Authors: Xu Ke , Shi Xiaoming , Shao Cancan , Dong Shouzhe , Huang Houbing 
Published: July 2024

AbstractElectrocaloric refrigeration which is environmentally benign has attracted considerable attention. In distinction to ferroelectric materials, which exhibit an extremely high positive electrocaloric effect near the Curie temperature, antiferroelectric materials represented by PbZrO3 have a specific negative electrocaloric effect, i.e., electric field decreases the temperature of the materials. However, the explanation of the microscopic mechanism of the negative electrocaloric effect is still unclear, and further research is still needed to provide a theoretical basis for the negative electrocaloric effect enhancement. Herein, the antiferroelectric phase-field model has been proposed to design polar boundaries enhancing antiferroelectric negative electrocaloric performance in PbZrO3-based materials. Based on this, we have simulated the polarization response and domain switching process of the temperature and electric field-induced antiferroelectric—ferroelectric phase transition. It is shown that the temperature range tends to increase as the density of polar boundaries increases from the antiferroelectric stripe domain, polymorphic domain to the nanodomain. Among them, the peak adiabatic temperature change of antiferroelectric nanodomains can reach −13.05 K at 84 kV/cm, and a wide temperature range of about 75 K can be realized at 42 kV/cm. We expect these discoveries to spur further interest in the potential applications of antiferroelectric materials for next-generation refrigeration devices.
Modeling habitat suitability of Dorema ammoniacum D Don. in the rangelands of central Iran
Authors: Zare Mostafa , Moameri Mehdi , Ghorbani Ardavan , Sahragard Hossein Piri , Mostafazadeh Raoof , Dadjou Farid , Biswas Asim 
Published: July 2024

AbstractThe purpose of this study was to evaluate the predictive accuracy of habitat suitability models, identifying the potential distribution range of Dorema ammoniacum, and its habitat requirements in the rangelands of Yazd province, central Iran. Bafgh, Mehriz and Nadoushan, were three habitats that were identified, and sampling was conducted in each habitat using a random-systematic method. A set of 10 plots were established (at equal distances) along 350 m long 18 transects. Soil samples (two depths: 0–30 and 30–60 cm from 36 profiles) were collected and measured in the laboratory. Elevation, slope, and aspect maps were derived, and climate information was collected from nearby meteorological stations. The habitat prediction of the species was modeled using Logistic Regression (LR), Maximum Entropy (MaxEnt), and Artificial Neural Network (ANN). The Kappa coefficient and the area under the curve (AUC) were calculated to assess the accuracy of the forecasted maps. The LR model for habitat prediction of the studied species in Mehriz (K = 0.67) and Nadoushan (K = 0.56) habitats were identified as good. The MaxEnt model predicted the habitat distribution for the selected species in Bafgh and Mehriz habitats as excellent (K = 0.89, AUC = 0.76, K = 0.89, AUC = 0.98), and in the Nadoushan habitat as very good (K = 0.78, AUC = 0.85). However, the ANN model predicted Bafgh and Nadoushan habitats as excellent and Mehriz habitat as very good (K = 0.87, K = 0.90, and K = 0.63, respectively). In general, in order to protect species D. ammoniacum, the development of its habitats in other areas of Yazd province and the habitats under study in conservation programs should be given priority.
The contribution of commonly consumed edible insects to nutrition security in the Eastern D.R. Congo
Authors: Ishara Jackson , Matendo Rehema , Ng’ang’a Jeremiah , Siddiqui Shahida Anusha , Niassy Saliou , Katcho Karume , Kinyuru John 
Published: July 2024

AbstractEdible insects are perceived as an incredible opportunity to mitigate the major challenge of sustainably producing healthy foods for a growing world population in the face of climate change uncertainties over the coming decade. In this study, we assessed the nutrient composition and sensory properties of Acheta domesticus, Apis mellifera, Gnathocera trivittata, Gryllotalpa africana, Imbrasia epimethea, Imbrasia oyemensis, Locusta migratoria, Macrotermes subhylanus, Nomadacris septemfasciata, Rhyncophorus phoenicis, Ruspolia differens and Rhynchophorus ferrugineus consumed in Eastern D. R. Congo. The investigated edible insects are highly appreciated and nutritious, with proteins (20.67–43.93 g/100 g) and fats (14.53–36.02 g/100 g) being the major macro-nutrients, proving their potential to improve diets through food enrichment. The high potassium (24–386.67 mg/100 g), sodium (152–257.82 mg/100 g), magnesium (32–64 mg/100 g), iron (5.3–16.13 mg/100 g), calcium (25–156.67 mg/100 g) and zinc (11–19.67 mg/100 g) content make the assessed edible insects a useful mineral-containing ingredient for preventing undernutrition in countries which are plagued by micronutrient deficiencies. A scatter plot of matrices and Pearson’s correlations between sensory attributes and nutritional composition showed a negative correlation (r = − 0.45) between protein and appearance. While no strong correlation was observed between nutritional attributes and sensory acceptance, a positive correlation was observed between potassium and aroma (r = 0.50), after-taste (r = 0.50) and acceptability (r = 0.52). Principal component analysis results indicated that the two axes accounted for up to 97.4% of the observed variability in the nutrient composition and sensory attributes of commonly consumed edible insects in the Eastern D. R. Congo. Given the significant delicacy and nutritional potential of edible insects highlighted in this paper, households can rely on the latter to meet their nutritional needs rather than conventional livestock, thus contributing to environmental and financial security through local business opportunities.
Effects of recycled waste on the modulus of elasticity of structural concrete
Authors: Gerges Najib N. , Issa Camille A. , Khalil Nariman J. , Aintrazi Sarah 
Published: July 2024

AbstractConcrete, the construction industry’s most utilized construction material, has transformed the environment and the modern built-up lifestyle. Although concrete is a first-rate supplier to the carbon footprint, it is imperative for buildings to display sustainable characteristics. Scholars have explored techniques to lessen the carbon footprint and the way to put into effect strategic waste control plans in which waste is reused. This study explores the dual benefits wherein concrete ingredients are replaced through abandoned waste which reduces the unwanted waste materials that have a substantial carbon footprint and thus results in the recycling of waste as part of a sustainable economic system. In this study, timber ash is utilized as a partial substitute for sand and cement, crumb rubber and waste glass as a partial substitute for sand, recycled concrete, and waste glass as a substitute for gravel. Characteristics studies were done to check the influence of each waste replacement on the modulus of elasticity of concrete. More than sixty-five combinations of waste have been examined to attain the modulus of elasticity of concrete. A total of about 200 concrete cylinders were cast to provide at least three cylinders for each generated data point. Three different ASTM standards were utilized to determine the modulus of elasticity of each mix. Four mixes comprising of the combination of two waste materials and two mixes comprising of the combination of three waste materials replacing natural materials were determined to exhibit an equal or superior modulus of elasticity of the control mix of 25 GPa.
Uncertainty quantification for probabilistic machine learning in earth observation using conformal prediction
Authors: Singh Geethen , Moncrieff Glenn , Venter Zander , Cawse-Nicholson Kerry , Slingsby Jasper , Robinson Tamara B. 
Published: July 2024

AbstractMachine learning is increasingly applied to Earth Observation (EO) data to obtain datasets that contribute towards international accords. However, these datasets contain inherent uncertainty that needs to be quantified reliably to avoid negative consequences. In response to the increased need to report uncertainty, we bring attention to the promise of conformal prediction within the domain of EO. Unlike previous uncertainty quantification methods, conformal prediction offers statistically valid prediction regions while concurrently supporting any machine learning model and data distribution. To support the need for conformal prediction, we reviewed EO datasets and found that only 22.5% of the datasets incorporated a degree of uncertainty information, with unreliable methods prevalent. Current open implementations require moving large amounts of EO data to the algorithms. We introduced Google Earth Engine native modules that bring conformal prediction to the data and compute, facilitating the integration of uncertainty quantification into existing traditional and deep learning modelling workflows. To demonstrate the versatility and scalability of these tools we apply them to valued EO applications spanning local to global extents, regression, and classification tasks. Subsequently, we discuss the opportunities arising from the use of conformal prediction in EO. We anticipate that accessible and easy-to-use tools, such as those provided here, will drive wider adoption of rigorous uncertainty quantification in EO, thereby enhancing the reliability of downstream uses such as operational monitoring and decision-making.
Role of elective neck dissection in cT2N0 maxillary sinus squamous cell carcinoma
Authors: Wang Jingjing , Fang Qigen , Zhang Xu , Dai Liyuan , Luo Ruihua 
Published: July 2024

AbstractOur objective was to examine the impact of elective neck dissection (END) on the prognosis of patients with cT2N0 maxillary sinus squamous cell carcinoma (MS-SCC) and to determine factors that predict the occurrence of occult metastasis in this patient population. A retrospective analysis was conducted using data from the SEER database. Patients with cT2N0 MS-SCC were included in the study and divided into two groups: those who received END and those who did not. The impact of END on disease-specific survival (DSS) and overall survival (OS) was assessed using propensity score matching. Multivariate logistic regression analysis was performed to determine predictors for occult metastasis. A total of 180 patients were included in the study, with 40 cases receiving END. Following propensity score matching, patients treated with END and those without showed similar DSS and OS rates. Occult metastasis was observed in 9 patients, corresponding to a rate of 22.5%. High-grade tumors were independently associated with a higher risk of occult metastasis compared to low-grade tumors (hazard ratio 1.52, 95% confidence interval 1.17–2.00). cT2 MS-SCC carries an occult metastasis rate of 22.5%, with histologic grade being the primary determinant of occult metastasis. END does not confer a significant survival benefit in this patient population.
Effects of kaempherol-3-rhamnoside on metabolic enzymes and AMPK in the liver tissue of STZ-induced diabetes in mice
Authors: Aodah Alhussain H. , Alkholifi Faisal K. , Alharthy Khalid M. , Devi Sushma , Foudah Ahmed I. , Yusufoglu Hasan S. , Alam Aftab 
Published: July 2024

AbstractDiabetes mellitus (DM) is a chronic metabolic disorder characterized by persistent hyperglycemia. It involves disturbances in carbohydrate, fat, and protein metabolism due to defects in insulin secretion, insulin action, or both. Novel therapeutic approaches are continuously being explored to enhance metabolic control and prevent complications associated with the disease. This study investigates the therapeutic potential of kaempherol-3-rhamnoside, a flavonoid, in managing diabetes by modulating the AMP-activated protein kinase (AMPK) pathway and improving metabolic enzyme activities in streptozotocin (STZ) -induced diabetic mice. Diabetic mice were treated with varying doses of kaempherol-3-rhamnoside and/or insulin over a 28-day period. Glycolytic and gluconeogenesis enzyme activities in the liver, fasting blood glucose levels, serum insulin levels, lipid profiles and oxidative stress markers were assessed. Treatment with kaempherol-3-rhamnoside significantly improved glycolytic enzyme activities, reduced fasting blood glucose, and enhanced insulin levels compared to diabetic controls. The compound also normalized lipid profiles and reduced oxidative stress in the liver, suggesting its potential in reversing diabetic dyslipidemia and oxidative damage. Furthermore, kaempherol-3-rhamnoside activated the AMPK pathway, indicating a mechanism through which it could exert its effects. Kaempherol-3-rhamnoside exhibits promising antidiabetic properties, potentially through AMPK pathway activation and metabolic enzyme modulation. These findings support its potential use as an adjunct therapy for diabetes management. Further clinical studies are warranted to validate these results in human subjects.
Quantification of circadian rhythms in mammalian lung tissue snapshot data
Authors: Grabe Saskia , Ananthasubramaniam Bharath , Herzel Hanspeter 
Published: July 2024

AbstractHealthy mammalian cells have a circadian clock, a gene regulatory network that allows them to schedule their physiological processes to optimal times of the day. When healthy cells turn into cancer cells, the circadian clock often becomes cancer specifically disturbed, so there is an interest in the extraction of circadian features from gene expression data of cancer. This is challenging, as clinical gene expression samples of cancer are snapshot-like and the circadian clock is best examined using gene expression time series. In this study, we obtained lists of intersecting circadian genes in public gene expression time series data of lung tissue of mouse and baboon. We base our circadian gene lists on correlations of gene expression levels of circadian genes, which are closely associated to the phase differences between them. Combining circadian gene expression patterns of diurnal and nocturnal species of different ages provides circadian genes that are also important in healthy and cancerous human lung tissue. We tested the quality of the representation of the circadian clock in our gene lists by PCA-based reconstructions of the circadian times of the mouse and baboon samples. Then we assigned potential circadian times to the human lung tissue samples and find an intact circadian clock in the healthy human lung tissue, but an altered, weak clock in the adjacent cancerous lung tissue.
The influence of recent bushfires on water quality and the operation of water purification systems in regional NSW
Authors: Jackson Reed , Krishna K. C. Bal , Li Miao , Sathasivan Arumugam , Senevirathna Lalantha 
Published: July 2024

AbstractOver the past decade, escalating extreme weather events have significantly affected New South Wales (NSW), Australia, with unprecedented droughts and intense fires. Yet, the impact on water quality and purification processes remains insufficiently studied. This research focuses on the immediate changes in NSW's environmental water quality and issues in water purification unit operations following the 2019 bushfires. Water samples and maintenance records from affected catchments, intakes, purification units, and reservoirs were analysed. Compared to control samples, post-bushfire water exhibited high turbidity. Sediment and ash shock loads posed significant threats to aquatic ecosystems. Elevated turbidity, suspended sediments, pH, and alkalinity were major concerns for water purification. Raw water samples showed turbidity exceeding 195 NTU, with flocculation and sedimentation most impacted. Immediate measures included sediment traps, aeration, pre-chlorination, and inline monitoring. These findings inform strategies to mitigate bushfire impacts on water quality and optimise water purification in fire-prone regions.
Diffractionless transmission of optical beams through a four-level atomic system affected by a plasmonic nanostructure
Authors: Lotfi Parvin , Sahrai Mostafa , Siahpoush Vahid , Vafafard Azar 
Published: July 2024

AbstractA nondiffracting propagation of an optical beam through a four-level double-V-type quantum system near a plasmonic nanostructure is investigated. We study the linear absorption and dispersion properties of the quantum system as it interacts with two laser fields. We discuss the effect of the control beam with a Laguerre-Gaussian (LG) profile on the focusing of the probe beam in the presence of a plasmonic nanostructure. An appropriately selected control beam excites one transition of the atomic system and generates a spatially varying refraction index modulation for a weak probe beam that couples to the other transition. We demonstrate that placing a plasmonic nanostructure at a nanometer distance from the atomic system and using a control field with the spatial structure leads to the diffraction-less propagation of the probe beam through the atomic system. Also, it is shown that the optical properties and probe beam focusing can be controlled by adjusting the distance of the plasmonic nanostructure from the atomic system. The proposed all-optical waveguide with high contrast and transmission can be used to implement applications such as image transfer through the medium and image processing.