bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and characterization of a DNA-launched Getah virus infectious clone
Authors: Cai Rongxuan , He Qi , Wang Qing , Wu XiaoFeng , Tian Lan , Chen Zhe , Yu Zhaorong , Sun Jiumeng , Shao Ying , Song Xiangjun , Qi Kezong , Tu Jian , Wang Zhenyu 
Published: October 2024

Abstract

Getah virus (GETV), a neglected and re-emerging mosquito-borne alphavirus, has becoming more serious and posing a potential threat to animal safety and public health. As there is a lack of antivirals and vaccines against GETV, it is necessary to continue the development of tools to further advance our efforts to combat these pathogens, including reverse genetics techniques. Herein, we describe the design and construction of a DNA-launched infectious clone for GETV. The full-length genome of GETV HuN1 strain, flanked by cytomegalovirus immediate-early (CMV) promoter sequence at the 5'-end and the hepatitis delta virus ribozyme along with the bovine growth hormone termination and polyadenylation signal sequences at the 3'-end, was packaged in bacterial artificial chromosome vector to establish a GETV infectious clone pBR322-GETV-HuN1. In parallel, the recombinant reporter viruses carrying the reporter gene EGFP between the E1 gene and the 3' UTR was constructed based on the established CMV-driven cDNA clone. Both in vivo and in vitro experiments have shown that the rescued recombinant virus possesses viral biological activity similar to the parental virus. Taken together, this study develops a concise and efficient GETV infectious cDNA clone and a recombinant virus carrying an EGFP reporter gene. The availability of the GETV infectious clone will facilitate further studies on understanding the molecular mechanisms of GETV virus biology, virulence determinants, molecular pathogenesis, vaccine development and virus-host interaction.
A simple and highly efficient protocol for 13 C-labeling of plant cell wall for structural and quantitative analyses via solid-state nuclear magnetic resonance
Authors: Javaid Tasleem , Venkataraghavan Akshayaa , Bhattarai Matrika , Debnath Debkumar , Zhao Wancheng , Wang Tuo , Faik Ahmed 
Published: October 2024

Abstract

Background
Plant cell walls are made of a complex network of interacting polymers that play critical role in plant development and responses to environmental changes. Thus, improving plant biomass and fitness requires the elucidation of the structural organization of plant cell walls in their native environment. The 13C-based multi-dimensional solid-state nuclear magnetic resonance (ssNMR) has been instrumental in revealing the structural information of plant cell walls through 2D and 3D correlation spectral analyses. However, the requirement of enriching plants with 13C limits the applicability of this method. To our knowledge, there is only a very limited set of methods currently available that achieve high levels of 13C-labeling of plant materials using 13CO2 and most of them require large amounts of 13CO2 in larger growth chambers.
Results
In this study, a simplified protocol for 13C-labeling of plant materials is introduced that allows ca 60% labeling of the cell walls, as quantified by comparison with commercially labeled samples. This level of 13C-enrichment is sufficient for all conventional 2D and 3D correlation ssNMR experiments for detailed analysis of plant cell wall structure. The protocol is based on a convenient and an easy setup to supply both 13C-labeled glucose and 13CO2 using a vacuum-desiccator. The protocol does not require large amounts of 13CO2.
Conclusion
This study shows that our 13C-labeling of plant materials can make the accessibility to ssNMR technique easy and affordable. The derived high-resolution 2D and 3D correlation spectra are used to extract structural information of plant cell walls. This helps to better understand the influence of polysaccharide-polysaccharide interaction on plant performance and allows for a more precise parametrization of plant cell wall models.
Ultrasensitive surface plasmon resonance-based biosensor for efficient detection of SARS-CoV-2 Virus in the near-infrared region
Authors: Runthala Rahul , Grover Nitika , Arora Pankaj 
Published: October 2024

Abstract

This work offers an ultra-sensitive multilayered surface plasmon resonance (SPR)-based biosensor that uses angular interrogation in the near-infrared (NIR) region to detect the novel coronavirus (SARS-CoV-2). The multi-layered biosensor consists of the bimetallic layer (Aluminum (Al) & Gold(Au)), a dielectric layer (MgF2), and an optimized number of 2D nanomaterial (MoS2) layers. The proposed SPR sensor is engineered using the transfer matrix and finite element methods to achieve high sensitivity, the figure of merit (FOM), and detection accuracy. The selection of plasmonic metal and optimization for the different layers have been proved crucial to improving the performance parameter of the proposed sensor. The biosensor configuration (Glass prism/Al/Au/MgF2/MoS2/sensing sample) is observed to exhibit the highest sensitivity of 372°/RIU, FOM of 1690 RIU-1, and detection accuracy of 4.54 degree-1 using the strong binding efficiency of the MoS2 layer and the high dielectric constant of the MgF2 layer. According to the investigation's findings, the proposed SPR-based biosensor exhibits excellent performance in the NIR region, demonstrating accurate real-time detection capabilities that will facilitate its use in field or clinical point-of-care testing applications.
Genetic and micromorphological differentiation within Sambacus ebulus (Adoxaceae) suggests divergence of populations from Iran
Authors: Bayrami Marzieh , Sattarian Ali , Salehi Mahmood , Amini Elham , Atazadeh Neda 
Published: October 2024

Abstract

Sambucus ebulus is mainly distributed in the northern, northwestern and northeastern regions of Iran and is characterized by its perennial growth habit and distinctive long, creeping and branched rhizomes. In this study, genetic diversity of seven populations S. ebulus based on molecular ISSR data and the micromorphology of seeds and leaves of this species in Iran were investigated. Micromorphological examination revealed the anomocytic type of stomata and indicated that the epidermal cells of various S. ebulus populations exhibited irregular cell shapes with anticlinal walls ranging from straight to curved. The seed shape was described as predominantly almond-shaped, and the surface of the seed coat of the studied taxa showed a reticulate pattern. The AMOVA (analysis of molecular variance) test showed that 87% of the total genetic variance was due to differences inter-populations genetic differences, while 13% was due to within-populations genetic variability, indicating a high degree of genetic variation among S. ebulus populations. The discriminating power of ISSR (inter simple sequence repeat) loci as determined by Gst against Nm (the number of migrants) analysis, showed that almost all ISSR loci have an excellent discriminating power. Thus, ISSR markers are efficient in differentiating of the studied S. ebulus populations. The Mantel test presented a significant correlation between genetic and geographic distance. These results suggest that the selected markers for genetic analysis represent different regions of the genome and effectively capture the genetic variation within the studied populations.
Barriers to the Adherence of ICU Nurses to the Tube Feeding Protocol: A Qualitative Study
Authors: Tabrizi Faranak Jabbarzadeh , Asghari Elnaz , Davoodi Arefeh 
Published: October 2024

Abstract

Background The heightened metabolic demands of critically ill patients on ventilators necessitate proper tube feeding for optimal recovery. Despite nurses being primarily responsible for administering tube feeding, evidence indicates a lack of adherence to evidence-based practices. This study aims to identify the barriers preventing ICU nurses from adhering to the tube feeding protocol. Methods This qualitative study utilized conventional content analysis. Participants included ICU nurses from Sina Hospital, Tabriz, Iran, in 2024. A combination of purposeful and snowball sampling was employed, achieving data saturation after 19 interviews. Data were collected through semi-structured interviews and analyzed using the Zhang & Wildemuth method. Results The analysis identified three primary barriers to adherence: the gap between theoretical knowledge and clinical practice, organizational and interpersonal challenges, and resistance to change. Conclusion The findings highlight that barriers to adherence are multifaceted, deeply rooted in organizational contexts. Policymakers and clinical educators can use these insights to develop targeted interventions. Future nurses can reflect on these findings to enhance their professional development and adjust protocols to bridge identified gaps. Additionally, organizational values and interventions for nursing staff should be revised to address these barriers effectively.
Ultrasonication-Enhanced Nanoencapsulation of Thymol and Cinnamaldehyde with Chitosan and Hydroxypropyl Methylcellulose: A Novel Approach to Improving Physicochemical Properties, Stability, and Bioactive Content
Authors: PHYO HSU MON , Al-Maqtari Qais Ali , Othman Norzila , Hussain Arif , Yuan Shaofeng , Yu Hang , Yao Weirong 
Published: October 2024

Abstract

This study presents a novel approach to enhancing the physicochemical properties, stability, and bioactive content of thymol and cinnamaldehyde-loaded nanocapsules (NCs) using chitosan (CH) and hydroxypropyl methylcellulose (H) as wall materials, optimized via ultrasonication at varying powers (200, 400, and 600 Watts). The results demonstrated that increasing ultrasonic power significantly improved the performance of NC-CH formulations. The NC-CH-400 formulation achieved optimal values in particle size (286.47 ± 19.11 nm), polydispersity index (0.24 ± 0.18), and ζ-potential (5.37 ± 0.24), while the NC-CH-600 formulation exhibited superior nanocapsule’s efficiency (97.8%), antioxidant activity (28.4%), antioxidant capacity (4.76 mg TE ml− 1), and other physical properties, including enhanced hygroscopicity, density, flowability, and porosity. Additionally, NC-CH-400 displayed the highest solubility (42.33%) and lowest water activity (0.45). Incorporating H with CH further improved nanocapsule’s yield (83.57%) and wettability (4.62 s) over CH alone. FTIR analysis confirmed successful nanocapsule without chemical modification, and the NC-CH-400 formulation showed the highest thermal stability, evidenced by the maximum glass transition temperature and melting points, suggesting superior storage durability. The nanocapsules also exhibited a smooth microstructure without surface cracking, and after 28 days, formulations treated with higher ultrasonic powers significantly enhanced the release of bioactive compounds, particularly in NC-CH. These findings underscore the potential of ultrasonication-enhanced nanocapsule for improving the stability and bioactive delivery of sensitive compounds, offering valuable applications in the food and pharmaceutical industries.
CircRNA-loaded DC vaccine in combination with low-dose gemcitabine induced potent anti-tumor immunity in pancreatic cancer model
Authors: Cai Zongyu , Wuri Qimuge , Song Yang , Qu Xueli , Hu Haotong , Cao Simiao , Wu Hui , Wu Jiaxin , Wang Chu , Yu Xianghui , Kong Wei , Zhang Haihong 
Published: October 2024

Abstract

Although promising, dendritic cell (DC) vaccines may not suffice to fully inhibit tumor progression alone, mainly due to the short expression time of the antigen in DC vaccines, immunosuppressive tumor microenvironment, and tumor antigenic modulation. Overcoming the limitations of DC vaccines is expected to further enhance their anti-tumor effects. In this study, we constructed a circRNA-loaded DC vaccine utilizing the inherent stability of circular RNA to enhance the expression level and duration of the antigen within the DC vaccine. Meanwhile we combined it with gemcitabine and validated their therapeutic efficacy in the Panc02 tumor model. We found that the use of DC vaccine alone can reach a tumor inhibition rate of 69%, and the effect was further enhanced when combined with gemcitabine, reaching a tumor inhibition rate of 89%. The combined treatment achieved a synergistic effect, which not only reduced immunosuppressive Tregs but also induced immunogenic cell death, leading to antigen spreading and reducing immune evasion caused by tumor antigenic modulation. As a result, the survival of the mice was significantly prolonged. Our research provides a promising approach for the clinical treatment of pancreatic cancer.
Effect of optoelectronic properties of vacancy defect in monolayer PtS 2 under strain: A first-principles study
Authors: Yang Hang , Yang Lu , Bao Jinlin , Liu Huaidong , Zhao Yanshen 
Published: October 2024

Abstract

In this paper, the optoelectronic properties of monolayer PtS2 under vacancy and strain are calculated based on density functional theory (DFT). Phonon spectrum verifies the stability of the model. Formation energy calculations show that the single S-atom defect system possesses lower energy and is easier to prepare experimentally. The single S-atom defect system is converted from an indirect bandgap to a direct bandgap, which is more favorable for electron transition. Under biaxial strain, the band gap of monolayer PtS2 decreases with increasing tensile strain and increases with increasing compressive strain. In addition, optical property calculations show that the initial absorption and reflection coefficients of the defect system gradually increase under tensile strain and decrease under compressive strain, and are located in the low-energy region where red-shift and blue-shift phenomena occur respectively. This paper reveals the modulation effect of strain on the electronic properties of monolayer PtS2 in the defect system, which is of great significance for the extension of material functionality and the optimization of device performance.
Genetic Analyses and Functional Validation of Ruminant SLAMs Reveal Potential Hosts for PPRV
Authors: Wei Xi , Lu Kejia , Chang Zhengwu , Guo Hanwei , Li Qinfeng , Yuan Binxuan , Liu Chen , Liu Haijin , Yang Zengqi 
Published: October 2024

Abstract

Peste des Petits Ruminants (PPR), caused by the Peste des Petits Ruminants virus (PPRV), is a highly contagious disease affecting ruminants. While goats and sheep are well-known hosts, PPRV has also spread to wild ruminants, and it remains unclear which ruminant species can be infected. SLAM (Signaling Lymphocytic Activation Molecule) acts as the primary receptor for PPRV, playing a crucial role in the viral infection process. Identifying which ruminant SLAMs can mediate PPRV infection is essential for understanding the potential hosts of PPRV, which is vital for effective eradication efforts. In this study, we first extracted SLAM sequences from 77 ruminant species using a ruminant genome database. Based on these sequences, we predicted the structures of ruminant SLAMs. The analysis revealed that SLAM conformation is similar across ruminant species, and the potential PPRV H protein binding domain residues were conserved among SLAMs of these 77 species. Phylogenetic analysis of SLAM grouped ruminants into six families. We then selected representative SLAMs from each ruminant family to assess their role in PPRV infection. Our findings demonstrated that ruminant SLAMs efficiently mediated PPRV infection, with enhanced viral amplification observed in cells expressing SLAM from Java Mouse Deer (Tragulidae) and Goat (Bovidae), compared to cells expressing SLAM from White Tailed Deer (Cervidae) and Giraffe (Giraffidae). These results underscore the need to consider a broader range of potential host populations beyond goat and sheep in efforts to prevent and eradicate PPRV.
Differential entropy as a measure of initial heterogeneity driving differentiation in the early mouse embryo
Authors: von Bonhorst Francisco Prista , Gandrillon Olivier , Chazaud Claire , Robert Corentin , De Decker Yannick , Gonze Didier , Dupont Geneviève 
Published: October 2024

Abstract

Background:
Heterogeneity in gene expression among single cells is critical for cell differentiation. In the preimplantation mammalian embryo, stochastic cell-to-cell expression heterogeneity is followed by signal reinforcement to initiate the differentiation of the Inner Cell Mass (ICM) cells into Epiblast (Epi) or Primitive Endoderm. A key question is to identify genes that initiate and drive coordination of pluripotency factors and specification of Epi cells alongside the key transcription factor NANOG.
Results:
To address this question, we fit single-cell expression data to gamma distributions and compute their inter-cellular differential entropy profile. Using five single-cell transcriptomic datasets (RT-qPCR and RNA-seq), we recover genes that are well-known to play a key role in Epi specification and identify candidate genes, whose coordinated heterogeneity in expression, alongside Nanog drives ICM cells differentiation. We show that other typical measures of variability, such as the Fano factor or the coefficient of variation, show a less robust temporal profile than differential inter-cellular entropy. Moreover, candidate genes would not have been identified with principal component and correlation analyses.
Conclusions:
The identified candidate genes, with a differential entropy time profile similar to that of Nanog, could play a crucial role in the differentiation of ICM cells. The estimation of cell-to-cell variability in gene expression based on inter-cellular differential entropy is robust among datasets and reveals insights that other standard methods such as principal component analysis and Fano factors do not. Differential entropy thus provides a useful quantity to assess gene regulation during early embryonic
development.
Measurements of buoyant plumes in a turbulent boundary layer
Authors: Pang Miaoyan , Chauhan Kapil , Talluru Krishna 
Published: October 2024

Abstract

This study presents a novel experimental setup designed to release a buoyant scalar plume and measure concentration and velocity simultaneously. Tracer gas is released from a point source in a low Reynolds number boundary layer ($Re_\tau \approx 1600$). The buoyant plume released consists of a mixture of varying proportions of tracer gas and a chemically stable base gas, resulting in density ratios relative to ambient air ($\rho_s/\rho_\infty$) of 1.48, 1, and 0.15. The concentration of the tracer gas (iso-butylene) is detected using a Photo-Ionisation Detector (PID) that ionises a small volume of the tracer gas within its chamber. Additionally, an $\times$-wire is employed to measure the streamwise and vertical components of velocity. Results of the mean and root-mean-square (RMS) concentration profiles for the positively and negatively buoyant plumes exhibit a Gaussian or reflected-Gaussian behaviour similar to a neutral plume, albeit with altered parameters such as the plume centreline that now vary with $\rho_s/\rho_\infty$. The data indicates that the half-width of the positively buoyant plume is wider than that of the neutral plume, and the spread of negatively buoyant plumes is thinner. Consequently, the maximum concentration of the negatively buoyant plume is the largest among the three $\rho_s/\rho_\infty$. Although power laws are fitted to describe the downstream evolution of plume spread and maximum mean and RMS values of concentration, the accuracy of the fit appears to be limited.
A Method to Identify Wildfire Ignition Points and Propagation Durations Using Genetic Algorithms
Authors: Hackett Conor , Moral Rafael de Andrade , Markham Charles 
Published: October 2024

Abstract

A critical research area regarding wildfire modelling that is often overlooked is the task of finding where a wildfire started and how long that wildfire burnt for. A review of the literature revealed that there are no automated methods for the detection of wildfire ignition points using wildfire burn scars. This paper describes a novel method called the WSGA (Wildfire Source Genetic Algorithm) to find the ignition points and the propagation time of a wildfire, given the environmental condition and the burn scar. The WSGA encodes a bitstring that corresponds to regions described by polygons within a wildfire simulating program called the IGS (Irregular Grid Software). In the bitstring, the bit value specifies whether that polygon contains a wildfire ignition point and is therefore a wildfire source polygon. The WSGA also generates a value representing the propagation time of the wildfire, called the simulation duration. Multiple bitstrings with simulation durations are generated. The WSGA uses these bitstrings and simulation durations to populate a genetic algorithm. The genetic algorithm compares the WSGA created wildfires seeded with the information in the bitstrings and the simulation durations to the original burn scar. The bitstring and simulation durations of the simulated wildfires that most closely resemble the original burn scar are then identified. These are then combined, and the process continues. This gradually generates a population of bitstrings and simulation durations that produce wildfires which more closely resemble the original burn scar. To evaluate the final outputted wildfires of the WSGA, a relative distance error was calculated by summing the Euclidian distances between source polygons produced by the WSGA and the source polygons of the original burn scar relative to the diameter of the original burn scar. Depending on the scenario the WSGA had a relative distance error in the range of [0, 1.25]. A relative simulation duration error was also calculated by finding the difference between the WSGA simulation duration and the original burn scar simulation duration, relative to the original burn scar simulation duration. Depending on the scenario the relative simulation duration error had a range of [0.0006, 0.49].
Associations of DNA methylation algorithms of aging with cardiovascular disease and mortality risk among US older adults
Authors: Li Xiangwei , Zhang Hui , Gong Yulu , Hao Darong , Yaqian Xu , Ding Chongyu , Wang Jing , Xian Cui , Sun Shiqun , An Tongyan , Du Jun 
Published: October 2024

Abstract

Recently, several DNA methylation (DNAm) algorithms have emerged as strong predictors of adverse health outcomes in older adults, offering insights into cardiovascular disease (CVD) risk stratification. Using data from the National Health and Nutrition Examination Survey (1999–2002), we assessed twelve DNAm algorithms (HannumAgeacc, PhenoAgeacc, GrimAgeMortacc, GrimAge2Mortacc, among others) in relation to CVD risk and mortality. The analysis included two subsets (n = 1,230 for CVD risk and n = 1,606 for CVD mortality). Significant associations were found between GrimAgeMortacc and GrimAge2Mortacc with coronary heart disease and heart attack risk. Additionally, HannumAgeacc, PhenoAgeacc, GrimAgeMortacc, and GrimAge2Mortacc showed significant associations with CVD mortality, with multivariable-adjusted hazard ratios per standard deviation increase of 1.15 (95% CI = 1.02–1.28), 1.15 (95% CI = 1.03–1.28), 1.72 (95% CI = 1.38–2.14), and 1.89 (95% CI = 1.52–2.29), respectively. DNAm algorithms, particularly GrimAgeMortacc and GrimAge2Mortacc, may serve as valuable tools for CVD risk stratification and mortality assessment.