bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein Signature Differentiating Neutrophils and Myeloid-Derived Suppressor Cells Determined Using a Human Isogenic Cell Line Model and Protein Profiling
Authors: Zhang Yuting , Hu Jin , Zhang Xiashiyao , Liang Minzhi , Wang Xuechun , Gan Dailin , Li Jun , Lu Xuemin , Wan Jun , Feng Shan , Lu Xin
Published: May 2024

Myeloid-derived suppressor cells (MDSCs) play an essential role in suppressing the antitumor activity of T lymphocytes in solid tumors, thus representing an attractive therapeutic target to enhance the efficacy of immunotherapy. However, the differences in protein expression between MDSCs and their physiological counterparts, particularly polymorphonuclear neutrophils (PMNs), remain inadequately characterized, making the specific identification and targeting of MDSCs difficult. PMNs and PMN-MDSCs share markers such as CD11b+CD14−CD15+/CD66b+, and some MDSC-enriched markers are emerging, such as LOX-1 and CD84. More proteomics studies are needed to identify the signature and markers for MDSCs. Recently, we reported the induced differentiation of isogenic PMNs or MDSCs (referred to as iPMNs and iMDSCs, respectively) from the human promyelocytic cell line HL60. Here, we profiled the global proteomics and membrane proteomics of these cells with quantitative mass spectrometry, which identified a 41-protein signature (“cluster 6”) that was upregulated in iMDSCs compared with HL60 and iPMN. We further integrated our cell line-based proteomics data with a published proteomics dataset of normal human primary monocytes and monocyte-derived MDSCs induced by cancer-associated fibroblasts. The analysis identified a 38-protein signature that exhibits an upregulated expression pattern in MDSCs compared with normal monocytes or PMNs. These signatures may provide a hypothesis-generating platform to identify protein biomarkers that phenotypically distinguish MDSCs from their healthy counterparts, as well as potential therapeutic targets that impair MDSCs without harming normal myeloid cells.
An Accurate Representation of the Number of bZIP Transcription Factors in the Triticum aestivum (Wheat) Genome and the Regulation of Functional Genes during Salt Stress
Authors: Liu Xin , Sukumaran Selvakumar , Viitanen Esteri , Naik Nupur , Hassan Sameer , Aronsson Henrik
Published: May 2024

Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many areas. A solution to this problem is increasing the salt tolerance of crop plants. Transcription factors (TFs) within crop plants represent a key to understanding salt tolerance, as these proteins play important roles in the regulation of functional genes linked to salt stress. The basic leucine zipper (bZIP) TF has a well-documented role in the regulation of salt tolerance. To better understand how bZIP TFs are linked to salt tolerance, we performed a genome-wide analysis in wheat using the Chinese spring wheat genome, which has been assembled by the International Wheat Genome Sequencing Consortium. We identified 89 additional bZIP gene sequences, which brings the total of bZIP gene sequences in wheat to 237. The majority of these 237 sequences included a single bZIP protein domain; however, different combinations of five other domains also exist. The bZIP proteins are divided into ten subfamily groups. Using an in silico analysis, we identified five bZIP genes (ABF2, ABF4, ABI5, EMBP1, and VIP1) that were involved in regulating salt stress. By scrutinizing the binding properties to the 2000 bp upstream region, we identified putative functional genes under the regulation of these TFs. Expression analyses of plant tissue that had been treated with or without 100 mM NaCl revealed variable patterns between the TFs and functional genes. For example, an increased expression of ABF4 was correlated with an increased expression of the corresponding functional genes in both root and shoot tissues, whereas VIP1 downregulation in root tissues strongly decreased the expression of two functional genes. Identifying strategies to sustain the expression of the functional genes described in this study could enhance wheat’s salt tolerance.
Structural, Dielectric, Electrical, and Magnetic Characteristics of Bi0.8Ba0.1Er0.1Fe0.96Cr0.02Mn0.02O3 Nanoparticles
Authors: Bougoffa A. , Benali E. M. , Benali A. , Tozri A. , Dhahri E. , Graça M. P. , Valente M. A. , Costa B. F. O.
Published: May 2024

Bi0.8Ba0.1Er0.1Fe0.96Cr0.02Mn0.02O3 (BBEFCMO) multiferroic ceramic was synthesized through the sol-gel route. The impact of incorporating various dopants into both A and B sites of the BiFeO3 was investigated, and structural, Raman, dielectric, electric, and magnetic properties were studied. X-ray diffraction analysis and Raman spectroscopy revealed a rhombohedral structure with the R3c space group for the doped material (BBEFCMO). Dielectric properties were examined across a frequency range of 102–106 Hz. The present multiferroic material exhibits a colossal dielectric constant and minimal dielectric loss tangent, making it suitable for applications in energy storage. Furthermore, the Cole-Cole type of relaxation was deduced from the imaginary part of the modulus for both grain and boundary-grain contributions. Overall, this study indicates that substituting ions in both A and B sites of BiFeO3 significantly enhances its multiferroic properties, as evidenced by dielectric and magnetic measurements.
Preclinical Testing of Chronic ICA-1S Exposure: A Potent Protein Kinase C-ι Inhibitor as a Potential Carcinoma Therapeutic
Authors: Apostolatos Christopher A. , Ratnayake Wishrawana S. , Breedy Sloan , Chuah Jacqueline Kai Chin , Miller James Alastair , Zink Daniele , Bourgeois Marie , Acevedo-Duncan Mildred
Published: May 2024

Protein kinase C-iota (PKC-ι) is an oncogene overexpressed in many cancer cells including prostate, breast, ovarian, melanoma, and glioma cells. Previous in vitro studies have shown that 5-amino-1-((1R,2S,3R,4R)-2-3-dihydroxy-4-(hydroxymethyl)cyclopentyl)-1H-imidazole-4-carboxamide (ICA-1S), a PKC-ι-specific inhibitor, has low toxicity in both acute and sub-acute mouse model toxicological testing and is an effective therapeutic against several cancer cell lines showing significant reductions in tumor growth when treating athymic nude mice with xenografted carcinoma cell lines. To further assess ICA-1S as a possible therapeutic agent, chronic mouse model toxicological testing was performed in vivo to provide inferences concerning the long-term effects and possible health hazards from repeated exposure over a substantial part of the animal’s lifespan. Subjects survived well after 30, 60, and 90 days of doses ranging from 50 mg/kg to 100 mg/kg. Heart, liver, kidney, and brain tissues were then analyzed for accumulations of ICA-1S including the measured assessment of aspartate transaminase (AST), alkaline phosphatase (ALK-P), gamma-glutamyl transferase (GGT), troponin, and C-reactive protein (CRP) serum levels to assess organ function. Predictive in vitro/in silico methods were used to predict compound-induced direct hepatocyte toxicity or renal proximal tubular cell (PTC) toxicity in humans based on the high-content imaging (HCI) of compound-treated cells in combination with phenotypic profiling. In conclusion, ICA-1S shows low toxicity in both acute and chronic toxicology studies, and shows promise as a potential therapeutic.
Essential Oil of Psidium glaziovianum Kiaersk Alleviates the Effects of Complete Freund’s Adjuvant (CFA)-Induced Arthritis by Regulating Inflammation and Oxidative Stress
Authors: Costa Wêndeo Kennedy , Alves João Victor de Oliveira , Fonseca Beatriz Meyruze Barros Da , Silva Valquíria Bruna Guimarães , Ferreira Rafael Jardim , Napoleão Thiago Henrique , Paiva Patrícia Maria Guedes , Correia Maria Tereza dos Santos , Oliveira Alisson Macário de , Silva Márcia Vanusa da
Published: May 2024

Rheumatoid arthritis (RA) is a chronic and debilitating condition that affects a significant number of individuals worldwide. Unfortunately, the currently available therapeutic approaches often yield unsatisfactory results and may be accompanied by harmful side effects. A medicinal plant called Psidium glaziovianum Kiaersk has potential benefits in the treatment of this condition due to its anti-inflammatory and analgesic properties. In this study, our objective was to investigate the potential therapeutic effects of P. glaziovianum essential oil (PgEO) in alleviating arthritis symptoms in mice induced by Complete Freund’s Adjuvant (CFA). The effect of P. glaziovianum essential oil was evaluated in mice with Complete Freund’s Adjuvant (CFA)-induced arthritis. Edema sizes, macroscopic and radiographic images, cytokine levels, and oxidative stress were evaluated. Administration of PgEO at dosages of 50 and 100 mg/kg effectively prevented CFA-induced osteoarticular changes in arthritic mice, resulting in a significant reduction in joint damage. Additionally, the PgEO treatment exhibited the ability to minimize edema, a common symptom associated with arthritis. Furthermore, PgEO can modulate the levels of pro-inflammatory cytokines and oxidative stress, both of which play crucial roles in the progression of the disease. In conclusion, our study suggests that PgEO holds great potential as a natural therapeutic agent for rheumatoid arthritis.
Characteristics of RNA Stabilizer RNApro for Peripheral Blood Collection
Authors: Gambarino Stefano , Galliano Ilaria , Clemente Anna , Calvi Cristina , Montanari Paola , Pau Anna , Dini Maddalena , Bergallo Massimiliano
Published: May 2024

Peripheral blood is the most practical tissue for human immune system gene expression profiling because it is easily accessible, whereas the site of primary infection in certain diseases may not be easily accessible. Due to the ex vivo instability of RNA transcripts, a key challenge in the gene expression analysis of blood samples is the rapid sample handling and stabilization of the mRNA by adding an RNA preservative (PAXgeneTM Blood RNA Tubes, TempusTM Blood RNA tubes, RNAlater Stabilization Reagent, RNAgard® Blood Tubes). BioMole (Turin, Italy) has developed a novel blood stabilizer, called RNApro, in which RNA is stabilized during phlebotomy and sample storage. In this study, RNApro performance intended as RNA yield, integrity, and stability was evaluated. Our results show that blood samples stored at −80 °C and re-extracted after 7 years show no differences in terms of quantity, quality, and amplificability. The samples in the RNAlater stabilization solution can be stored at room temperature for up to one week or at 4 °C for up to one month. Similar results can also be observed for PAXgene tubes, Tempus tubes, and RNAgard tubes. In agreement with these data, the RNApro stabilization solution preserves the RNA from degradation for up to 1 month at 4 °C and 1 week at room temperature. RNApro can be stored indifferently at −80, −20, 4 °C, or room temperature for up to 2 months after, and then could be stored at −80 °C for up to seven years. In summary, our study is the first to analyze the performance of an RNA stabilizer called RNApro. We can conclude that several studies have shown significant differences in gene expression analysis when the sample was preserved in different RNA stabilizers. Therefore, it is desirable to standardize the method of nucleic acid conservation when comparing data from transcriptomic analyses.
Relativistic Roots of κ-Entropy
Authors: Kaniadakis Giorgio
Published: May 2024

The axiomatic structure of the κ-statistcal theory is proven. In addition to the first three standard Khinchin–Shannon axioms of continuity, maximality, and expansibility, two further axioms are identified, namely the self-duality axiom and the scaling axiom. It is shown that both the κ-entropy and its special limiting case, the classical Boltzmann–Gibbs–Shannon entropy, follow unambiguously from the above new set of five axioms. It has been emphasized that the statistical theory that can be built from κ-entropy has a validity that goes beyond physics and can be used to treat physical, natural, or artificial complex systems. The physical origin of the self-duality and scaling axioms has been investigated and traced back to the first principles of relativistic physics, i.e., the Galileo relativity principle and the Einstein principle of the constancy of the speed of light. It has been shown that the κ-formalism, which emerges from the κ-entropy, can treat both simple (few-body) and complex (statistical) systems in a unified way. Relativistic statistical mechanics based on κ-entropy is shown that preserves the main features of classical statistical mechanics (kinetic theory, molecular chaos hypothesis, maximum entropy principle, thermodynamic stability, H-theorem, and Lesche stability). The answers that the κ-statistical theory gives to the more-than-a-century-old open problems of relativistic physics, such as how thermodynamic quantities like temperature and entropy vary with the speed of the reference frame, have been emphasized.
Constraints and Opportunities of Agricultural Development in Haor Ecosystem of Bangladesh
Authors: Bokhtiar Shaikh Mohammad , Islam Md. Jahirul , Samsuzzaman Syed , Jahiruddin Mohammad , Panaullah Golam Mohammad , Salam Md. Abdus , Hossain Mohammad Anwar
Published: May 2024

The Haors in Bangladesh are saucer-shaped, low-lying land depressions that form deep basins; they remain submerged for approximately half of the year, typically from June onwards. This fragile ecosystem spans over 2.0 million hectares in the northeastern region of the country, accounting for roughly 14% of the total areas, where approximately 19.4 million people reside. Factors including floods, flash floods, and low winter temperatures constrain agricultural productivity in the haor areas. It is a great challenge to change the haor areas from less productive to more productive land. This is a comprehensive analysis of the biophysical and socioeconomic characteristics of haors which also highlights the constraints and opportunities in agricultural production. It explores strategies for significantly increasing crop, livestock, and fish production within the haor ecosystem, in alignment with government policies. Some of the proposed agricultural development strategies for the haor areas include the development of short-duration, cold-tolerant crop varieties, such as Boro rice, utilizing relatively flood-free elevated lands and homesteads for vegetable production and promoting agricultural mechanization, livestock rearing, fisheries, and agribusiness development. The recommendations presented in this paper focus on enhancing crop yields, increasing cropping intensity, and boosting livestock and fish production; ultimately, they contribute to food security, poverty reduction, and improved livelihoods for the inhabitants of the haor areas.
Effect of Boxing Exercises on the Functional Ability and Quality of Life of Individuals with Parkinson’s Disease: A Systematic Review
Authors: Chrysagis Nikolaos , Trompouki Georgia , Petropaulis Dimitris , Koumantakis George A. , Krekoukias Georgios , Theotokatos Georgios , Skordilis Emmanouil , Sakellari Vasiliki
Published: May 2024

Parkinson’s disease (PD) is a neurological disorder caused by the loss of dopamine-producing cells in the substantia nigra and characterized by motor and non-motor symptoms. Boxing is a type of complementary therapy to improve symptoms in PD. The purpose of the present study was to examine the effect of boxing training on the functionality and quality of life of patients with PD. The literature search was performed on PubMed, Scopus, PEDro, Cochrane Library, and Google Scholar search engines. The PEDro scale was used to assess the methodological quality of the studies. This systematic review included three studies that examined disease severity, mobility, physical activity, balance, and quality of life. According to the PEDro scale criteria, the three articles included were of high methodological quality. Statistically significant improvements after the implementation of boxing training was shown for balance and quality of life in contrast to the other variables. Boxing training intervention programs had a positive effect on balance and quality of life in patients with PD; however, the results are conflicting regarding certain functionality variables. Therefore, it is necessary to conduct further research to examine the effectiveness of boxing training on the functionality and quality of life of patients with Parkinson’s disease.
Correction: Miletić et al. Quantifying Forest Cover Loss as a Response to Drought and Dieback of Norway Spruce and Evaluating Sensitivity of Various Vegetation Indices Using Remote Sensing. Forests 2024, 15, 662
Authors: Miletić Boban R. , Matović Bratislav , Orlović Saša , Gutalj Marko , Đorem Todor , Marinković Goran , Simović Srđan , Dugalić Mirko , Stojanović Dejan B.
Published: May 2024

In the original publication [...]
AI-Empowered Multimodal Hierarchical Graph-Based Learning for Situation Awareness on Enhancing Disaster Responses
Authors: Chen Jieli , Seng Kah Phooi , Ang Li Minn , Smith Jeremy , Xu Hanyue
Published: May 2024

Situational awareness (SA) is crucial in disaster response, enhancing the understanding of the environment. Social media, with its extensive user base, offers valuable real-time information for such scenarios. Although SA systems excel in extracting disaster-related details from user-generated content, a common limitation in prior approaches is their emphasis on single-modal extraction rather than embracing multi-modalities. This paper proposed a multimodal hierarchical graph-based situational awareness (MHGSA) system for comprehensive disaster event classification. Specifically, the proposed multimodal hierarchical graph contains nodes representing different disaster events and the features of the event nodes are extracted from the corresponding images and acoustic features. The proposed feature extraction modules with multi-branches for vision and audio features provide hierarchical node features for disaster events of different granularities, aiming to build a coarse-granularity classification task to constrain the model and enhance fine-granularity classification. The relationships between different disaster events in multi-modalities are learned by graph convolutional neural networks to enhance the system’s ability to recognize disaster events, thus enabling the system to fuse complex features of vision and audio. Experimental results illustrate the effectiveness of the proposed visual and audio feature extraction modules in single-modal scenarios. Furthermore, the MHGSA successfully fuses visual and audio features, yielding promising results in disaster event classification tasks.
BPET: A Unified Blockchain-Based Framework for Peer-to-Peer Energy Trading
Authors: Fan Caixiang , Khazaei Hamzeh , Musilek Petr
Published: May 2024

Recent years have witnessed a significant dispersion of renewable energy and the emergence of blockchain-enabled transactive energy systems. These systems facilitate direct energy trading among participants, cutting transmission losses, improving energy efficiency, and fostering renewable energy adoption. However, developing such a system is usually challenging and time-consuming due to the diversity of energy markets. The lack of a market-agnostic design hampers the widespread adoption of blockchain-based peer-to-peer energy trading globally. In this paper, we propose and develop a novel unified blockchain-based peer-to-peer energy trading framework, called BPET. This framework incorporates microservices and blockchain as the infrastructures and adopts a highly modular smart contract design so that developers can easily extend it by plugging in localized energy market rules and rapidly developing a customized blockchain-based peer-to-peer energy trading system. Additionally, we have developed the price formation mechanisms, e.g., the system marginal price calculation algorithm and the pool price calculation algorithm, to demonstrate the extensibility of the BPET framework. To validate the proposed solution, we have conducted a comprehensive case study using real trading data from the Alberta Electric System Operator. The experimental results confirm the system’s capability of processing energy trading transactions efficiently and effectively within the Alberta electricity wholesale market.
Current Status of Research on Wildland Fire Impacts on Soil Environment and Soil Organisms and Hotspots Visualization Analysis
Authors: Cheng Zhichao , Wu Song , Wei Dan , Pan Hong , Fu Xiaoyu , Lu Xinming , Yang Libin
Published: May 2024

Ecosystems are frequently disturbed by fires that have an important impact on the soil environment and the composition of soil organisms. In order to provide a baseline for the current research and identify trends on the effects of wildland fire on soil environment and biological changes, the available literature was identified from the Web of Science database, covering the period from 1998/1998/1999 (the year of the earliest publication in this field) to 2023. A bibliometric analysis was performed and the data were visually displayed for the number of publications, countries, authors, research institutions, and keywords representing research hotspots. Specifically, the effects of wildland fire on the soil environment, on soil microorganisms and on soil fauna were analyzed. The results show that the annual number of publications describing effects of wildland fire on the soil environment and on soil microorganisms are increasing over time, while those describing effects on soil fauna are fewer and their number remains constant. The largest number of papers originate from the United States, with the United States Department of Agriculture as the research institution with the largest output. The three authors with the largest number of publications are Stefan H. Doerr, Manuel Esteban Lucas-Borja and Jan Jacob Keizer. The research hotspots, as identified by keywords, are highly concentrated on wildfire, fire, organic matter, and biodiversity, amongst others. This study comprehensively analyzes the current situation of the research on the effects of wildland fire on changes in the soil environment and organisms, and provides reference for relevant scientific researchers in this trend and future research hotspots.
A Numerical Study on the Influence of Riparian Vegetation Patch on the Transportation of Suspended Sediment in a U-Bend Channel Flow
Authors: Wang Mingyang , Yu Qian , Xu Yuan , Li Na , Wang Jing , Cao Bo , Wang Lu , Avital Eldad J.
Published: May 2024

Bend sections are ubiquitous in natural sandy river systems. This study employs Computational Fluid Dynamics–Discrete Phase Model (CFD-DPM) methodology to analyze particle transport dynamics in U-bend channel flows, focusing on the distinctions between partially vegetated (Case No.1) and non-vegetated (Case No.2) scenarios. The research aims to unravel the intricate relationships among bending channel-induced secondary flow, vegetation blockage, and particle aggregation, employing both quantitative and qualitative approaches. (I) The key findings reveal that vegetation near the inner walls of curved channels markedly diminishes the intensity of secondary circulation. This reduction in circulation intensity is observed not only within vegetated areas but also extends to adjacent non-vegetated zones. Additionally, the study identifies a close correlation between vertical vortices and particle distribution near the channel bed. While particle distribution generally aligns with the vortices’ margin, dynamic patch-scale eddies near vegetation patches induce deviations, creating wave-like patterns in particle distribution. (II) The application of the Probability Density Function (PDF) provides insights into the radius-wise particle distribution. In non-vegetated channels, particle distribution is primarily influenced by secondary flow and boundary layers. In contrast, the presence of vegetation leads to a complex mixing layer, altering the particle distribution pattern and maximizing PDF values in non-vegetated free flow subzones. (III) Furthermore, the research quantifies spatial–temporal sediment heterogeneity through PDF variance. The findings demonstrate that variance in non-vegetated channels increases towards the outer wall in bending regions. Vegetation-induced turbulence causes higher variance, particularly in the mixing layer subzone, underscoring the significance of eddy size in sediment redistribution. (IV) The study of vertical concentration profiles in vegetated U-bend channels offers additional insights, while secondary flow in non-vegetated channels facilitates upward sediment transport and vegetation presence, although increasing the Turbulent Kinetic Energy (TKE), restricts channel space, and impedes secondary flow, thereby reducing vertical particle suspension. Sediment concentrations are found to be higher in the lower layers of vegetated bends, contrary to the pattern in non-vegetated bends. These findings highlight the complex interplay between vegetation, secondary flow, and sediment transport, illustrating the reduced effectiveness of secondary flow in promoting vertical particle transportation in bending channels due to the vegetation obstruction.
Adaptive Neural Control for a Class of Random Fractional-Order Multi-Agent Systems with Markov Jump Parameters and Full State Constraints
Authors: Yao Yuhang , Yuan Jiaxin , Chen Tao , Zhang Chen , Yang Hui
Published: May 2024

Based on an adaptive neural control scheme, this paper investigates the consensus problem of random Markov jump multi-agent systems with full state constraints. Each agent is described by the fractional-order random nonlinear uncertain system driven by random differential equations, where the random noise is the second-order stationary stochastic process. First, in order to deal with the unknown functions with Markov jump parameters, a radial basis function neural network (RBFNN) structure is introduced to achieve approximation. Second, for the purpose of keeping the agents’ states from violating the constraint boundary, the tan-type barrier Lyapunov function is employed. By using the stochastic stability theory and adopting the backstepping technique, a novel adaptive neural control design method is presented. Furthermore, to cope with the differential explosion problem in the design course, the extended state observer (ESO) is developed instead of neural network (NN) approximation or command filtering techniques. Finally, the exponentially noise-to-state stability in the mean square is analyzed rigorously by the Lyapunov method, which guarantees the consensus of the considered multi-agent systems and all the agents’ outputs are bounded in probability. Two simulation examples are provided to verify the effectiveness of the suggested control strategy.
The Optimal Branch Width Convergence Ratio to Maximize the Transport Efficiency of the Combined Electroosmotic and Pressure-Driven Flow within a Fractal Tree-like Convergent Microchannel
Authors: Jing Dalei , Qi Peng
Published: May 2024

Building upon the efficient transport capabilities observed in the fractal tree-like convergent structures found in nature, this paper numerically studies the transport process of the combined electroosmotic and pressure-driven flow within a fractal tree-like convergent microchannel (FTCMC) with uniform channel height. The present work finds that the flow rate of the combined flow first increases and then decreases with the increasing branch width convergence ratio under the fixed voltage difference and pressure gradient along the FTCMC, which means that there is an optimal branch width convergence ratio to maximize the transport efficiency of the combined flow within the FTCMC. The value of the optimal branch convergence ratio is highly dependent on the ratio of the voltage difference and pressure gradient to drive the combined flow. By adjusting the structural and dimensional parameters of the FTCMC, the dependencies of the optimal branch convergence ratio of the FTCMC on the branching level convergence ratio, the length ratio, the branching number, and the branching level are also investigated. The findings in the present work can be used for the optimization of FTCMC with high transport efficiency for combined electroosmotic and pressure-driven flow.
Genetic Analysis of the ts-Lethal Mutant Δpa0665/pTS-pa0665 Reveals Its Role in Cell Morphology and Oxidative Phosphorylation in Pseudomonas aeruginosa
Authors: Zhu Jiayin , Zhao Hulin , Yang Zhili
Published: May 2024

Pa0665 in Pseudomonas aeruginosa shares homologous sequences with that of the essential A-type iron–sulfur (Fe-S) cluster insertion protein ErpA in Escherichia coli. However, its essentiality in P. aeruginosa and its complementation with E. coli erpA has not been experimentally examined. To fulfill this task, we constructed plasmid-based ts-mutant Δpa0665/pTS-pa0665 using a three-step protocol. The mutant displayed growth defects at 42 °C, which were complemented by expressing ec.erpA. Microscopic observations indicated a petite cell phenotype for Δpa0665/pTS-pa0665 at 42 °C, correlated with the downregulation of the oprG gene. RNA sequencing revealed significant transcriptional changes in genes associated with the oxidative phosphorylation (OXPHOS) system, aligning with reduced ATP levels in Δpa0665/pTS-pa0665 under 42 °C. Additionally, the ts-mutant showed heightened sensitivity to H2O2 at 42 °C. Overall, our study demonstrates the essential role of pa0665 for OXPHOS function and is complemented by ec.erpA. We propose that the plasmid-based ts-allele is useful for genetic analysis of essential genes of interest in P. aeruginosa.
The Association between Mutational Signatures and Clinical Outcomes among Patients with Early-Onset Breast Cancer
Authors: Basmadjian Robert B. , O’Sullivan Dylan E. , Quan May Lynn , Lupichuk Sasha , Xu Yuan , Cheung Winson Y. , Brenner Darren R.
Published: May 2024

Early-onset breast cancer (EoBC), defined by a diagnosis <40 years of age, is associated with poor prognosis. This study investigated the mutational landscape of non-metastatic EoBC and the prognostic relevance of mutational signatures using 100 tumour samples from Alberta, Canada. The MutationalPatterns package in R/Bioconductor was used to extract de novo single-base substitution (SBS) and insertion–deletion (indel) mutational signatures and to fit COSMIC SBS and indel signatures. We assessed associations between these signatures and clinical characteristics of disease, in addition to recurrence-free (RFS) and overall survival (OS). Five SBS and two indel signatures were extracted. The SBS13-like signature had higher relative contributions in the HER2-enriched subtype. Patients with higher than median contribution tended to have better RFS after adjustment for other prognostic factors (HR = 0.29; 95% CI: 0.08–1.06). An unsupervised clustering algorithm based on absolute contribution revealed three clusters of fitted COSMIC SBS signatures, but cluster membership was not associated with clinical variables or survival outcomes. The results of this exploratory study reveal various SBS and indel signatures may be associated with clinical features of disease and prognosis. Future studies with larger samples are required to better understand the mechanistic underpinnings of disease progression and treatment response in EoBC.
Predictive Modelling of Postpartum Haemorrhage Using Early Risk Factors: A Comparative Analysis of Statistical and Machine Learning Models
Authors: Holcroft Shannon , Karangwa Innocent , Little Francesca , Behoor Joelle , Bazirete Oliva
Published: May 2024

Postpartum haemorrhage (PPH) is a significant cause of maternal morbidity and mortality worldwide, particularly in low-resource settings. This study aimed to develop a predictive model for PPH using early risk factors and rank their importance in terms of predictive ability. The dataset was obtained from an observational case–control study in northern Rwanda. Various statistical models and machine learning techniques were evaluated, including logistic regression, logistic regression with elastic-net regularisation, Random Forests, Extremely Randomised Trees, and gradient-boosted trees with XGBoost. The Random Forest model, with an average sensitivity of 80.7%, specificity of 71.3%, and a misclassification rate of 12.19%, outperformed the other models, demonstrating its potential as a reliable tool for predicting PPH. The important predictors identified in this study were haemoglobin level during labour and maternal age. However, there were differences in PPH risk factor importance in different data partitions, highlighting the need for further investigation. These findings contribute to understanding PPH risk factors, highlight the importance of considering different data partitions and implementing cross-validation in predictive modelling, and emphasise the value of identifying the appropriate prediction model for the application. Effective PPH prediction models are essential for improving maternal health outcomes on a global scale. This study provides valuable insights for healthcare providers to develop predictive models for PPH to identify high-risk women and implement targeted interventions.
An Adaptive Simplification Method for Coastlines Using a Skeleton Line “Bridge” Double Direction Buffering Algorithm
Authors: Tang Lulu , Zhang Lihua , Dong Jian , Wei Hongcheng , Wei Shuai
Published: May 2024

Aiming at the problem that the current double direction buffering algorithm is easy to use to seal the “bottleneck” area when simplifying coastlines, an adaptive simplification method for coastlines using a skeleton line “bridge” double direction buffering algorithm is proposed. Firstly, from the perspective of visual constraints, the relationship between the buffer distance and the coastline line width and the minimum recognition distance of the human eye is theoretically derived and determined. Then, based on the construction of the coastline skeleton binary tree, the “bridge” skeleton line is extracted using the “source tracing” algorithm. Finally, the shoreline adaptive simplification is realized by constructing a visual buffer of “bridge” skeleton lines to bridge the original resulting coastline and the local details. The experimental results show that the proposed method can effectively solve the problem that the current double direction buffering algorithm has, which can significantly improve the quality of simplification.
A Multi-Feature Fusion Method for Urban Functional Regions Identification: A Case Study of Xi’an, China
Authors: Wang Zhuo , Bai Jianjun , Feng Ruitao
Published: May 2024

Research on the identification of urban functional regions is of great significance for the understanding of urban structure, spatial planning, resource allocation, and promoting sustainable urban development. However, achieving high-precision urban functional region recognition has always been a research challenge in this field. For this purpose, this paper proposes an urban functional region identification method called ASOE (activity–scene–object–economy), which integrates the features from multi-source data to perceive the spatial differentiation of urban human and geographic elements. First, we utilize VGG16 (Visual Geometry Group 16) to extract high-level semantic features from the remote sensing images with 1.2 m spatial resolution. Then, using scraped building footprints, we extract building object features such as area, perimeter, and structural ratios. Socioeconomic features and population activity features are extracted from Point of Interest (POI) and Weibo data, respectively. Finally, integrating the aforementioned features and using the Random Forest method for classification, the identification results of urban functional regions in the main urban area of Xi’an are obtained. After comparing with the actual land use map, our method achieves an identification accuracy of 91.74%, which is higher than other comparative methods, making it effectively identify four typical urban functional regions in the main urban area of Xi’an (e.g., residential regions, industrial regions, commercial regions, and public regions). The research indicates that the method of fusing multi-source data can fully leverage the advantages of big data, achieving high-precision identification of urban functional regions.
RETRACTED: Serebrovska et al. Intermittent Hypoxia-Hyperoxia Training Improves Cognitive Function and Decreases Circulating Biomarkers of Alzheimer’s Disease in Patients with Mild Cognitive Impairment: A Pilot Study. Int. J. Mol. Sci. 2019, 20, 5405
Authors: Serebrovska Zoya O. , Serebrovska Tetiana V. , Kholin Viktor A. , Tumanovska Lesya V. , Shysh Angela M. , Pashevin Denis A. , Goncharov Sergii V. , Stroy Dmytro , Grib Oksana N. , Shatylo Valeriy B. , Bachinskaya Natalia Yu. , Egorov Egor , Xi Lei , Dosenko Victor E.
Published: May 2024

The journal Int [...]
Special Issue “Recent Process Design and Development Strategies for Dental Materials”
Authors: Melo Mary Anne S.
Published: May 2024

The field of dental materials is rapidly evolving, and this Special Issue of the International Journal of Molecular Sciences offers a comprehensive examination of the latest advancements in process design and development strategies [...]
The Role of microRNA in the Regulation of Cortisol Metabolism in the Adipose Tissue in the Course of Obesity
Authors: Podraza Jakub , Gutowska Klaudia , Lenartowicz Anna , Wąsowski Michał , Jonas Marta Izabela , Bartoszewicz Zbigniew , Lisik Wojciech , Jonas Maurycy , Binda Artur , Jaworski Paweł , Tarnowski Wiesław , Noszczyk Bartłomiej , Puzianowska-Kuźnicka Monika , Kuryłowicz Alina
Published: May 2024

The similarity of the clinical picture of metabolic syndrome and hypercortisolemia supports the hypothesis that obesity may be associated with impaired expression of genes related to cortisol action and metabolism in adipose tissue. The expression of genes encoding the glucocorticoid receptor alpha (GR), cortisol metabolizing enzymes (HSD11B1, HSD11B2, H6PDH), and adipokines, as well as selected microRNAs, was measured by real-time PCR in adipose tissue from 75 patients with obesity, 19 patients following metabolic surgery, and 25 normal-weight subjects. Cortisol levels were analyzed by LC-MS/MS in 30 pairs of tissues. The mRNA levels of all genes studied were significantly (p < 0.05) decreased in the visceral adipose tissue (VAT) of patients with obesity and normalized by weight loss. In the subcutaneous adipose tissue (SAT), GR and HSD11B2 were affected by this phenomenon. Negative correlations were observed between the mRNA levels of the investigated genes and selected miRNAs (hsa-miR-142-3p, hsa-miR-561, and hsa-miR-579). However, the observed changes did not translate into differences in tissue cortisol concentrations, although levels of this hormone in the SAT of patients with obesity correlated negatively with mRNA levels for adiponectin. In conclusion, although the expression of genes related to cortisol action and metabolism in adipose tissue is altered in obesity and miRNAs may be involved in this process, these changes do not affect tissue cortisol concentrations.
A New Approach in Lipase-Octyl-Agarose Biocatalysis of 2-Arylpropionic Acid Derivatives
Authors: Siódmiak Joanna , Dulęba Jacek , Kocot Natalia , Mastalerz Rafał , Haraldsson Gudmundur G. , Marszałł Michał Piotr , Siódmiak Tomasz
Published: May 2024

The use of lipase immobilized on an octyl-agarose support to obtain the optically pure enantiomers of chiral drugs in reactions carried out in organic solvents is a great challenge for chemical and pharmaceutical sciences. Therefore, it is extremely important to develop optimal procedures to achieve a high enantioselectivity of the biocatalysts in the organic medium. Our paper describes a new approach to biocatalysis performed in an organic solvent with the use of CALB-octyl-agarose support including the application of a polypropylene reactor, an appropriate buffer for immobilization (Tris base—pH 9, 100 mM), a drying step, and then the storage of immobilized lipases in a climatic chamber or a refrigerator. An immobilized lipase B from Candida antarctica (CALB) was used in the kinetic resolution of (R,S)-flurbiprofen by enantioselective esterification with methanol, reaching a high enantiomeric excess (eep = 89.6 ± 2.0%). As part of the immobilization optimization, the influence of different buffers was investigated. The effect of the reactor material and the reaction medium on the lipase activity was also studied. Moreover, the stability of the immobilized lipases: lipase from Candida rugosa (CRL) and CALB during storage in various temperature and humidity conditions (climatic chamber and refrigerator) was tested. The application of the immobilized CALB in a polypropylene reactor allowed for receiving over 9-fold higher conversion values compared to the results achieved when conducting the reaction in a glass reactor, as well as approximately 30-fold higher conversion values in comparison with free lipase. The good stability of the CALB-octyl-agarose support was demonstrated. After 7 days of storage in a climatic chamber or refrigerator (with protection from humidity) approximately 60% higher conversion values were obtained compared to the results observed for the immobilized form that had not been stored. The new approach involving the application of the CALB-octyl-agarose support for reactions performed in organic solvents indicates a significant role of the polymer reactor material being used in achieving high catalytic activity.
Design and Synthesis of Biomedical Polymer Materials
Authors: Chen Jie
Published: May 2024

Due to their biocompatibility and non-toxic nature, biomedical polymer materials have found widespread applications and significantly propelled the progress of the biomedical field [...]
Synthesis, In Silico Study, and In Vitro Antifungal Activity of New 5-(1,3-Diphenyl-1H-Pyrazol-4-yl)-4-Tosyl-4,5-Dihydrooxazoles
Authors: Tlapale-Lara Neively , López Julio , Gómez Elizabeth , Villa-Tanaca Lourdes , Barrera Edson , Escalante Carlos H. , Tamariz Joaquín , Delgado Francisco , Andrade-Pavón Dulce , Gómez-García Omar
Published: May 2024

The increase in multi-drug resistant Candida strains has caused a sharp rise in life-threatening fungal infections in immunosuppressed patients, including those with SARS-CoV-2. Novel antifungal drugs are needed to combat multi-drug-resistant yeasts. This study aimed to synthesize a new series of 2-oxazolines and evaluate the ligands in vitro for the inhibition of six Candida species and in silico for affinity to the CYP51 enzymes (obtained with molecular modeling and protein homology) of the same species. The 5-(1,3-diphenyl-1H-pyrazol-4-yl)-4-tosyl-4,5-dihydrooxazoles 6a-j were synthesized using the Van Leusen reaction between 1,3-diphenyl-4-formylpyrazoles 4a-j and TosMIC 5 in the presence of K2CO3 or KOH without heating, resulting in short reaction times, high compound purity, and high yields. The docking studies revealed good affinity for the active site of the CYP51 enzymes of the Candida species in the following order: 6a-j > 4a-j > fluconazole (the reference drug). The in vitro testing of the compounds against the Candida species showed lower MIC values for 6a-j than 4a-j, and for 4a-j than fluconazole, thus correlating well with the in silico findings. According to growth rescue assays, 6a-j and 4a-j (like fluconazole) inhibit ergosterol synthesis. The in silico toxicity assessment evidenced the safety of compounds 6a-j, which merit further research as possible antifungal drugs.
Chronological Changes in the Histology of Infection-Related Glomerulonephritis in Renal Allograft: A Case Report
Authors: Tominaga Kenta , Oda Takashi , Iwama Sachiko , Kojima Tadasu , Konno Osamu , Yamada Muneharu , Nakabayashi Iwao , Iwamoto Hitoshi
Published: May 2024

We report the histological changes over time for a patient with infection-related glomerulonephritis (IRGN) that developed in a transplanted kidney. A 47-year-old man had undergone renal transplantation 3 years ago for end-stage kidney disease (ESKD). After several episodes of acute rejection, the patient was in a stable CKD condition. The abrupt development of severe microscopic hematuria and renal dysfunction was observed approximately 2 weeks after the onset of a phlegmon in his right leg. An allograft biopsy showed prominent glomerular endocapillary proliferation on light microscopy, granular C3 deposition on immunofluorescent microscopy, and subepithelial electron-dense deposits on electron microscopy, suggesting IRGN accompanied by moderate interstitial fibrosis and tubular atrophy (IFTA). Positive glomerular staining for nephritis-associated plasmin receptor (NAPlr) and plasmin activity, which are biomarkers of bacterial IRGN, supported the diagnosis. Although the infection was completely cured with antibiotic therapy, renal dysfunction persisted. A re-biopsy of the allograft 2 months later revealed resolution of the glomerular endocapillary proliferation and negative staining for NAPlr/plasmin activity, with worsening IFTA. We showed, for the first time, the chronological changes in infiltrating cells and histological markers of IRGN in transplanted kidneys. Glomerular changes, including NAPlr/plasmin activity staining, almost disappeared after the cessation of infection, while interstitial changes continuously progressed, contributing to ESKD progression.
DNA Methylation Analysis of Growth Differences between Upright and Inverted Cuttings of Populus yunnanensis
Authors: Guo Haiyang , Guo Tiansu , Li Hailin , Ma Shaojie , Zhang Xiaolin , He Chengzhong , Zong Dan
Published: May 2024

DNA methylation is an important mechanism for epigenetic modifications that have been shown to be associated with responses to plant development. Previous studies found that inverted Populus yunnanensis cuttings were still viable and could develop into complete plants. However, the growth status of inverted cuttings was weaker than that of upright cuttings, and the sprouting time of inverted cuttings was later than that of upright cuttings. There is currently no research on DNA methylation patterns in inverted cuttings of Populus yunnanensis. In this study, we detected genome-wide methylation patterns of stem tips of Populus yunnanensis at the early growth stage and the rapid growth stage by Oxford Nanopore Technologies (ONT) methylation sequencing. We found that the methylation levels of CpG, CHG, CHH, and 6mA were 41.34%, 33.79%, 17.27%, and 12.90%, respectively, in the genome of inverted poplar cuttings, while the methylation levels of the four methylation types were higher in the genome of upright poplar cuttings than in inverted cuttings, 41.90%, 34.57%, 18.09%, and 14.11%, suggesting important roles for DNA methylation in poplar cells. In all comparison groups, CpG-type methylation genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were annotated to pathways associated with carbon metabolism, ribosome biogenesis in eukaryotes, glycolysis/gluconeogenesis, pyruvate metabolism, and mRNA detection pathways, suggesting that different biological processes are activated in upright and inverted cuttings. The results show that methylation genes are commonly present in the poplar genome, but only a few of them are involved in the regulation of expression in the growth and development of inverted cuttings. From this, we screened the DET2 gene for significant differences in methylation levels in upright or inverted cuttings. The DET2 gene is a key gene in the Brassinolide (BRs) synthesis pathway, and BRs have an important influence on the growth and development process of plants. These results provide important clues for studying DNA methylation patterns in P. yunnanensis.