bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemoinformatic study of spiramycin in comparison with other antibiotics
Authors: Gromovа O. A. , Torshin I. Yu. 
Published: February 2025

Background. Antibiotics have different spectra of action on bacterial pathogens, including their antibiotic-resistant strains. Establishing the spectra of action of antibiotics and mechanisms of resistance to them is an important task for finding effective and safe antibiotic therapy.Objective: a chemoinformatic study of the macrolide spiramycin in comparison with moxifloxacin, josamycin, azithromycin and clarithromycin.Material and methods. The analysis was carried out using modern data analysis methods (theories of labeled graph analysis, metric data analysis, combinatorial solvability theory, topological theory of ill-formalized problem analysis) developed within the framework of the algebraic approach to recognition.Results. Chemomicrobiome and pharmacoinformatic profiling of spiramycin indicated significant differences between the spiramycin molecule and the comparison molecules in terms of efficacy, safety and mechanisms of action. Characteristic features of spiramycin action were inhibition of protein synthesis by influencing the ribosome, with possible inhibition of bacterial topoisomerase, DNA synthesis and with anti-membrane activity, including through ionophore mechanisms. Analysis of correlations between chemogenomic profiles of molecules indicated a pronounced similarity of the effects of three of the five studied molecules (josamycin, azithromycin, clarithromycin) with a significant difference in the effects of spiramycin from the effects of other studied macrolides. Mechanisms of resistance to spiramycin potentially include genes from the functional groups “assembly of the outer membrane of gram-negative bacteria”, “sorbitol transport”, “transmembrane transporter of L-leucine” etc. Spiramycin was characterized by the best safety profile in terms of “antimicronutrient” effects (increase in the risk of excretion of a particular micronutrient by only 7%).Conclusion. The significant difference between the chemogenomic, chemomicrobiomic and pharmacoinformatic profiles of spiramycin and other antibiotics (including other macrolides) suggests low resistance to spiramycin at the population level.
SOX9 regulation of Hexokinase 1 controls neuroinflammatory astrocyte subtypes in neuropathic pain
Authors: Liu Jessica Aijia , CHEN Yonglong , LIAO Yu , WU Zhaoming , WAN Yutong , CAI Haoyang , FENG Xianglan , FAN Chaoyang , ZHAN Dengcheng , ZHU Huazhang , Cheung Martin , CHEUNG Chiwai 
Published: February 2025

Abstract

Neuropathic pain (NeP) results from nerve damage or disease, lacking effective treatments. Astrocytes contribute to long-lasting neuroinflammation in the dorsal horn, driving NeP development. Directly targeting astrocytes is not feasible due to their roles in supporting neuronal homeostasis and pain resolution. Despite this understanding, the heterogeneity of astrocytes and the regulation of deleterious subsets emergence in pain remain less known. Through a comprehensive approach involving metabolomic, single-cell transcriptomic, epigenomic profiling and regional astrocyte-specific perturbation studies, we identified distinct astrocyte clusters under physiological and pathological pain conditions, and elucidated mechanisms by which metabolic regulation of neuroinflammatory astrocyte subsets during pain pathogenesis. We found an astrocyte specifier, Sox9, transcriptionally regulates Hexokinase1 (HK1), a critical enzyme that catalyzes the first step in glucose metabolism irreversibly, contributing to astrocytic glycolysis homeostasis. Initial nerve damage induced abnormal phosphorylation of Sox9, triggering aberrantly activation of HK1 for high-rate glycolysis in astrocytes. Moreover, the excessive lactate production from heightened glycolysis remodeled histones of gene promoters via lactylation, H3K9la, promoting transcriptional modules of genes governing pro-inflammatory and neurotoxic signaling, which induced pathogenic astrocyte properties while reducing beneficial populations, ultimately causing persistent pain state. Importantly, we demonstrate that targeted modulation of the SOX9-HK1-H3K9la axis specifically dampens deleterious astrocyte subsets, promoting long-lasting recovery of NeP. Collectively, our findings unveil a novel immunometabolic mechanism and identify multiple potential targets for effective therapeutic interventions in the treatment of NeP.
Hidden structural states of proteins revealed by conformer selection with AlphaFold-NMR
Authors: Montelione Gaetano , Huang Yuanpeng , Ramelot Theresa , Spaman Laura , Kobayashi Naohiro 
Published: February 2025

Abstract

We introduce AlphaFold-NMR, a novel approach to NMR structure determination that reveals previously undetected protein conformational states. Unlike conventional NMR methods which rely on NOE-derived spatial restraints, AlphaFold-NMR combines AI-driven conformational sampling with Bayesian scoring of realistic protein models against NOESY and chemical shift data. This method uncovers alternative conformational states of the enzyme Gaussia luciferase, involving large-scale changes in the lid, binding pockets, and other surface cavities. It also identifies similar yet distinct conformational states of the human tumor suppressor Cyclin-Dependent Kinase 2-Associated Protein 1. These studies demonstrate the potential of AI-based modeling with enhanced sampling to generate diverse structural models, followed by conformer selection and validation with experimental data, as an alternative to traditional restraint-satisfaction protocols for protein NMR structure determination. The AlphaFold-NMR framework enables discovery of conformational heterogeneity and cryptic pockets that conventional NMR analysis methods do not distinguish, providing new insights into protein structure-function relationships.
Classification of agroforestry systems by photo-interpretation of satellite imagery
Authors: Tahiri Ouadya , Beillouin Damien , Dumas Patrice , Prudhomme Rémi , Makowski David 
Published: February 2025

Abstract

Effective and large-scale monitoring of agroforestry (AF) systems is essential to assess the environmental benefits of agroforestry and support sustainable land management strategies. However, a standardized method for classifying these systems using satellite imagery is still missing. Here, we present a novel operational framework to classify agroforestry systems into three categories—Alley cropping, Scattered agroforestry, and Hedgerows—and to distinguish these systems from Cropland without trees, Natural trees, and Orchards. The proposed procedure relies on a classification tree based on photo-interpretation of satellite imagery. The accuracy and robustness of this classification tree were evaluated by five interpreters across 300 agroforestry and non-agroforestry plots spanning all continents. Results show that the classification tree accurately distinguishes agroforestry categories from one another and from non-agroforestry systems, with an overall accuracy ranging from 0.75 to 0.81 depending on the interpreter. After eliminating the interpreters’ errors, the potential classification accuracy increases to 0.86. While hedgerows were accurately classified in most cases with an omission error of 2% and no commission error (0%), the study revealed challenges in differentiating between Alley cropping and Orchards which were frequently confounded. Similarly, plots with Scattered agroforestry were also misclassified as Natural trees leading to a commission error of 19% for this class. Despite these limitations, the proposed classification tree represents a valuable tool for large-scale monitoring of agroforestry systems. Future adaptations of this framework could address regional specificities, further improving its applicability and accuracy.
Structural and Computational Insights into New Nano-sized Cu(II) Metal- Organic Coordination Particles: Synthesis, Crystal Analysis, and Hirshfeld Surface Analysis
Authors: rajabzadeh Halimeh 
Published: February 2025

Abstract

The synthesis of novel nano-structures of a Cu(II) metal-organic coordination complex (MOC), referred to as [Cu2(ox)(phen)2(H2O)2](NO3)2{1}, where ox =C2O4-2 (oxalate) and phen= C12H8N2 (1,10-Phenanthroline), was accomplished using two distinct experimental approaches: solvothermal as well as sonochemical techniques. Notably, both methods resulted in the formation of an identical crystalline structure. A range of characterization techniques, including Powder X-ray diffraction (PXRD), Scanning Electron Microscopy (SEM), and Fourier Transform Infrared Spectroscopy (FT-IR), were utilized to analyze the compounds. The complex is characterized by single-crystal X-ray diffraction (SCXRD) which is shown Cu atoms (Cu2+) that are 5-coordinated. The effects of various parameters, including sonication time and temperature, were examined for the final morphology of the compounds produced by the sonochemical method. Ultimately, a Hirshfeld Surface Analysis (HSA) was conducted on the 1. Analyzing geometric and electronic using DFT/PBE/6-311++G*/lanl2dz level of theory shows that the Cu(II) structure with the high chemical softness (2.03eV) has a high tendency for interacting with the protein of prostate cancer, Eint=-16.7 kJ mol-1; this interaction involves electrostatic, hydrogen, and steric.
A Novel Phenoplast-Based Structural Electrolyte with High Ionic Conductivity and Fire Resistance for Advanced Energy Storage Composites
Authors: Sha Zhao , Gao Ziyan , Shen Yingkun , Wang Cheng , Xu Jiangtao , Wu Shuying , Brown Sonya , Peng Shuhua , Zhang Jin , Wang Chun 
Published: February 2025

Abstract

Structural energy storage composites are a promising lightweight solution for many applications, enabling structures to store electricity. However, there is a significant challenge in engendering polymer electrolytes with high flame retardancy, ionic conductivity, and mechanical properties. In this study, we introduce a novel fire-resistant polymer electrolyte that is highly ionic conductive and mechanically strong by designing a co-continuous composite electrolyte consisting of phenolic resin (or phenoplasts), ionic liquid (EMIM TFSI), and lithium salt (LiTFSI). The ionic liquid and lithium salt work synergistically as a hybrid surfactant to facilitate the emulsion polymerization of the phenolic resin, forming unique microstructures where the Li⁺ ions complex with hydroxyl groups in the phenoplasts creates ion-conductive pathways in the solid phase. This design yields significantly enhanced ionic conductivities up to 2.87 mS/cm, comparable to those of ionic liquids. For structural electrolyte applications, certain formulations achieved an ionic conductivity of approximately 0.15 mS/cm, a tensile strength around 19 MPa, and a tensile modulus of about 1.2 GPa. These properties demonstrate a well-balanced performance between electrochemical and mechanical characteristics, making the electrolytes suitable for advanced structural energy storage applications. The resulting phenoplast-based electrolyte not only maintains mechanical strength and structural integrity but also achieves the highest flame retardancy rating of V-0. A composite structural supercapacitor fabricated using this electrolyte demonstrated excellent electrochemical performance and safety features. This development presents a significant advancement in creating safe, efficient, and multifunctional materials for advanced structural energy storage applications.
Combination and Interaction of Seven Trace Elements and the Risk of Protein-Energy Malnutrition in School-Aged Children in Shenzhen, China
Authors: Yu Mingtao , Tan Leyun , Chen Yuhui , Shang Jianhui , You Yingbin , Xie Haimin , Pang Nan , Liang Rimei , Zhang Qingying 
Published: February 2025

Abstract

Background
The imbalance of trace elements plays an important role in childhood malnutrition, but previous studies are usually specific to certain elements. We aimed to examine the individual and joint associations between multiple elements and the risk of protein-energy malnutrition (PEM) in young school children.
Methods
This study measured the serum levels of Zinc (Zn), Copper (Cu), Chromium (Cr), Cobalt (Co), Vanadium (V), Manganese (Mn), and Nickel (Ni) in 1832 out of 5152 children aged 6 to 9 years by using inductively coupled plasma mass spectrometry. The individual and joint association of element and risk of PEM were appraised using logistic regression, restricted cubic splines model (RCS), bayesian kernel machine regression (BKMR), and weighted quantile sum regression (WQS) model, respectively.
Results
Serum concentrations of Zn, Cu, Co, V, Mn, and Ni were significantly lower in the PEM group than in controls (all P < 0.005). Higher quartile concentrations of Zn (OR = 0.52), Cu (0.59), V (0.52), Mn (0.51), and Ni (0.68) were associated with lower PEM risk (all Ptrend < 0.05). RCS model indicated non-linear relationships between Zn, Cu, Cr, Co, V, Mn, and PEM risk. Interactions were found between Zn, Mn, and Co on the risk of PEM. Both BKMR and WQS models revealed a negative joint association of seven elements with PEM risk (OR = -0.102), Mn (40.4%), and Zn (19.1%) as the strongest contributors.
Conclusion
Serum concentrations of Zn, Cu, Co, V, and Mn were relatively lower in Children with PEM and exhibited non-linear associations with the risk of PEM. The joint association of seven trace elements was negative with the risk of PEM, in which Mn and Zn contribute the most. Additionally, Mn, Zn, and Co exhibited pairwise interactions. These findings highlight the importance of maintaining balanced trace element levels to mitigate PEM in children.
Classification and Interpretation of Histopathology Images: Leveraging Ensemble of EfficientNetV1 and EfficientNetV2 Models
Authors: Kalati Mahdi Azmoodeh , Shabani Hasti , Maghareh Mohammad Sadegh , Barzegar Zeynab , Lashgari Reza 
Published: February 2025

Abstract

Breast cancer is the second leading cause of cancer-related deaths among women, following lung cancer, as of 2024. Conventional cancer diagnosis relies on manual examination of biopsied tissues by pathologists which is a time-consuming process and based on pathologist experience may vary. Early detection and accurate diagnosis are critical for effective treatment planning and patient care. The invention of whole-slide scanners has revolutionized this process by enabling the adoption of Computer-Aided Detection (CAD) systems for automated analysis. Convolutional Neural Networks (CNNs) within CAD systems play a pivotal role in the automated classification of breast tissues. This study utilizes state-of-the-art CNNs called EfficientNetV1 and EfficientNetV2 for binary classification of BreakHis dataset ,a collection of histopathological images categorized as benign and malignant breast tissues. To address the challenge posed by the limited availability of annotated data, data augmentation and transfer learning techniques were applied. Model interpretability was enhanced using the Grad-CAM technique, which generates localization maps highlighting critical regions relevant to predictions. Finally, ensemble learning is employed for further improving performance. we utilized unweighted averaging and majority voting to combine predictions of multiple trained models. Furthermore, We define two ensemble architecture combining different trained EfficientNets. The proposed framework was able to achieve a classification accuracy of 99.58% outperforming conventional CNN models on BreakHis dataset. This study underscores the potential of ensemble learning to improve diagnostics accuracy in breast cancer detection.
Общественно-политические взгляды раннего Э. Бёрка(50-е – начало 60-х годов XVIII века)
Authors: Ковалев М.А. 
Published: February 2025

В статье рассматриваются взгляды британского мыслителя и политика XVIII века, основателя консерватизма Эдмунда Бёрка. Автор ограничивается изучением раннего периода творчества этого мыслителя, когда он еще не вышел на широкую политическую арену. Именно в этот период Берк написал несколько значительных работ, которые заложили основу для реализации всей его дальнейшей политической перспективы. В статье также уделяется значительное внимание философским взглядам мыслителя, поскольку они легли в основу его социальных и политических идей.
The article deals with the views of the XVIIIth century British thinker and politician, founder of the ideology of conservatism Edmund Burke. The author is limited to studying the early period of creativity of this thinker when he has not yet entered the broad political arena. It was during this period that Burke wrote some of significant works that laid the foundations for all his further political outlook. The article also pays considerable attention to the philosophical views of the thinker, as they were the basis of his social and political ideas.
Adopting a socio-technical perspective to challenges and barriers of Blue-Green Infrastructure (BGI) transition
Authors: Sadegh Koohestani Somayeh , Mukheibir Pierre , Wakefield-Rann Rachael , Santamouris Mattheos 
Published: February 2025

ABSTRACT
Blue-Green Infrastructure is widely recognized as one of the keys to addressing climate change impacts and rapid urbanization challenges. Integrating nature-based solutions enhances cities’ resiliency through sustainable stormwater management, mitigating flood risks while providing various ecosystem services. However, despite these multiple benefits and co-benefits, BGI remains far from mainstream adoption. We conducted a selective literature review to explore this practical gap guided by the socio-technical transition theory. We then employed a multi-level perspective to conceptualize the results, as it helps elucidate the complex nature of this problem beyond the standard variables considered in the existing literature on challenges and barriers to BGI uptake. Finally, we argued the necessity of societal and institutional considerations in addition to the technical aspects while investigating it systematically. We categorized the findings into five clusters including institutional and governance, economics and finance, knowledge and experience, socio-cultural challenges, and spatial planning practices. These clusters are highly interconnected and influenced by one another, revealing the complexity of this issue. Based on these findings, we suggest approaching BGI transitions as a complex problem by using systems thinking practices. This would necessitate dynamic interdisciplinary and connective collaborations among different organizations to bridge this gap.
Covalent Inhibitors - An Overview of Design Process, Challenges and Future Directions
Authors: Mugisa Simon , Murahari Manikanta 
Published: February 2025

Abstract:
Covalent inhibitor drugs or targeted covalent inhibitors (TCI) are a type of drug category that interact
with their target by covalent bond formation. They represent a unique category having desired properties
such as high potency and longer duration of action, making them an attractive opportunity to pursue by researchers
in drug discovery. In history, covalent inhibitors were often discovered serendipitously (e.g. aspirin
and penicillin). However, modern times have witnessed numerous cases of rational design of these drugs,
which has caused their rise to occupy a significant fraction of marketed drugs (over 30%). Here, we have given
an overview of the discovery process of covalent inhibitors, including target identification/validation, warhead
selection and optimization, linker design and conjugation and the role of computational tools in covalent inhibitors.
To conclude, the challenges facing in this field and future directions to foresee are discussed. The objective
of this article is to provide a summary of the general development process of covalent inhibitors as well
as prospects or research gaps awaiting to be solved to overcome the challenges that hinder the discovery of
covalent drugs.
Synthesis of Novel Substituted Bis(benzimidazole)amine, N-Benzimidazole (benzothiazole)amine, and N-Benzimidazole(benzoxazole)amine Under
Ultrasound Irradiation via Copper-Catalyzed Reaction
Authors: nematpour manijeh 
Published: February 2025

Abstract:
In this work, novel bis(benzimidazole)amine, N-benzimidazole(benzothiazole)amine, and
N-benzimidazole(benzoxazole)amine have been synthesized via a one-pot, intramolecular cyclization
of 2-iodoaniline and 2-aminobenzimidazoles (thiazoles and oxazoles)-trichloroacetonitrile adduct
using copper(I) iodide and DMF under ultrasound-assisted reaction with moderate to good yields.
Using basic materials and simple and available reagents, gentle copper-catalyzed reaction conditions,
easy purification with the help of solvent, good yields, non-addition of ligands, application of a simple
and efficient sonochemical method, short reaction times, and the synthesis of 15 new heterocycle
compounds have been appreciable features of this protocol.
Prevalence and Adverse Outcomes of Iron Deficiency in Heart Failure
Authors: Habeeb Habeeb Abdulkareem , Todd Fraser , Valsalan Rohith , Schembri Emily , Noyhar John K. , Yip Gary , Anpalahan Mahesan 
Published: February 2025

Introduction/Objective:
Outcomes of iron deficiency (ID) in heart failure (HF) with
preserved ejection fraction (HFpEF) or in samples with mixed heart failure subtypes are variably
described. Hence, we investigated the prevalence and adverse outcomes of ID in a sample of
mixed heart failure subtypes.

Methods:
Adult patients admitted with HF over a six-month period were retrospectively studied.
ID was defined as serum ferritin<100mcg/L, or serum ferritin 100-300mcg/L with serum transferrin
saturation<20%. For each case of ID, sex- and age-matched (within five years) controls
were selected. The primary outcome was the composite of all-cause mortality or readmissions up
to 12 months post-index admission.

Results:
Of the 245 patients admitted with HF [HFpEF: 83 (70.3%), HFrEF: 35 (29.6%)], 233
met the inclusion criteria. Iron studies were available for 131 patients and 59 (45%) had ID. ID
had a significant univariate association with the primary outcome (OR: 3.80, 95% CI: 1.42–
10.18, P=0.008), and it remained significant after controlling for age, anaemia, comorbidities,
and frailty (OR: 6.04, 95% CI: 1.18–30.85, P=0.031). ID also had a significant independent association
with readmissions (OR: 4.61, 95% CI: 1.15–18.43, P=0.03), but not with mortality
(OR: 1.17, 95% CI: 0.67-4.35, P=0.257). In post-hoc analysis, ID exhibited a significant association
with primary outcome in patients with HFrEF (OR: 14.12, 95% CI: 1.7-0-117.33,
P=0.014), but not in patients with HFpEF (OR: 1.8, 95% CI: 0.71-4.58, P=0.214).

Conclusion:
ID is common in patients hospitalised for heart failure and has been found to have a
significant association with the composite primary outcome, largely due to its effect on readmissions.
ID may have a differential effect on adverse outcomes with respect to heart failure subtypes.