bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis, Antimicrobial Activities, and Molecular Modeling Studies of Agents for the Sortase A Enzyme
Authors: Tatar Yilmaz Gizem , Yayli Nurettin , Tüzüner Tamer , Bozdal Gözde , Salmanli Merve , Renda Gülin , Korkmaz Büşra , Bozdeveci Arif , Alpay Karaoğlu Şengül 
Published: February 2024

AbstractSortase A (SrtA) is an attractive target for developing new anti‐infective drugs that aim to interfere with essential virulence mechanisms, such as adhesion to host cells and biofilm formation. Herein, twenty hydroxy, nitro, bromo, fluoro, and methoxy substituted chalcone compounds were synthesized, antimicrobial activities and molecular modeling strategies against the SrtA enzyme were investigated. The most active compounds were found to be T2, T4, and T19 against Streptococcus mutans (S. mutans) with MIC values of 1.93, 3.8, 3.94 μg/mL, and docking scores of −6.46, −6.63, −6.73 kcal/mol, respectively. Also, these three active compounds showed better activity than the chlorohexidine (CHX) (MIC value: 4.88 μg/mL, docking score: −6.29 kcal/mol) in both in vitro and in silico. Structural stability and binding free energy analysis of S.mutans SrtA with active compounds were measured by molecular dynamic (MD) simulations throughout 100 nanoseconds (ns) time. It was observed that the stability of the critical interactions between these compounds and the target enzyme was preserved. To prove further, in vivo biological evaluation studies could be conducted for the most promising precursor compounds T2, T4, and T19, and it might open new avenues to the discovery of more potent SrtA inhibitors.
Pterostilbene protects against H2O2‐induced oxidative stress by regulating GAS6/Axl signaling in HL‐1 cells
Authors: Di Wencheng , Zhao Aizhen , Li Xiaoru , Chen Junmin , Dai Yongbin , Li Jiawen , Lei Wangrui , Yang Yang , Lu Hongzhou 
Published: February 2024

AbstractPterostilbene (PTE, trans‐3,5‐dimethoxy‐4′‐hydroxystilbene), a natural plant polyphenol, possesses numerous pharmacological effects, including antioxidant, antidiabetic, antiatherosclerotic, and neuroprotective aspects. This study aims to investigate whether PTE plays a protective role against oxidative stress injury by GAS6/Axl signaling pathway in cardiomyocytes. Hydrogen peroxide (H2O2)‐induced oxidative stress HL‐1 cells were used as models. The mechanism by which PTE protected oxidative stress is investigated by combining cell viability, cell ROS levels, apoptosis assay, molecular docking, quantitative real‐time PCR, and western blot analysis. GAS6 shRNA was performed to investigate the involvement of GAS6/Axl pathways in PTE's protective role. The results showed that PTE treatment improved the cell morphology and viability, and inhibited the apoptosis rate and ROS levels in H2O2‐injured HL‐1 cells. Particularly, PTE treatment upregulated the levels of GAS6, Axl, and markers related to oxidative stress, apoptosis, and mitochondrial function related. Molecular docking showed that PTE and GAS6 have good binding ability. Taken together, PTE plays a protective role against oxidative stress injury through inhibiting oxidative stress and apoptosis and improving mitochondrial function. Particularly, GAS6/Axl axis is the surprisingly prominent in the PTE‐mediated pleiotropic effects.
Phylogeny‐guided Characterization of Bacterial Hydrazine Biosynthesis Mediated by Cupin/methionyl tRNA Synthetase‐like Enzymes
Authors: Matsuda Kenichi , Nakahara Yuto , Choirunnisa Atina Rizkiya , Arima Kuga , Wakimoto Toshiyuki 
Published: February 2024

AbstractCupin/methionyl‐tRNA synthetase (MetRS)‐like didomain enzymes catalyze nitrogen‐nitrogen (N−N) bond formation between Nω‐hydroxylamines and amino acids to generate hydrazines, key biosynthetic intermediates of various natural products containing N−N bonds. While the combination of these two building blocks leads to the creation of diverse hydrazine products, the full extent of their structural diversity remains largely unknown. To explore this, we herein conducted phylogeny‐guided genome‐mining of related hydrazine biosynthetic pathways consisting of two enzymes: flavin‐dependent Nω‐hydroxylating monooxygenases (NMOs) that produce Nω‐hydroxylamine precursors and cupin/MetRS‐like enzymes that couple the Nω‐hydroxylamines with amino acids via N−N bonds. A phylogenetic analysis identified the largely unexplored sequence spaces of these enzyme families. The biochemical characterization of NMOs demonstrated their capabilities to produce various Nω‐hydroxylamines, including those previously not known as precursors of N−N bonds. Furthermore, the characterization of cupin/MetRS‐like enzymes identified five new hydrazine products with novel combinations of building blocks, including one containing non‐amino acid building blocks: 1,3‐diaminopropane and putrescine. This study substantially expanded the variety of N−N bond forming pathways mediated by cupin/MetRS‐like enzymes.
Ruthenium NNN‐Based Pincer Complexes with Metal Ligand Cooperation as Catalysts for N‐Methylation of Anilines and Nitroarenes with Methanol as a C1 Source
Authors: Garg Nitish K. , Goriya Yogesh , Manojveer Seetharaman , Wendt Ola F. , Johnson Magnus T. 
Published: February 2024

AbstractA novel phosphine‐free ruthenium pincer complex based on an NNN pincer ligand has been prepared and fully characterized. The complex was subsequently employed as an efficient catalyst for the N‐methylation of amines and the direct N‐methylation of nitroarenes using methanol as a C1 source under mild reaction conditions following the borrowing‐hydrogen approach. Both of the catalytic transformations were performed with only catalytic amounts of base under closed air conditions without using any other additives.
Metal‐Organic Framework Catalyzed Hydrogen Atom Transfer for Photocatalytic Organic Synthetic Applications
Authors: Ouyang Jing , Quan Yangjian 
Published: February 2024

AbstractThis concept paper aims to summarize recent research on the design and synthetic applications of metal‐organic frameworks (MOFs)‐based hydrogen atom transfer (HAT) catalysts. Functional MOFs have emerged as highly promising heterogeneous catalysts, leveraging their tunable, ordered structure and abundant active sites to enhance catalytic efficiency in various reactions. HAT, a versatile method for generating active open‐shell radical species through selective hydrogen abstraction, has been well explored in homogeneous photocatalysis. In contrast, heterogeneous HAT catalysis remains less developed, albeit their great potential in industry. This paper will provide a timely overview of the advancements in MOFs‐based HAT photocatalysis, classified according to catalytic centers including aromatic ketones, polyoxometalates, xanthene dyes, thiols, and alcohols, highlighting their design principles and practical applications in photocatalytic organic synthesis.
Tailoring the Properties of Gel Polymer Electrolytes for Sodium‐Ion Batteries Using Ionic Liquids: A Review
Authors: Gabryelczyk Agnieszka , Swiderska‐Mocek Agnieszka 
Published: February 2024

AbstractIonic liquids are an extraordinary group of compounds, fully ionic in structure like inorganic salts but with low melting points, that resemble organic molecular solvents. Their chemical, electrochemical, and thermal stability is what draws the attention and enables their use in many applications, including electrochemical power sources. Even though they are no longer considered eco‐friendly because of nonnegligible toxicity and long bioaccumulation, they can still be efficiently recovered, purified, and reused. These attributes can be harvested to enhance the properties of gel polymer electrolytes for the emerging sodium‐ion batteries. The variety of anions and cations for ILs and their influence on the final properties of the compound opens the road to tuning the properties of gel polymer electrolytes. Ionic liquids as plasticizers constitute a major part of gel polymer electrolytes (average of 70 wt%) and hence, they affect the fundamental properties of gel electrolytes like ionic conductivity and electrochemical window. They also improve the safety features of sodium‐ion batteries, which is relevant for their anticipated applications in stationary energy storage and electric vehicles. The presented review paper aims to explain the relationship between the cation and anion in ionic liquid and the properties of gel electrolytes for sodium‐ion batteries.
2’,3’‐Protected Nucleotides as Building Blocks for Enzymatic de novo RNA Synthesis
Authors: Pichon Maëva , Levi‐Acobas Fabienne , Kitoun Camélia , Hollenstein Marcel 
Published: February 2024

AbstractBesides being a key player in numerous fundamental biological processes, RNA also represents a versatile platform for the creation of therapeutic agents and efficient vaccines. The production of RNA oligonucleotides, especially those decorated with chemical modifications, cannot meet the exponential demand. Due to the inherent limits of solid‐phase synthesis and in vitro transcription, alternative, biocatalytic approaches are in dire need to facilitate the production of RNA oligonucleotides. Here, we present a first step towards the controlled enzymatic synthesis of RNA oligonucleotides. We have explored the possibility of a simple protection step of the vicinal cis‐diol moiety to temporarily block ribonucleotides. We demonstrate that pyrimidine nucleotides protected with acetals, particularly 2′,3′‐O‐isopropylidene, are well‐tolerated by the template‐independent RNA polymerase PUP (polyU polymerase) and highly efficient coupling reactions can be achieved within minutes – an important feature for the development of enzymatic de novo synthesis protocols. Even though purines are not equally well‐tolerated, these findings clearly demonstrate the possibility of using cis‐diol‐protected ribonucleotides combined with template‐independent polymerases for the stepwise construction of RNA oligonucleotides.
Modulating β‐Keto‐enamine‐Based Covalent Organic Frameworks for Photocatalytic Atom‐Transfer Radical Addition Reaction
Authors: Zhao Yuting , Li Lei , Zang Jiyuan , Young David J. , Ren Zhi‐Gang , Li Hai‐Yan , Yu Lei , Bian Guo‐Qing , Li Hong‐Xi 
Published: February 2024

AbstractThe atom‐transfer radical addition (ATRA) reaction simultaneously forges carbon‐carbon and carbon‐halogen bonds. However, frequently‐used photosensitizers such as precious transition metal complexes, or organic dyes have limitations in terms of their potential toxicity and recyclability. Three β‐ketoenamine‐linked covalent organic frameworks (COFs) from 1,3,5‐triformylphloroglucinol and 1,4‐phenylenediamines with variable transient photocurrent and photocatalytic activity have been prepared. A COF bearing electron‐deficient Cl atoms displayed the highest photocatalytic activity toward the ATRA reaction of polyhalogenated alkanes to give halogenated olefins under visible light at room temperature. This heterogeneous photocatalyst exhibited good functional group tolerance and could be recycled without significant loss of activity.
Advances Toward Amphidinolides C, F and U: Isolations, Synthetic Studies and Total Syntheses
Authors: Ciss Ismaila , Seck Matar , Figadère Bruno , Ferrié Laurent 
Published: February 2024

AbstractAmphidinolides C, F, and U, including C2‐C4 analogs, are highly cytotoxic marine macrolides, mainly isolated from dinoflagellates of the genus Amphidinium. All these polyketides share a 75 % or more similar structure, highlighted by a macrolactone ring, at least one trans‐2,5‐substituted‐THF motif and a characteristic polyenic side chain. From their isolation and absolute configurational assignment, the total synthesis of these marine macrolides represented an intense challenge to the organic synthesis community over the last 15 years, with around 14 research groups engaged in this inspiring task. In the first part of this review, we present the different approaches to the isolation and characterization of these natural products, including the most recent analogs, which may cast doubt on the biogenetic origin of these compounds. The various synthetic approaches to the total synthesis of C, F, and U amphidinolides are presented in a second part, focusing on key reactions and/or innovative strategies. The review concludes in a third section summarizing the successful approaches leading to the total synthesis of one of the members of this amphidinolide subfamily.
Reversibly Tuning the Viscosity of Peptide‐Based Solutions Using Visible Light
Authors: Bianco Simona , Wimberger Laura , Ben‐Tal Yael , Williams George T. , Smith Andrew J. , Beves Jonathon E. , Adams Dave J. 
Published: February 2024

AbstractLight can be used to design stimuli–responsive systems. We induce transient changes in the assembly of a low molecular weight gelator solution using a merocyanine photoacid. Through our approach, reversible viscosity changes can be achieved via irradiation, delivering systems where flow can be controlled non‐invasively on demand.
Clicked BODIPY‐Fullerene‐Peptide Assemblies: Studies of Electron Transfer Processes in Self‐Assembled Monolayers on Gold Surfaces
Authors: Rabah Jad , Nasrallah Houssein , Wright Karen , Gérard Isabelle , Fensterbank Hélène , Bui Thi‐Tuyet‐Van , Marrot Jérôme , Tran Thu‐Trang , Fatima Anam , Ha‐Thi Minh‐Huong , Méallet Rachel , Burdzinski Gotard , Clavier Gilles , Boujday Souhir , Cachet Hubert , Debiemme‐Chouvy Catherine , Maisonhaute Emmanuel , Vallée Anne , Allard Emmanuel 
Published: February 2024

AbstractTwo BODIPY‐C60‐peptide assemblies were synthesized by CuAAC reactions of BODIPY‐C60 dyads and a helical peptide functionalized with a terminal alkyne group and an azide group, respectively. The helical peptide within these assemblies was functionalized at its other end by a disulfide group, allowing formation of self‐assembled monolayers (SAMs) on gold surfaces. Characterizations of these SAMs, as well as those of reference molecules (BODIPY‐C60‐alkyl, C60‐peptide and BODIPY‐peptide), were carried out by PM‐IRRAS and cyclic voltammetry. BODIPY‐C60‐peptide SAMs are more densely packed than BODIPY‐C60‐alkyl and BODIPY‐peptide based SAMs. These findings were attributed to the rigid peptide helical conformation along with peptide‐peptide and C60‐C60 interactions within the monolayers. However, less dense monolayers were obtained with the target assemblies compared to the C60‐peptide, as the BODIPY entity likely disrupts organization within the monolayers. Finally, electron transfer kinetics measurements by ultra‐fast electrochemistry experiments demonstrated that the helical peptide is a better electron mediator in comparison to alkyl chains. This property was exploited along with those of the BODIPY‐C60 dyads in a photo‐current generation experiment by converting the resulting excited and/or charge separated states from photo‐illumination of the dyad into electrical energy.
Computational Analysis of B‐Cell Receptor (BCR) Immune Repertoires with Abalign
Authors: Wei Jiachen , Li Junxian , Zong Fanjie , Xiao Zhi‐Xiong , Cao Yang 
Published: February 2024

AbstractThe widespread application of high‐throughput sequencing technology has generated massive sequences of B‐cell receptor (BCR) immune repertoires. Computational analysis of these data has gained significant attention due to the increasing importance of immunotherapy and precision medicine. It not only reveals the diversity and dynamic changes in immune responses, contributing to the study of associated diseases, but also provides valuable information for immunodiagnostics and drug development. Recently, we introduced a BCR‐specific multiple sequence alignment (MSA) method along with a comprehensive platform software called Abalign, which stands out as an excellent choice for analyzing BCR immune repertoires due to its unique high‐throughput processing capability. It offers ultra‐fast MSA functionality and a wide range of analytical features, including BCR/antibody extraction, clonal grouping, lineage tree construction, mutation profiling, diversity statistics, VJ gene assignment, antibody humanization, and more. Importantly, users can perform these analyses using the graphical user interface without any programming skills or scripts. In this article, we present a series of protocols that integrate Abalign's analysis modules into a cohesive workflow. This step‐by‐step workflow provides detailed instructions for software installation, data preparation, and comprehensive analysis of BCR immune repertoires. This workflow facilitates the efficient acquisition of comprehensive results in profiling BCR immune repertoires, offering insights into the impacts of infectious diseases, allergies, autoimmune disorders, tumor immunology, and antibody drugs. Abalign is freely available at http://cao.labshare.cn/abalign/. © 2024 Wiley Periodicals LLC.Basic Protocol 1: Resource preparationBasic Protocol 2: Analyzing BCR immune repertoiresSupport Protocol 1: Aiding antibody humanizationSupport Protocol 2: Constructing B‐cell lineage treesAlternate Protocol: Running with Linux command lineBasic Protocol 3: Comparing BCR immune repertoires
A Theoretical Insight into the Physical Characteristics of Double Perovskite Rb2TlInBr6 for Renewable Energy Applications
Authors: Qaid Saif M. H. , Ain Quratul , Akhtar Masoofa , Murtaza Hudabia , Ghaithan Hamid M. , Ahmed Abdullah Ahmed Ali , Munir Junaid 
Published: February 2024

AbstractMetal halide perovskites have gained prominence in optoelectronics recently, thanks to their unique optical and electrical properties, along with their adaptable morphologies. The current work reports the electronic, structural, mechanical, optical, and thermoelectric traits of Rb2TlInBr6 for the very first time. The confirmation of thermodynamic stability is evidenced by the negative value of the formation energy, while structural stability is established by calculating values for the tolerance factor and octahedral tilting. Elastic constants (Cij) and mechanical attributes are evaluated to assess perovskites’ ability to resist external strains. Electronic band structures computed with GGA and mBJ potentials depict a semiconducting nature containing indirect bandgap of 1.8 and 2.42 eV, respectively. Optical characteristics of Rb2TlInBr6 ensure that it can be used effectively for optoelectronic applications. An insight into the thermoelectric characteristic is assessed through BoltzTraP code. The electrical conductivity and ZT reveal the ability of Rb2TlInBr6 to be utilized in green energy devices.
First‐Principles Calculations to Investigate the Ground State, Mechanical Stability, Electronic Structure, and Optical Properties of Tl2SnX3 (X = S, Se, Te)
Authors: Alhussain Hanen , Ferjani Hela , Ben Smida Youssef 
Published: February 2024

AbstractIn this work, the Density Functional Theory (DFT) analysis of the Tl2SnX3 series (X = S, Se, Te) is performed, and the ground states are confirmed by the calculation of the elastic constant Cij. Based on the DFT calculation, the Tl2SnX3 structures are direct‐gap semiconductors with bandgaps of 1.434, 1.181, and 0.907 eV, respectively. Chalcogen substitution significantly impacts their electronic structures, notably increasing the Density of States (DOS) width in the valence band from sulfur to tellurium, and shifting the dielectric function's real part, ε1(ω), toward lower energies. This change means that the optical activity and response to electric fields are better, with Tl2SnTe3 showing the best polarization response and light‐matter interaction abilities. Optical tests show that Tl2SnTe3 has very high optical absorption, peaking at ≈17 × 104 cm−1 along [010], and reflectivity levels above 90%, marking its suitability for high‐reflectivity applications. Moreover, loss energy function analysis also shows that Tl2SnTe3 has a strong electron loss resonance at lower energies, which means it has strong interactions with electrons.
Hopf bifurcation analytical expression and control strategy in direct‐drive permanent magnet synchronous generator
Authors: Li Qiangqiang , Chen Wei , Wei Zhanhong , Wang Kun , Wang Bo 
Published: February 2024

SummaryThe unstable operation of a direct‐drive permanent magnet synchronous generator (DPMSG) is exacerbated by periodic oscillation, having a significant impact on the safe and stable functioning of wind energy generation systems. This paper proposes an approximate solution method for analyzing the periodic oscillation of the Hopf bifurcation and a method for suppressing its bifurcation through H∞ robust control. Firstly, a three‐dimensional nonlinear dynamic model of the DPMSG is constructed. Secondly, the Hopf bifurcation of the system with changes in internal parameters is solved using the time domain and frequency domain methods, and the harmonic balancing method is used to approximate the periodic solution at the point of Hopf bifurcation. The order of the Hopf bifurcation neighborhood is then decreased using the central manifold theorem. Finally, this study suggests a H∞ output feedback control employing bifurcation parameters. The Nyquist criteria are used for evaluating small signal stability and convergence speed of the response system in DPMSG before and after dimensionality reduction. The simulation results suggest that the proposed strategy helps to tackle the periodic solution expression and instability difficulties caused by Hopf bifurcation. This paper provides theoretical suggestions for the future reliable operation of new energy generation systems.
Homologous blood transfusion and doping: Where are we now?
Authors: Marchand Alexandre , Ericsson Magnus 
Published: February 2024

AbstractHomologous blood transfusion (HBT) is used for doping in endurance sports since the 1960s. The blood comes from a compatible donor, that is, someone with a compatible ABO and rhesus blood group. Despite been prohibited by the IOC in 1985, no detection method was available until 2003. Then came the idea to use red blood cells (RBC) minor blood groups antigens that constitute an “identity” card of someone's RBC to detect the presence of a second RBC population. The method validated for doping control samples uses flow cytometry after incubation of isolated RBC with eight to 12 primary antibodies against specific minor blood groups antigens. The presence of double populations of RBC is revealed by a major and a minor peak in a fluorescence histogram. The sensitivity was estimated sufficient to detect HBT for a few weeks. Despite the complexity and cost of the method, right after its application in 2004, several cases of HBT were identified but the number of cases dropped rapidly over the years. In the 2010s, other ways to detect HBT were developed and evaluated: indirect detection using the Athlete Biological Passport approach, and a few years later forensic DNA analysis to establish the presence of two different DNA in a blood sample after HBT. Despite the high specificity of the latter, the sensitivity was recently questioned in vivo. Nowadays, the flow cytometry method remains the method of choice for HBT detection and recent investigations helped to simplify the method and increase its specificity and sensitivity.