bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mathematical model of osteophyte development with the first attempt to identify a biomechanical parameter
Authors: Bednarczyk Ewa , Sikora Szymon , Jankowski Krzysztof , Żołek-Tryznowska Zuzanna , Murawski Tomasz , Bańczerowski Jakub , Lu Yanfei , Senderowski Cezary 
Published: January 2024

AbstractThe paper presents research on identifying a biomechanical parameter from a theoretical model of changes during osteoarthritis. In vitro experiments were carried out on quasi-3D chondrocyte cultures seeded on corn-starch hydrogel materials and subjected to mechanical stress on a designed and constructed stand. The results were adapted to a mathematical model and calculated on a simplified two-dimensional specimen. Numerical simulations have been performed to illustrate the growth of bone spurs. The observed changes of variables which determine osteophytes are qualitative and more correlated to the real-life observations.
Ursolic acid acetate and iso-mukaadial acetate bind to Plasmodium falciparum Hsp90, abrogating its chaperone function in vitro
Authors: Nndwammbi Andani A. T , Dongola Tendamudzimu Harmfree , Shonhai Addmore , Mokoena Fortunate , Pooe Ofentse J. , Simelane Mthokozisi B. C 
Published: January 2024

AbstractPlasmodium falciparum is the most lethal malaria parasite. Increasing incidences of drug resistance of P. falciparum have prompted the need for discovering new and effective antimalarial compounds with an alternative mode of action. Heat shock protein 90 (PfHsp90) facilitates protein folding and is a promising antimalarial drug target. We have previously reported that iso-mukaadial acetate (IMA) and ursolic acid acetate (UAA) exhibit antimalarial activity. We investigated the abilities of IMA and UAA to bind PfHsp90 by molecular docking and dynamics simulations. The in silico predictions were validated by biochemical assays conducted on recombinant PfHsp90. The interaction between the ligands and PfHsp90 was evaluated using ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FTIR), and surface plasmon resonance (SPR) analysis. The results obtained by docking calculations and MD dynamics simulation predicted that UAA and IMA preferentially bound to PfHsp90 via the N-terminal domain, with UAA binding more stable than IMA. UV-vis-based data suggest that PfHsp90 harbors buried aromatic amino acids, which were exposed in the presence of either IMA or UAA. In addition, data obtained using FTIR suggested that IMA and UAA destabilized the secondary structure of PfHsp90. Of the two compounds, UAA bound to PfHsp90 within the micromolar range based on surface plasmon resonance (SPR)-based binding assay. Furthermore, both compounds disrupted the holdase chaperone function of PfHsp90 as the chaperone failed to suppress heat-induced aggregation of the model proteins, malate dehydrogenase (MDH), luciferase, and citrate synthase in vitro. In addition, both compounds lowered the ATPase activity of PfHsp90. The molecular dynamics simulation analysis indicated that the docked complexes were mostly stable for 100 ns, validating the data obtained through the biochemical assays. Altogether, this study expands the repository of antiplasmodial compounds that have PfHsp90 among their possible targets.
Biosynthesis of Bt-Ag2O nanoparticles using Bacillus thuringiensis and their pesticidal and antimicrobial activities
Authors: Ge Jiajia , Hu Jianzhong , Cui Sufen , Wang Yirong , Xu Caijiayi , Liu Wenzhuo 
Published: January 2024

Abstract
Nanosilver oxide exhibits strong antibacterial and photocatalytic properties and has shown great application potential in food packaging, biochemical fields, and other fields involving diseases and pest control. In this study, Ag2O nanoparticles were synthesized using Bacillus thuringiensis (Bt-Ag2O NPs). The physicochemical characteristics of the Bt-Ag2O NPs were analyzed by UV‒vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscope (SEM), inductively coupled plasma emission spectrometry (ICP), high-resolution transmission electron microscopy (HR-TEM), and zeta potential. The phis-chemical characterization revealed that the Bt-Ag2O NPs are in spherical shape with the small particle size (18.24 nm), high crystallinity, well dispersity, and stability. The biopesticidal and antifungal effects of Bt-Ag2O NPs were tested against Tribolium castaneum, Aspergillus flavus, and Penicillium chrysogenum. The survival, growth, and reproduction of tested pests and molds were significantly inhibited by Bt-Ag2O NPs in a dose-dependent manner. Bt-Ag2O NPs showed higher pesticidal activities against T. castaneum than Bt and commercial Ag2O NPs. The LC50 values of Bt, Ag2O NPs, and Bt-Ag2O NPs were 0.139%, 0.072%, and 0.06% on day 14, respectively. The Bt-Ag2O NPs also showed well antifungal activities against A. flavus and P. chrysogenum, while it resulted a small inhibition zone than commercial Ag2O NPs did. In addition, A. flavus showed much more sensitive to Bt-Ag2O NP treatments, compared to P. chrysogenum. Our results revealed that Bt-Ag2O NPs synthesized using B. thuringiensis could act as pesticides and antifungal agents in stored-product fields.

Key points
• Bt-Ag2O NPs could be synthesized using Bacillus thuringiensis (Bt).
• The NPs showed a high degree of crystallinity, spherical shape, and small particle size.
• The NPs also showed excellent insecticidal and antifungal activity.
Combined 6-benzylaminopurine and H2O2 stimulate the astaxanthin biosynthesis in Xanthophyllomyces dendrorhous
Authors: Torres-Haro Alejandro , Verdín Jorge , Kirchmayr Manuel R. , Arellano-Plaza Melchor 
Published: January 2024

Abstract
Astaxanthin is one of the most attractive carotenoids due to its high antioxidant activity and beneficial biological properties, while Xanthophyllomyces dendrorhous is one of its main microbial sources. Since astaxanthin is synthesized as a response to oxidative stress, several oxidative agents have been evaluated to increase X. dendrorhous astaxanthin yields. However, the extent of the stimulation is determined by the cellular damage caused by the applied oxidative agent. Phytohormones have also been reported as stimulants of astaxanthin biosynthesis acting directly on its metabolic pathway and indirectly promoting cellular resistance to reactive oxygen species. We reasoned that both oxidative agents and phytohormones lead to increased astaxanthin synthesis, but the latter could mitigate the drawbacks of the former. Thus, here, the stimulation on astaxanthin biosynthesis, as well as the cellular and transcriptional responses of wild type X. dendrorhous to phytohormones (6-benzylaminopurine, 6-BAP; abscisic acid, ABA; and indole-3-acetic acid, IAA), and oxidative agents (glutamate, menadione, H2O2, and/or Fe2+) were evaluated as a single or combined treatments. ABA and 6-BAP were the best individual stimulants leading to 2.24- and 2.60-fold astaxanthin biosynthesis increase, respectively. Nevertheless, the effect of combined 6-BAP and H2O2 led to a 3.69-fold astaxanthin synthesis increase (0.127 ± 0.018 mg astaxanthin/g biomass). Moreover, cell viability (> 82.75%) and mitochondrial activity (> 82.2%) remained almost intact in the combined treatment (6-BAP + H2O2) compared to control (< 52.17% cell viability; < 85.3% mitochondrial activity). On the other hand, mRNA levels of hmgR, idi, crtYB, crtR, and crtS, genes of the astaxanthin biosynthetic pathway, increased transiently along X. dendrorhous fermentation due to stimulations assayed in this study.

Key points
• Combined 6-BAP and H2O2 is the best treatment to increase astaxanthin yields in X. dendrorhous.
• 6-BAP preserves cell integrity under oxidative H2O2 stress conditions.
• 6-BAP and H2O2 increase transcriptional responses of hmgR, idi, and crt family genes transiently.

Graphical abstract
Metagenomic analysis of hot spring soil for mining a novel thermostable enzybiotic
Authors: Pantiora Panagiota D. , Georgakis Nikolaos D. , Premetis Georgios E. , Labrou Nikolaos E. 
Published: January 2024

Abstract
The misuse and overuse of antibiotics have contributed to a rapid emergence of antibiotic-resistant bacterial pathogens. This global health threat underlines the urgent need for innovative and novel antimicrobials. Endolysins derived from bacteriophages or prophages constitute promising new antimicrobials (so-called enzybiotics), exhibiting the ability to break down bacterial peptidoglycan (PG). In the present work, metagenomic analysis of soil samples, collected from thermal springs, allowed the identification of a prophage-derived endolysin that belongs to the N-acetylmuramoyl-L-alanine amidase type 2 (NALAA-2) family and possesses a LysM (lysin motif) region as a cell wall binding domain (CWBD). The enzyme (Ami1) was cloned and expressed in Escherichia coli, and its bactericidal and lytic activity was characterized. The results indicate that Ami1 exhibits strong bactericidal and antimicrobial activity against a broad range of bacterial pathogens, as well as against isolated peptidoglycan (PG). Among the examined bacterial pathogens, Ami1 showed highest bactericidal activity against Staphylococcus aureus sand Staphylococcus epidermidis cells. Thermostability analysis revealed a melting temperature of 64.2 ± 0.6 °C. Overall, these findings support the potential that Ami1, as a broad spectrum antimicrobial agent, could be further assessed as enzybiotic for the effective treatment of bacterial infections.

Key points
• Metagenomic analysis allowed the identification of a novel prophage endolysin
• The endolysin belongs to type 2 amidase family with lysin motif region
• The endolysin displays high thermostability and broad bactericidal spectrum
Enhanced chlorobenzene removal by internal magnetic field through initial cell adhesion and biofilm formation
Authors: Chen Dong-zhi , Qiu Jinfeng , Sun Haimin , Liu Yanting , Ye Jiexu , Chen Jian-Meng , Lu Lichao 
Published: January 2024

Abstract
Magnetic fields (MF) have been proven efficient in bioaugmentation, and the internal MFs have become competitive because they require no configuration, despite their application in waste gas treatment remaining largely unexplored. In this study, we firstly developed an intensity-regulable bioaugmentation with internal MF for gaseous chlorobenzene (CB) treatment with modified packing in batch bioreactors, and the elimination capacity increased by up to 26%, surpassing that of the external MF. Additionally, the microbial affinity to CB and the packing surface was enhanced, which was correlated with the ninefold increased secreted ratio of proteins/polysaccharides, 43% promoted cell surface hydrophobicity, and half reduced zeta potential. Furthermore, the dehydrogenase content was promoted over 3 times, and CB removal steadily increased with the rising intensity indicating enhanced biofilm activity and reduced CB bioimpedance; this was further supported by kinetic analysis, which resulted in improved cell adhesive ability and biological utilisation of CB. The results introduced a novel concept of adjustable magnetic bioaugmentation and provided technical support for industrial waste gas treatments.

Key points
• Regulable magnetic bioaugmentation was developed to promote 26% chlorobenzene removal
• Chlorobenzene mineralisation was enhanced under the magnetic field
• Microbial adhesion was promoted through weakening repulsive forces

Graphical abstract
Microfluidics for adaptation of microorganisms to stress: design and application
Authors: Zoheir Ahmed E. , Stolle Camilla , Rabe Kersten S. 
Published: January 2024

Abstract
Microfluidic systems have fundamentally transformed the realm of adaptive laboratory evolution (ALE) for microorganisms by offering unparalleled control over environmental conditions, thereby optimizing mutant generation and desired trait selection. This review summarizes the substantial influence of microfluidic technologies and their design paradigms on microbial adaptation, with a primary focus on leveraging spatial stressor concentration gradients to enhance microbial growth in challenging environments. Specifically, microfluidic platforms tailored for scaled-down ALE processes not only enable highly autonomous and precise setups but also incorporate novel functionalities. These capabilities encompass fostering the growth of biofilms alongside planktonic cells, refining selection gradient profiles, and simulating adaptation dynamics akin to natural habitats. The integration of these aspects enables shaping phenotypes under pressure, presenting an unprecedented avenue for developing robust, stress-resistant strains, a feat not easily attainable using conventional ALE setups. The versatility of these microfluidic systems is not limited to fundamental research but also offers promising applications in various areas of stress resistance. As microfluidic technologies continue to evolve and merge with cutting-edge methodologies, they possess the potential not only to redefine the landscape of microbial adaptation studies but also to expedite advancements in various biotechnological areas.

Key points
• Microfluidics enable precise microbial adaptation in controlled gradients.
• Microfluidic ALE offers insights into stress resistance and distinguishes between resistance and persistence.
• Integration of adaptation-influencing factors in microfluidic setups facilitates efficient generation of stress-resistant strains.
The Statistical Theory of the Angiogenesis Equations
Authors: Birnir Björn , Bonilla Luis , Carretero Manuel , Terragni Filippo 
Published: January 2024

AbstractAngiogenesis is a multiscale process by which a primary blood vessel issues secondary vessel sprouts that reach regions lacking oxygen. Angiogenesis can be a natural process of organ growth and development or a pathological one induced by a cancerous tumor. A mean-field approximation for a stochastic model of angiogenesis consists of a partial differential equation (PDE) for the density of active vessel tips. Addition of Gaussian and jump noise terms to this equation produces a stochastic PDE that defines an infinite-dimensional Lévy process and is the basis of a statistical theory of angiogenesis. The associated functional equation has been solved and the invariant measure obtained. The results of this theory are compared to direct numerical simulations of the underlying angiogenesis model. The invariant measure and the moments are functions of a Korteweg–de Vries-like soliton, which approximates the deterministic density of active vessel tips.
Extreme low-frequency waves on the Ofu, American Samoa, reef flat
Authors: Cheriton Olivia M. , Storlazzi Curt D. , Oberle Ferdinand K. J. , Rosenberger Kurt J. , Brown Eric K. 
Published: January 2024

AbstractThe southern fringing reef along Ofu, American Samoa, has been a focus of coral research owing to the presence of super-heated pools on the reef flat, where corals thrive in elevated sea temperatures. Here, we present the first documentation of exceptionally large low-frequency (periods > 100 s) waves over this reef flat. During a large, southerly swell event, low-frequency waves on the inner reef flat had mean heights of 0.7 m and periods of 2–4 min and are estimated to have contributed up to 50% of the total water levels. One observed low-frequency wave had a trough-to-peak vertical height of 1.5 m, possibly representing the largest low-frequency wave ever directly observed on a reef flat. These large, low-frequency waves, which were likely amplified by reef resonance, are important factors in coastal hazards such as flooding and erosion and may also be relevant to coral health and resilience.
Crickets in the spotlight: exploring the impact of light on circadian behavior
Authors: Levy Keren , Barnea Anat , Tauber Eran , Ayali Amir 
Published: January 2024

AbstractCrickets serve as a well-established model organism in biological research spanning various fields, such as behavior, physiology, neurobiology, and ecology. Cricket circadian behavior was first reported over a century ago and prompted a wealth of studies delving into their chronobiology. Circadian rhythms have been described in relation to fundamental cricket behaviors, encompassing stridulation and locomotion, but also in hormonal secretion and gene expression. Here we review how changes in illumination patterns and light intensity differentially impact the different cricket behaviors as well as circadian gene expression. We further describe the cricket’s circadian pacemaker. Ample anatomical manipulations support the location of a major circadian pacemaker in the cricket optic lobes and another in the central brain, possibly interconnected via signaling of the neuropeptide PDF. The cricket circadian machinery comprises a molecular cascade based on two major transcriptional/translational negative feedback loops, deviating somewhat from the canonical model of Drosophila and emphasizing the significance of exploring alternative models. Finally, the nocturnal nature of crickets has provided a unique avenue for investigating the repercussions of artificial light at night on cricket behavior and ecology, underscoring the critical role played by natural light cycles in synchronizing cricket behaviors and populations, further supporting the use of the cricket model in the study of the effects of light on insects. Some gaps in our knowledge and challenges for future studies are discussed.
Association between telomere length and neuropsychological function at 4–5 years in children from the INMA project: a cross-sectional study
Authors: Campos-Sánchez Irene , Navarrete-Muñoz Eva María , Hurtado-Pomares Miriam , Júlvez Jordi , Lertxundi Nerea , Martens Dries S. , Fernández-Somoano Ana , Riaño-Galán Isolina , Guxens Mònica , Ibarluzea Jesús María , Nawrot Tim , Valera-Gran Desirée 
Published: January 2024

AbstractShortened telomere length (TL) has been associated with lower cognitive performance, different neurological diseases in adults, and certain neurodevelopmental disorders in children. However, the evidence about the association between TL and neuropsychological developmental outcomes in children from the general population is scarce. Therefore, this study aimed to explore the association between TL and neuropsychological function in children 4–5 years of age. We included 686 children from the INMA Project, a population-based birth cohort in Spain. Leucocyte TL was determined by quantitative PCR method, and neuropsychological outcomes were measured using the McCarthy Scales of Children’s Abilities (MCSA). Multiple linear regression models were used to estimate associations adjusted for potential confounding variables. Main findings showed that a longer TL was associated with a higher mean working memory score (β = 4.55; 95% CI = 0.39, 8.71). In addition, longer TL was associated with a higher mean global quantitative score (β = 3.85; 95% CI = −0.19, 7.89), although the association was marginally significant. To our knowledge, this is the first study that shows a positive association between TL and better neuropsychological outcomes in children. Although further research is required to confirm these results, this study supports the hypothesis that TL is essential in protecting and maintaining a child’s health, including cognitive functions such as working memory.
Effects of small heat shock proteins from thermotolerant bacteria on the stress resistance of Escherichia coli to temperature, pH, and hyperosmolarity
Authors: Sato Yu , Okano Kenji , Honda Kohsuke 
Published: January 2024

AbstractSmall heat shock proteins (HSPs), such as HSP20, represent cellular thermal resistance mechanisms, to avoid protein aggregation at elevated temperatures. Recombinantly expressed HSP20s serve as a molecular tool for improving the tolerance of living cells to various physical and chemical stressors. Here, we aimed to heterologously express 18 HSP20s from 12 thermotolerant bacteria in Escherichia coli and evaluate their effects on various physical and chemical cellular stresses. Seventeen HSP20s were successfully expressed as soluble proteins. Recombinant E. coli cells were subjected to heat, cold, acidic, alkaline, and hyperosmolar stress to evaluate the effects of HSP20 proteins on stress resistance. Notably, the overexpression of 15 HSP20s enhanced the stress resistance of E. coli compared to that of the control strain. In particular, HSPs from Tepidimonas sediminis and Oceanithermus profundus improved the stress tolerance of E. coli under all tested conditions. In addition, E. coli harboring HSP20 from T. sediminis retained cell viability even after heat treatment at 52 °C for 5 days. To our knowledge, this is the first report of E. coli tolerance to prolonged (> 100 h) high-temperature stress. These findings indicate the potential of thermotolerant HSPs as molecular tools for improving stress tolerance in E. coli.
Risk factors, outcomes, and epidemiological and etiological study of hospitalized COVID-19 patients with bacterial co-infection and secondary infections
Authors: Duan Yishan , Wang Jing , Wang Suyan , Zhang Rui , Hu Jinrui , Li Weimin , Chen Bojiang 
Published: January 2024

Abstract
Background
As a common complication of viral respiratory tract infection, bacterial infection was associated with higher mortality and morbidity. Determining the prevalence, culprit pathogens, outcomes, and risk factors of co-infection and secondary infection occurring in hospitalized patients with coronavirus disease 2019 (COVID-19) will be beneficial for better antibiotic management.

Methods
In this retrospective cohort research, we assessed clinical characteristics, laboratory parameters, microbiologic results, and outcomes of laboratory-confirmed COVID-19 patients with bacterial co-infection and secondary infection in West China Hospital from 2022 December 2nd to 2023 March 15th.

Results
The incidence of bacterial co-infection and secondary infection, as defined by positive culture results of clinical specimens, was 16.3% (178/1091) and 10.1% (110/1091) respectively among 1091 patients. Acinetobacter, Klebsiella, and Pseudomonas were the most commonly identified bacteria in respiratory tract samples of COVID-19 patients. In-hospital mortality of COVID-19 patients with co-infection (17.4% vs 9.5%, p = 0.003) and secondary infection (28.2% vs 9.5%, p < 0.001) greatly exceeded that of COVID-19 patients without bacterial infection. Cardiovascular disease (1.847 (1.202–2.837), p = 0.005), severe COVID-19 (1.694 (1.033–2.778), p = 0.037), and critical COVID-19 (2.220 (1.196–4.121), p = 0.012) were proved to be risk factors for bacterial co-infection, while only critical COVID-19 (1.847 (1.202–2.837), p = 0.005) was closely related to secondary infection.

Conclusions
Bacterial co-infection and secondary infection could aggravate the disease severity and worsen clinical outcomes of COVID-19 patients. Notably, only critical COVID-19 subtype was proved to be an independent risk factor for both co-infection and secondary infection. Therefore, standard empirical antibiotics was recommended for critically ill COVID-19 rather than all the inpatients according to our research.