bluuebunny/crossref_metadata_2025 huggingface dataset:
Blockchain-Based Unbalanced PSI with Public Verification and Financial Security
Authors: Wang Zhanshan , Ma Xiaofeng
Published: May 2024

Private set intersection (PSI) enables two parties to determine the intersection of their respective datasets without revealing any information beyond the intersection itself. This paper particularly focuses on the scenario of unbalanced PSI, where the sizes of datasets possessed by the parties can significantly differ. Current protocols for unbalanced PSI under the malicious security model exhibit low efficiency, rendering them impractical in real-world applications. By contrast, most efficient unbalanced PSI protocols fail to guarantee the correctness of the intersection against a malicious server and cannot even ensure the client’s privacy. The present study proposes a blockchain-based unbalanced PSI protocol with public verification and financial security that enables the client to detect malicious behavior from the server (if any) and then generate an irrefutable and publicly verifiable proof without compromising its secret. The proof can be verified through smart contracts, and some economic incentive and penalty measures are executed automatically to achieve financial security. Furthermore, we implement the proposed protocol, and experimental results demonstrate that our scheme exhibits low online communication complexity and computational overhead for the client. At the same time, the size of the generated proof and its verification complexity are both O(logn), enabling cost-effective validation on the blockchain.
On Some Multipliers Related to Discrete Fractional Integrals
Authors: Cheng Jinhua
Published: May 2024

This paper explores the properties of multipliers associated with discrete analogues of fractional integrals, revealing intriguing connections with Dirichlet characters, Euler’s identity, and Dedekind zeta functions of quadratic imaginary fields. Employing Fourier transform techniques, the Hardy–Littlewood circle method, and a discrete analogue of the Stein–Weiss inequality on product space through implication methods, we establish ℓp→ℓq bounds for these operators. Our results contribute to a deeper understanding of the intricate relationship between number theory and harmonic analysis in discrete domains, offering insights into the convergence behavior of these operators.
Exploring Trust Dynamics in Online Social Networks: A Social Network Analysis Perspective
Authors: Kridera Stavroula , Kanavos Andreas
Published: May 2024

This study explores trust dynamics within online social networks, blending social science theories with advanced machine-learning (ML) techniques. We examine trust’s multifaceted nature—definitions, types, and mechanisms for its establishment and maintenance—and analyze social network structures through graph theory. Employing a diverse array of ML models (e.g., KNN, SVM, Naive Bayes, Gradient Boosting, and Neural Networks), we predict connection strengths on Facebook, focusing on model performance metrics such as accuracy, precision, recall, and F1-score. Our methodology, executed in Python using the Anaconda distribution, unveils insights into trust formation and sustainability on social media, highlighting the potent application of ML in understanding these dynamics. Challenges, including the complexity of modeling social behaviors and ethical data use concerns, are discussed, emphasizing the need for continued innovation. Our findings contribute to the discourse on trust in social networks and suggest future research directions, including the application of our methodologies to other platforms and the study of online trust over time. This work not only advances the academic understanding of digital social interactions but also offers practical implications for developers, policymakers, and online communities.
The Role of Nitrate Supply in Bioactive Compound Synthesis and Antioxidant Activity in the Cultivation of Porphyra linearis (Rhodophyta, Bangiales) for Future Cosmeceutical and Bioremediation Applications
Authors: Pereira Débora Tomazi , Korbee Nathalie , Vega Julia , Figueroa Félix L.
Published: May 2024

Porphyra sensu lato has economic importance for food and pharmaceutical industries due to its significant physiological activities resulting from its bioactive compounds (BACs). This study aimed to determine the optimal nitrate dosage required in short-term cultivation to achieve substantial BAC production. A nitrate experiment using varied concentrations (0 to 6.5 mM) revealed optimal nitrate uptake at 0.5 mM in the first two days and at 3 and 5 mM in the last five days. Polyphenols and carbohydrates showed no differences between treatments, while soluble proteins peaked at 1.5 and 3 mM. Total mycosporine-like amino acids (MAAs) were highest in algae incubated at 5 and 6.5 mM, and the highest antioxidant activity was observed in the 5 mM, potentially related to the MAAs amount. Total carbon and sulfur did not differ between treatments, while nitrogen decreased at higher nitrate. This discovery highlights the nuanced role of nitrate in algal physiology, suggesting that biological and chemical responses to nitrate supplementation can optimize an organism’s health and its commercially significant bioactive potential. Furthermore, given its ability to absorb high doses of nitrate, this alga can be cultivated in eutrophic zones or even in out-/indoor tanks, becoming an excellent option for integrated multi-trophic aquaculture (IMTA) and bioremediation.
Humidification during Invasive and Non-Invasive Ventilation: A Starting Tool Kit for Correct Setting
Authors: Re Riccardo , Lassola Sergio , De Rosa Silvia , Bellani Giacomo
Published: May 2024

The humidification process of medical gases plays a crucial role in both invasive and non-invasive ventilation, aiming to mitigate the complications arising from bronchial dryness. While passive humidification systems (HME) and active humidification systems are prevalent in routine clinical practice, there is a pressing need for further evaluation of their significance. Additionally, there is often an incomplete understanding of the operational mechanisms of these devices. The current review explores the historical evolution of gas conditioning in clinical practice, from early prototypes to contemporary active and passive humidification systems. It also discusses the physiological principles underlying humidity regulation and provides practical guidance for optimizing humidification parameters in both invasive and non-invasive ventilation modalities. The aim of this review is to elucidate the intricate interplay between temperature, humidity, and patient comfort, emphasizing the importance of individualized approaches to gas conditioning.
Clinical Evaluation of VITEK MS PRIME with PICKME Pen for Bacteria and Yeasts, and RUO Database for Filamentous Fungi
Authors: Lee Hyeyoung , Koo Jehyun , Oh Junsang , Cho Sung-Il , Lee Hyunjoo , Lee Hyun Ji , Sung Gi-Ho , Kim Jayoung
Published: May 2024

The VITEK MS PRIME (bioMérieux, Marcy-l’Étoile, France), a newly developed matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, alongside the VITEK PICKME pen (PICKME), offers easy sample preparation for bacteria and yeasts. The VITEK MS PRIME also offers two software platforms for filamentous fungi: the IVD database and the RUO database. Our study evaluated its identification agreement on 320 clinical isolates of bacteria and yeasts, comparing PICKME and traditional wooden toothpick sampling techniques against MicroIDSys Elite (ASTA) results. Additionally, we assessed the IVD (v3.2) and SARAMIS (v4.16) RUO databases on 289 filamentous fungi against molecular sequencing. The concordance rates for species-level identification of bacteria and yeasts were about 89.4% (286/320) between the PICKME and wooden toothpick, and about 83.4–85.3% between the VITEK MS PRIME and ASTA MicroIDSys Elite. Retesting with PICKME improved concordance to 91.9%. For filamentous fungi, species-level identification reached 71.3% with the IVD database and 85.8% with RUO, which significantly enhanced basidiomycetes’ identification from 35.3% to 100%. Some strains in the IVD database, like Aspergillus versicolor, Exophiala xenobiotica, and Nannizzia gypsea, failed to be identified. The VITEK MS PRIME with PICKME offers reliable and efficient microorganism identification. For filamentous fungi, combined use of the RUO database can be beneficial, especially for basidiomycetes.
Metallo-Glycodendrimeric Materials against Enterotoxigenic Escherichia coli
Authors: El Riz Aly , Tchoumi Neree Armelle , Mousavifar Leila , Roy René , Chorfi Younes , Mateescu Mircea Alexandru
Published: May 2024

Conjugation of carbohydrates to nanomaterials has been extensively studied and recognized as an alternative in the biomedical field. Dendrimers synthesized with mannose at the end group and with entrapped zero-valent copper/silver could be a potential candidate against bacterial proliferation. This study is aimed at investigating the bactericidal activity of metal-glycodendrimers. The Cu(I)-catalyzed azide–alkyne cycloaddition (CuAAC) reaction was used to synthesize a new mannosylated dendrimer containing 12 mannopyranoside residues in the periphery. The enterotoxigenic Escherichia coli fimbriae 4 (ETEC:F4) viability, measured at 600 nm, showed the half-inhibitory concentration (IC50) of metal-free glycodendrimers (D), copper-loaded glycodendrimers (D:Cu) and silver-loaded glycodendrimers (D:Ag) closed to 4.5 × 101, 3.5 × 101 and to 1.0 × 10−2 µg/mL, respectively, and minimum inhibitory concentration (MIC) of D, D:Cu and D:Ag of 2.0, 1.5 and 1.0 × 10−4 µg/mL, respectively. The release of bacteria contents onto broth and the inhibition of ETEC:F4 biofilm formation increased with the number of metallo-glycodendrimer materials, with a special interest in silver-containing nanomaterial, which had the highest activity, suggesting that glycodendrimer-based materials interfered with bacteria-bacteria or bacteria–polystyrene interactions, with bacteria metabolism and can disrupt bacteria cell walls. Our findings identify metal–mannose-dendrimers as potent bactericidal agents and emphasize the effect of entrapped zero-valent metal against ETEC:F4.
Point-of-Care Method T2Bacteria®Panel Enables a More Sensitive and Rapid Diagnosis of Bacterial Blood Stream Infections and a Shorter Time until Targeted Therapy than Blood Culture
Authors: Clodi-Seitz Tamara , Baumgartner Sebastian , Turner Michael , Mader Theresa , Hind Julian , Wenisch Christoph , Zoufaly Alexander , Presterl Elisabeth
Published: May 2024

Background: Rapid diagnosis and identification of pathogens are pivotal for appropriate therapy of blood stream infections. The T2Bacteria®Panel, a culture-independent assay for the detection of Escherichia coli, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa in blood, was evaluated under real-world conditions as a point-of-care method including patients admitted to the internal medicine ward due to suspected blood stream infection. Methods: Patients were assigned to two groups (standard of care—SOC vs. T2). In the SOC group 2 × 2 blood culture samples were collected, in the T2 group the T2Bacteria®Panel was performed additionally for pathogen identification. Results: A total of 94 patients were included. Pathogens were detected in 19 of 50 patients (38%) in the T2 group compared to 16 of 44 patients (36.4%) in the SOC group. The median time until pathogen detection was significantly shorter in the T2 group (4.5 h vs. 60 h, p < 0.001), as well as the time until targeted therapy (antibiotic with the narrowest spectrum and maximal effectiveness) (6.4 h vs. 42.2 h, p = 0.043). Conclusions: The implementation of the T2Bacteria®Panel for patients with sepsis leads to an earlier targeted antimicrobial therapy resulting in earlier sufficient treatment and decreased excessive usage of broad-spectrum antimicrobials.
Interruption after Short-Term Nitrogen Additions Improves Ecological Stability of Larix olgensis Forest Soil by Affecting Bacterial Communities
Authors: Qu Tongbao , Zhao Xiaoting , Yan Siyu , Liu Yushan , Ameer Muhammad Jamal , Zhao Lei
Published: May 2024

Atmospheric nitrogen deposition can alter soil microbial communities and further impact the structure and function of forest ecosystems. However, most studies are focused on positive or negative effects after nitrogen addition, and few studies pay attention to its interruption. In order to investigate whether interruption after different levels of short-term N additions still benefit soil health, we conducted a 2-year interruption after a 4-year short-term nitrogen addition (10 and 20 kg N·hm−2·yr−1) experiment; then, we compared soil microbial diversity and structure and analyzed soil physicochemical properties and their correlations before and after the interruption in Larix olgensis forest soil in northeast China. The results showed that soil ecological stabilization of Larix olgensis forest further improved after the interruption compared to pre-interruption. The TN, C:P, N:P, and C:N:P ratios increased significantly regardless of the previous nitrogen addition concentration, and soil nutrient cycling was further promoted. The relative abundance of the original beneficial microbial taxa Gemmatimonas, Sphingomonas, and Pseudolabrys increased; new beneficial bacteria Ellin6067, Massilia, Solirubrobacter, and Bradyrhizobium appeared, and the species of beneficial soil microorganisms were further improved. The results of this study elucidated the dynamics of the bacterial community before and after the interruption of short-term nitrogen addition and could provide data support and a reference basis for forest ecosystem restoration strategies and management under the background of global nitrogen deposition.
Long Non-Coding RNA Analysis: Severe Pathogenicity in Chicken Embryonic Visceral Tissues Infected with Highly Virulent Newcastle Disease Virus—A Comparison to the Avirulent Vaccine Virus
Authors: Sha Yuxin , Liu Xinxin , Yan Weiwen , Wang Mengjun , Li Hongjin , Jiang Shanshan , Wang Sijie , Ren Yongning , Zhang Kexin , Yin Renfu
Published: May 2024

There are significant variations in pathogenicity among different virulent strains of the Newcastle disease virus (NDV). Virulent NDV typically induces severe pathological changes and high mortality rates in infected birds, while avirulent NDV usually results in asymptomatic infection. Currently, the understanding of the specific mechanisms underlying the differences in host pathological responses and symptoms caused by various virulent NDV strains remains limited. Long non-coding RNA (lncRNA) can participate in a range of biological processes and plays a crucial role in viral infection and replication. Therefore, this study employed RNA-Seq to investigate the transcriptional profiles of chicken embryos’ visceral tissues (CEVTs) infected with either the virulent NA-1 strain or avirulent LaSota strain at 24 hpi and 36 hpi. Using bioinformatic methods, we obtained a total of 2532 lncRNAs, of which there were 52 and 85 differentially expressed lncRNAs at 24 hpi and 36 hpi, respectively. LncRNA analysis revealed that the severe pathological changes and symptoms induced by virulent NDV infection may be partially attributed to related target genes, regulated by differentially expressed lncRNAs such as MSTRG.1545.5, MSTRG.14601.6, MSTRG.7150.1, and MSTRG.4481.1. Taken together, these findings suggest that virulent NDV infection exploits the host’s metabolic resources and exerts an influence on the host’s metabolic processes, accompanied by excessive activation of the immune response. This impacts the growth and development of each system of CEVTs, breaches the blood–brain barrier, inflicts severe damage on the nervous system, and induces significant lesions. These observations may be attributed to variations in pathology. Consequently, novel insights were obtained into the intricate regulatory mechanisms governing NDV and host interactions. This will aid in unraveling the molecular mechanisms underlying both virulent and avirulent forms of NDV infection.
Ironing out Persisters? Revisiting the Iron Chelation Strategy to Target Planktonic Bacterial Persisters Harboured in Carbapenem-Resistant Escherichia coli
Authors: Yeo Jia Hao , Begam Nasren , Leow Wan Ting , Goh Jia Xuan , Zhong Yang , Cai Yiying , Kwa Andrea Lay-Hoon
Published: May 2024

Antibiotic resistance is a global health crisis. Notably, carbapenem-resistant Enterobacterales (CRE) pose a significant clinical challenge due to the limited effective treatment options. This problem is exacerbated by persisters that develop upon antibiotic exposure. Bacteria persisters can tolerate high antibiotic doses and can cause recalcitrant infections, potentially developing further antibiotic resistance. Iron is a critical micronutrient for survival. We aimed to evaluate the utility of iron chelators, alone and in combination with antibiotics, in managing persisters. We hypothesized that iron chelators eradicate CRE persisters in vitro, when administered in combination with antibiotics. Our screening revealed three clinical isolates with bacteria persisters that resuscitated upon antibiotic removal. These isolates were treated with both meropenem and an iron chelator (deferoxamine mesylate, deferiprone or dexrazoxane) over 24 h. Against our hypothesis, bacteria persisters survived and resuscitated upon withdrawing both the antibiotic and iron chelator. Pursuing our aim, we next hypothesized that iron chelation is feasible as a post-antibiotic treatment in managing and suppressing persisters’ resuscitation. We exposed bacteria persisters to an iron chelator without antibiotics. Flow cytometric assessments revealed that iron chelators are inconsistent in suppressing persister resuscitation. Collectively, these results suggest that the iron chelation strategy may not be useful as an antibiotic adjunct to target planktonic bacteria persisters.
Spatial Distribution Patterns and Assembly Processes of Abundant and Rare Fungal Communities in Pinus sylvestris var. mongolica Forests
Authors: Mumin Reyila , Wang Dan-Dan , Zhao Wen , Huang Kai-Chuan , Li Jun-Ning , Sun Yi-Fei , Cui Bao-Kai
Published: May 2024

Revealing the biogeography and community assembly mechanisms of soil microorganisms is crucial in comprehending the diversity and maintenance of Pinus sylvestris var. mongolica forests. Here, we used high-throughput sequencing techniques and null model analysis to explore the distribution patterns and assembly processes of abundant, rare, and total fungal communities in P. sylvestris var. mongolica forests based on a large-scale soil survey across northern China. Compared to the abundant and total taxa, the diversity and composition of rare taxa were found to be more strongly influenced by regional changes and environmental factors. At the level of class, abundant and total taxa were dominated by Agaricomycetes and Leotiomycetes, while Agaricomycetes and Sordariomycetes were dominant in the rare taxa. In the functional guilds, symbiotrophic fungi were advantaged in the abundant and total taxa, and saprotrophic fungi were advantaged in the rare taxa. The null model revealed that the abundant, rare, and total taxa were mainly governed by stochastic processes. However, rare taxa were more influenced by deterministic processes. Precipitation and temperature were the key drivers in regulating the balance between stochastic and deterministic processes. This study provides new insights into both the biogeographical patterns and assembly processes of soil fungi in P. sylvestris var. mongolica forests.
Intestinal Emphysema and Gut Bacterial Microbiota Composition
Authors: Hattab Jasmine , Rosamilia Alfonso , Guarnieri Chiara , Sciota Domenico , Marruchella Giuseppe , Tiscar Pietro Giorgio
Published: May 2024

Pneumatosis cystoides intestinalis, or intestinal emphysema, is a condition characterized by the presence of multiple cystic structures within the gut wall and on the serosal surface of the intestine. Intestinal emphysema represents an accidental finding in swine, although it can be clinically relevant in humans. Its etiology is unknown, and many theories have been proposed. Among them, a bacterial etiology is considered the most likely. Therefore, in this study, the V3-V4 region of the 16S rRNA gene was sequenced from 19 swine ileal tracts, 12 with intestinal emphysema and 7 without lesions, to detect a possible bacterial agent. In parallel, prevalence was estimated. Escherichia–Shigella (13.15%), Clostridium_sensu_stricto_1; s__uncultured_bacterium (7.09%), and Fusobacterium; s_uncultured bacterium (6.60%) were the most abundant species identified. No statistically relevant differences were observed between the pathological and physiological groups. Prevalence ranged from 1.25 to 5.12% depending on the batch. Our results suggest that the gut wall bacterial microbiota greatly match the normal gut microbiota, and that the etiological agent of intestinal emphysema may be (1) undetectable due to the chronicity of the lesions, (2) not considered statistically relevant in comparing the two groups (p < 0.05) and likewise in causing lesions, and (3) undetectable due to contamination. Regarding prevalence, the condition is moderately frequent.
Machine Learning-Based Identification of Mating Type and Metalaxyl Response in Phytophthora infestans Using SSR Markers
Authors: Agho Collins A. , Śliwka Jadwiga , Nassar Helina , Niinemets Ülo , Runno-Paurson Eve
Published: May 2024

Phytophthora infestans is the causal agent of late blight in potato. The occurrence of P. infestans with both A1 and A2 mating types in the field may result in sexual reproduction and the generation of recombinant strains. Such strains with new combinations of traits can be highly aggressive, resistant to fungicides, and can make the disease difficult to control in the field. Metalaxyl-resistant isolates are now more prevalent in potato fields. Understanding the genetic structure and rapid identification of mating types and metalaxyl response of P. infestans in the field is a prerequisite for effective late blight disease monitoring and management. Molecular and phenotypic assays involving molecular and phenotypic markers such as mating types and metalaxyl response are typically conducted separately in the studies of the genotypic and phenotypic diversity of P. infestans. As a result, there is a pressing need to reduce the experimental workload and more efficiently assess the aggressiveness of different strains. We think that employing genetic markers to not only estimate genotypic diversity but also to identify the mating type and fungicide response using machine learning techniques can guide and speed up the decision-making process in late blight disease management, especially when the mating type and metalaxyl resistance data are not available. This technique can also be applied to determine these phenotypic traits for dead isolates. In this study, over 600 P. infestans isolates from different populations—Estonia, Pskov region, and Poland—were classified for mating types and metalaxyl response using machine learning techniques based on simple sequence repeat (SSR) markers. For both traits, random forest and the support vector machine demonstrated good accuracy of over 70%, compared to the decision tree and artificial neural network models whose accuracy was lower. There were also associations (p < 0.05) between the traits and some of the alleles detected, but machine learning prediction techniques based on multilocus SSR genotypes offered better prediction accuracy.
Antibiotic Resistance Profiles in Eye Infections: A Local Concern with a Retrospective Focus on a Large Hospital in Northern Italy
Authors: Drago Lorenzo , Minasi Vincenzo , Lembo Andrea , Uslenghi Angela , Benedetti Sofia , Covi Matteo , Nucci Paolo , Deflorio Loredana
Published: May 2024

The emergence of antibiotic resistance poses a significant threat to public health worldwide, affecting various medical fields, including ophthalmology. Eye infections, ranging from conjunctivitis to more severe conditions like keratitis, are commonly treated with antibiotics. However, the misuse and overuse of these drugs have led to the development of resistant strains of bacteria, allowing traditional treatments ineffective. This paper aims to examine the current situation of antibiotic resistance in eye infections globally, with a specific focus on a large group of hospitals located in Milan (Italy) with considerable experience in cataract and cornea surgery as well as in retinopathy. The results of the study show the prevalence of Gram-positives in the tested samples and a low resistance of fluoroquinolones and glycopeptides. The results also highlight the need to implement sample collection methods for ocular infections, as the quantity of positive samples is rather low compared to the total number of samples. In conclusion, the study, although with limited data, shows that resistance to aminoglycosides and cephalosporins is a situation to be monitored. These data also show the critical need to improve and guide the biological sample collection modalities in order to make the diagnosis more reliable.
Veratryl Alcohol Attenuates the Virulence and Pathogenicity of Pseudomonas aeruginosa Mainly via Targeting las Quorum-Sensing System
Authors: Fu Songzhe , Song Wenxu , Han Xiaofeng , Chen Lin , Shen Lixin
Published: May 2024

Pseudomonas aeruginosa is an opportunistic pathogen that usually causes chronic infections and even death in patients. The treatment of P. aeruginosa infection has become more challenging due to the prevalence of antibiotic resistance and the slow pace of new antibiotic development. Therefore, it is essential to explore non-antibiotic methods. A new strategy involves screening for drugs that target the quorum-sensing (QS) system. The QS system regulates the infection and drug resistance in P. aeruginosa. In this study, veratryl alcohol (VA) was found as an effective QS inhibitor (QSI). It effectively suppressed the expression of QS-related genes and the subsequent production of virulence factors under the control of QS including elastase, protease, pyocyanin and rhamnolipid at sub-inhibitory concentrations. In addition, motility activity and biofilm formation, which were correlated with the infection of P. aeruginosa, were also suppressed by VA. In vivo experiments demonstrated that VA could weaken the pathogenicity of P. aeruginosa in Chinese cabbage, Drosophila melanogaster, and Caenorhabditis elegans infection models. Molecular docking, combined with QS quintuple mutant infection analysis, identified that the mechanism of VA could target the LasR protein of the las system mainly. Moreover, VA increased the susceptibility of P. aeruginosa to conventional antibiotics of tobramycin, kanamycin and gentamicin. The results firstly demonstrate that VA is a promising QSI to treat infections caused by P. aeruginosa.
Comparative Genomics Unveils Functional Diversity, Pangenome Openness, and Underlying Biological Drivers among Bacillus subtilis Group
Authors: Wang Taiquan , Shi Yiling , Zheng Mengzhuo , Zheng Jinshui
Published: May 2024

The Bacillus subtilis group (Bs group), with Bacillus subtilis as its core species, holds significant research and economic value in various fields, including science, industrial production, food, and pharmaceuticals. However, most studies have been confined to comparative genomics analyses and exploration within individual genomes at the level of species, with few conducted within groups across different species. This study focused on Bacillus subtilis, the model of Gram-positive bacteria, and 14 other species with significant research value, employing comparative pangenomics as well as population enrichment analysis to ascertain the functional enrichment and diversity. Through the quantification of pangenome openness, this work revealed the underlying biological drivers and significant correlation between pangenome openness and various factors, including the distribution of toxin–antitoxin- and integrase-related genes, as well as the number of endonucleases, recombinases, repair system-related genes, prophages, integrases, and transfer mobile elements. Furthermore, the functional enrichment results indicated the potential for secondary metabolite, probiotic, and antibiotic exploration in Bacillus licheniformis, Bacillus paralicheniformis, and Bacillus spizizenii, respectively. In general, this work systematically exposed the quantification of pangenome openness, biological drivers, the pivotal role of genomic instability factors, and mobile elements, providing targeted exploration guidance for the Bs group.
Infective Endocarditis—Characteristics and Prognosis According to the Affected Valves
Authors: Dobreva-Yatseva Bistra , Nikolov Fedya , Raycheva Ralitsa , Tokmakova Mariya
Published: May 2024

Background: Infective endocarditis (IE) continues to be a disease with high mortality despite medical advances. Objective: The objective of this study was to investigate the characteristics and prognosis of IE according to the affected valves. Materials and methods: This study was retrospective and single-centered, and it included 270 patients with a diagnosis of IE, for the period 2005–2021, who received treatment at the University Hospital “St. Georgi” in Plovdiv, Bulgaria. Results: Single-valve IE (SIE) was found in 82.6% (n-223), multivalvular IE (MIE) in 16.66% (n = 45) and device IE (CDRIE) in 0.74% (n = 2) of patients. The most commonly affected valve was the aortic valve, in 44.8% (n = 121). The predominant multivalvular involvement was aortic–mitral valves (AV-MV) (13.7%, n = 37). The patients with tricuspid valve (TV) IE were significantly younger, at 39 (30) years, and were more frequently male (80.8%). Mortality was higher in MIE than in SIE (31.1% vs. 23.8%) and was the highest in multivalve aortic–tricuspid (AV-TV) IE (75%). Early surgery was performed most in AV-MV IE, in 29.7% (n = 11). The Charlson comorbidity index (CCI) was significantly higher in MV 4 (4) and AV 3 (3) vs. TV IE 1 (5) (p = 0.048 and p = 0.011, respectively). Septic shock occurred most frequently in AV-TV involvement (75%; p = 0.0001). The most common causative agents were of the Staphylococcus group. Staphylococcus aureus more often affected TV alone (46.2%, n = 124) vs. AV (9.9%, n = 14; p = 0.0001) and vs. MV (22.6%, n = 17; p = 0.022); Staphylococcus coagulase-negative (CNG) was the prevalent cause of MV IE (22.7%, n = 17) vs. AV-MV (2.7%, n = 1; p = 0.007). Streptococci were represented in a low percentage and only in left-sided IE, more frequently in AV-MV (18.9%, n = 7) vs. AV (6.6%, n = 8; p = 0.025). Conclusions: The aortic valve is the most frequently affected valve, as single-valve IE or as multivalve AV-MV, with the predominant causative agents being of the Staphylococcus group. AV-TV IE has the worst prognosis, with the most common complication of septic shock and the highest in-hospital mortality.
Distinct Gastrointestinal and Reproductive Microbial Patterns in Female Holobiont of Infertility
Authors: Marcos Ana T. , Rus Maria J. , Areal-Quecuty Victoria , Simon-Soro Aurea , Navarro-Pando José Manuel
Published: May 2024

The microbiota is in symbiosis with the human body as a holobiont. Infertility conditions affect the female reproductive tract (FRT) and its resident microbiota. However, a disturbance in homeostasis could influence the FRT and other distal body sites, such as the gastrointestinal tract (GIT). We included 21 patients with endometriosis and other infertility-associated diseases with clinical profiles and biological samples from the FRT (endometrium, endometrial fluid, and vagina), and GIT samples (oral and feces). We performed a 16S rRNA analysis of site-specific microbial communities and estimated diversity metrics. The study found body site-specific microbial patterns in the FRT–GIT. In both study groups, Lactobacillus was the most shared Amplicon Sequence Variant (ASV), a precise identifier of microbial sequences, between endometrial and vagina samples. However, shared Gardnerella and Enterobacteriaceae ASVs were linked to other conditions but not endometriosis. Remarkably, Haemophilus was a specific GIT-shared taxon in endometriosis cases. In conclusion, infertility influences distinctly the FRT and GIT microbiomes, with endometriosis showing unique microbial characteristics. We proposed the concept of ‘female holobiont’ as a community that comprises the host and microbes that must maintain overall homeostasis across all body sites to ensure a woman’s health. Insights into these microbial patterns not only advance our understanding of the pathophysiology of infertility but also open new avenues for developing microbe-based therapeutic interventions aimed at restoring microbial balance, thereby enhancing fertility prospects.
Epidemiological Investigation of Goose Astrovirus in Hebei Province, China, 2019–2021
Authors: Chen Ligong , Cui Huan , Li Jiaqi , Zhang Yuxin , Wang Heng , Yang Yejin , Wang Xuejing , Zhang Cheng , Liu Juxiang
Published: May 2024

The goose astrovirus (GAstV), a key pathogen causing visceral gout and high mortality in geese, has spread widely in China, with frequent outbreaks in recent years. Outbreaks and transmissions of this virus have been reported across China, causing considerable economic losses to the goose industry worldwide, with losses exceeding tens of billions in China alone. However, there is still no effective prevention strategy against this virus. Therefore, continuous monitoring of the genetic diversity of dominant GAstV strains is crucial for developing targeted vaccines and appropriate therapeutics. As a crucial region for goose breeding in China, Hebei Province has previously lacked reports on the epidemiology of GAstV. Hence, investigating the epidemiology of GAstV in Hebei Province is highly important. From January 2019 to December 2021, 474 samples suspected of having a GAstV infection were collected in Hebei Province in this study. Through detailed histological observations, pathological examinations, virus isolation and identification, and genetic diversity analysis, we found that GAstV-2 has become the predominant circulating genotype. However, the presence of GAstV-1 and mixed infections cannot be ignored and should receive increased attention. The findings of this study not only deepened our understanding of GAstV in waterfowl in China but also provided scientific evidence for developing effective prevention and control measures, thereby promoting the healthy development of the goose industry in China.
Secreted Metabolites from Pseudomonas, Staphylococcus, and Borrelia Biofilm: Modulation of Immunogenicity by a Nutraceutical Enzyme and Botanical Blend
Authors: Cruickshank Dina , Hamilton Debby E. , Iloba Ifeanyi , Jensen Gitte S.
Published: May 2024

Bacterial biofilms are hardy, adaptable colonies, evading immune recognition while triggering and sustaining inflammation. The goals for this study were to present a method for testing the immunogenicity of secreted metabolites from pathogenic biofilm and to document whether biofilm treated with a nutraceutical enzyme and botanical blend (NEBB) showed evidence of reprogrammed bacterial metabolism, potentially becoming more recognizable to the immune system. We screened immune-modulating properties of metabolites from established biofilm from Pseudomonas aeruginosa (Pa), Stapholycoccus simulans (Ss), and Borrelia burgdorferi (Bb). Secreted metabolites significantly increased the cytokine production by human peripheral blood mononuclear cells, including Interleukin-1-beta (IL-1β), Interleukin-6 (IL-6), macrophage inflammatory protein-1-alpha (MIP-1α), tumor necrosis factor-alpha (TNF-α), interleukin-1 receptor antagonist (IL-1ra), and interleukin-10 (IL-10). Pa metabolites triggered the most robust increase in IL-1β, whereas Bb metabolites triggered the most robust increase in IL-10. NEBB-disrupted biofilm produced metabolites triggering altered immune modulation compared to metabolites from untreated biofilm. Metabolites from NEBB-disrupted biofilm triggered increased MIP-1α levels and reduced IL-10 levels, suggesting a reduced ability to suppress the recruitment of phagocytes compared to untreated biofilm. The results suggest that nutraceutical biofilm disruption offers strategies for inflammation management in chronic infectious illnesses. Further clinical studies are warranted to evaluate clinical correlations in infected human hosts.
Source Analysis and Bioavailability of Soil Cadmium in Poyang Lake Plain of China Based on Principal Component Analysis and Positive Definite Matrix Factor
Authors: Wen Bangyong , Jiang Hongyu , Gao Yuan , Zhou Qiangqiang , Qie Haiman
Published: May 2024

In order to identify the source and bioavailability of soil Cd in the alluvial geological high background area, 3799 topsoil samples and 140 root soil samples were collected from the Jiulong area on the south bank of Poyang Lake, Jiangxi Province. The results confidently indicate that the range of topsoil Cd content is 0.02~8.12 ppm, with an exceedance rate of 14.6%. It is noteworthy that exceedance points were mostly distributed in quaternary sediments. The geostatistical analysis clearly shows that the spatial distribution characteristic of topsoil Cd is higher in the north and lower in the south. The area with extremely high values (>90% quantile) is predominantly located in the tidal flat and low-lying areas of the mainstream of the Xinjiang River. The PCA analysis confirms that the main source of topsoil Cd is man-made activities related to industry and mining. Soil Cd is primarily derived from upstream industrial and mining discharge (58.5%), as revealed by the PMF model analysis. The active Cd content in root soil is 77 ppb, with higher levels observed in the north and lower levels in the south. These findings suggest a significant risk of Cd diffusion along the upstream stream and deposition in the low-lying parts of the north. It is worth noting that Cd’s bioavailability and active forms in paddy fields are the highest, which can have a detrimental effect on food security. The correlation analysis suggests that genetic sources primarily control the bioavailability of soil Cd, followed by soil physicochemical properties such as SOC, Fe-Al oxides, and soil texture. Preventing source pollution and cutting off water system transmission are effective methods for preventing and controlling soil Cd pollution. These methods ensure the safety of cultivated land in the lakeside area of Poyang Lake Plain.
Screening Antioxidant Components in Different Parts of Dandelion Using Online Gradient Pressure Liquid Extraction Coupled with High-Performance Liquid Chromatography Antioxidant Analysis System and Molecular Simulations
Authors: Cao Xia , Li Gaoquan , Xie Juying , Wu Mengqi , Wang Wenhao , Xiao Li , Qian Zhengming
Published: May 2024

Utilizing online gradient pressure liquid extraction (OGPLE) coupled with a high-performance liquid chromatography antioxidant analysis system, we examined the antioxidative active components present in both the aerial parts and roots of dandelion. By optimizing the chromatographic conditions, we identified the ferric reducing–antioxidant power system as the most suitable for online antioxidant reactions in dandelion. Compared to offline ultrasonic extraction, the OGPLE method demonstrated superior efficiency in extracting chemical components with varying polarities from the samples. Liquid chromatography–mass spectrometry revealed twelve compounds within the dandelion samples, with nine demonstrating considerable antioxidant efficacy. Of these, the aerial parts and roots of dandelion contained nine and four antioxidant constituents, respectively. Additionally, molecular docking studies were carried out to investigate the interaction between these nine antioxidants and four proteins associated with oxidative stress (glutathione peroxidase, inducible nitric oxide synthase, superoxide dismutase, and xanthine oxidase). The nine antioxidant compounds displayed notable binding affinities below −5.0 kcal/mol with the selected proteins, suggesting potential receptor–ligand interactions. These findings contribute to enhancing our understanding of dandelion and provide a comprehensive methodology for screening the natural antioxidant components from herbs.
Antimalarial Activity of Aqueous Extracts of Nasturtium (Tropaeolum majus L.) and Benzyl Isothiocyanate
Authors: Pintão Ana Maria , Santos Tiago , Nogueira Fátima
Published: May 2024

Malaria remains an important and challenging infectious disease, and novel antimalarials are required. Benzyl isothiocyanate (BITC), the main breakdown product of benzyl glucosinolate, is present in all parts of Tropaeolum majus L. (T. majus) and has antibacterial and antiparasitic activities. To our knowledge, there is no information on the effects of BITC against malaria. The present study evaluates the antimalarial activity of aqueous extracts of BITC and T. majus seeds, leaves, and stems. We used flow cytometry to calculate the growth inhibition (GI) percentage of the extracts and BITC against unsynchronized cultures of the chloroquine-susceptible Plasmodium falciparum 3D7 − GFP strain. Extracts and/or compounds with at least 70% GI were validated by IC50 estimation against P. falciparum 3D7 − GFP and Dd2 (chloroquine-resistant strain) unsynchronized cultures by flow cytometry, and the resistance index (RI) was determined. T. majus aqueous extracts showed some antimalarial activity that was higher in seeds than in leaves or stems. BITC’s GI was comparable to chloroquine’s. BITC’s IC50 was similar in both strains; thus, a cross-resistance absence with aminoquinolines was found (RI < 1). BITC presented features that could open new avenues for malaria drug discovery.
Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning
Authors: Chen Jianzhong , Wang Jian , Yang Wanchun , Zhao Lu , Zhao Juan , Hu Guodong
Published: May 2024

The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the phosphorylation-mediated effect on conformational dynamics of the GTP-bound KRAS. The DL finds that the switch domains are involved in obvious differences in conformation contacts and suggests that the switch domains play a key role in the function of KRAS. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of pY32, pY64, and pY137 leads to more disordered states of the switch domains than the wild-type (WT) KRAS and induces conformational transformations between the closed and open states. The results from principal component analysis (PCA) indicate that principal motions PC1 and PC2 are responsible for the closed and open states of the phosphorylated KRAS. Interaction networks were analyzed and the results verify that the phosphorylation alters interactions of GTP and magnesium ion Mg2+ with the switch domains. It is concluded that the phosphorylation pY32, pY64, and pY137 tune the activity of KRAS through changing conformational dynamics and interactions of the switch domains. We anticipated that this work could provide theoretical aids for deeply understanding the function of KRAS.
Synthesis, Characterization and Antimicrobial and Anticancer Evaluations of Some Novel Heteroannulated Difuro[3,2-c:3′,2′-g]Chromenes
Authors: Alshaye Najla A. , Ibrahim Magdy A. , Badran Al-Shimaa
Published: May 2024

The goal of this study was directed to synthesize a novel class of annulated compounds containing difuro[3,2-c:3′,2′-g]chromene. Friedländer condensation of o-aminoacetyl derivative 3 was performed with some active methylene ketones, namely, 1,3-cyclohexanediones, pyrazolones, 1,3-thiazolidinones and barbituric acids, furnished furochromenofuroquinolines (4,5), furochromenofuropyrazolopyridines (6–8), furochromenofurothiazolopyridines (9,10) and furochromenofuropyridopyrimidines (11, 12), respectively. Also, condensation of substrate 3 with 5-amine-3-methyl-1H-pyrazole and 6-amino-1,3-dimethyluracil, as cyclic enamines, resulted in polyfused systems 13 and 14, respectively. In vitro antimicrobial efficiency of the prepared heterocycles against microbial strains exhibited variable inhibition action, where compound 3 was the most effective against all kinds of microorganisms. A significant cytotoxic activity was seen upon the annulation of the starting compound with thiazolopyridine (9 and 10) as well as pyridopyrimidine moieties (11, 12 and 14). The spectroscopic and analytical results were used to infer the structures of the novel synthesized compounds.
Robust Ferromagnetism in Hexagonal Honeycomb Transition Metal Nitride Monolayer
Authors: Ma Xiaolin , Wang Zengqian , Yue Yuanfang , Gao Miao , Ma Fengjie , Yan Xun-Wang
Published: May 2024

Two-dimensional intrinsic magnetic materials with high Curie temperature are promising candidates for next-generation spintronic devices. In this work, we design two kinds of two-dimensional transition metal nitrides, VN2 and FeN2, both with a hexagonal honeycomb lattice. Based on the formation energy, and phonon spectra calculations as well as the molecular dynamics simulations, their structural stability is demonstrated. Then, we determine the ferromagnetic ground states of VN2 and FeN2 monolayers through the energy calculations, and the Curie temperatures of 222 K and 238 K are estimated by solving the Heisenberg model using the Monte Carlo simulation method. Hence, the VN2 and FeN2 monolayers are demonstrated to be new two-dimensional ferromagnetic materials with high temperature ferromagnetism or large-gap half-metallicity.
Discovery and Synthesis of Hydroxy-l-Proline Blockers of the Neutral Amino Acid Transporters SLC1A4 (ASCT1) and SLC1A5 (ASCT2)
Authors: Lyda Brent R. , Leary Gregory P. , Farnsworth Jill , Seaver Benjamin , Silvius Derek , Kavanaugh Michael P. , Esslinger C. Sean , Natale Nicholas R.
Published: May 2024

As a conformationally restricted amino acid, hydroxy-l-proline is a versatile scaffold for the synthesis of diverse multi-functionalized pyrrolidines for probing the ligand binding sites of biological targets. With the goal to develop new inhibitors of the widely expressed amino acid transporters SLC1A4 and SLC1A5 (also known as ASCT1 and ASCT2), we synthesized and functionally screened synthetic hydroxy-l-proline derivatives using electrophysiological and radiolabeled uptake methods against amino acid transporters from the SLC1, SLC7, and SLC38 solute carrier families. We have discovered a novel class of alkoxy hydroxy-pyrrolidine carboxylic acids (AHPCs) that act as selective high-affinity inhibitors of the SLC1 family neutral amino acid transporters SLC1A4 and SLC1A5. AHPCs were computationally docked into a homology model and assessed with respect to predicted molecular orientation and functional activity. The series of hydroxyproline analogs identified here represent promising new agents to pharmacologically modulate SLC1A4 and SLC1A5 amino acid exchangers which are implicated in numerous pathophysiological processes such as cancer and neurological diseases.