bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quenching of quorum sensing in multi-drug resistant Pseudomonas aeruginosa: insights on halo-bacterial metabolites and gamma irradiation as channels inhibitors
Authors: Talaat Reham , Abu El-naga Mohamed N. , El-Bialy Heba Abd Alla , El-Fouly Mohie Z. , Abouzeid Mohamed A. 
Published: April 2024

Abstract
Background
Anti-virulence therapy is a promising strategy to treat multi-drug resistant (MDR) pathogens. Pseudomonas aeruginosa is a potent opportunistic pathogen because of an array of virulence factors that are regulated by quorum sensing systems.

Methods
The virulence features of four multi-drug resistant P. aeruginosa strains were investigated upon exposure to the sub-lethal dose of gamma rays (1 kGy), and sub-inhibitory concentrations of bioactive metabolites recovered from local halophilic strains in comparison to control. Then, the gene expression of AHL-mediated quorum sensing systems (las/rhl) was quantitatively determined in treated and untreated groups by real-time PCR.

Results
The bioactive metabolites recovered from halophilic strains previously isolated from saline ecosystems were identified as Halomonas cupida (Halo-Rt1), H. elongate (Halo-Rt2), Vigibacillus natechei (Halo-Rt3), Sediminibacillus terrae (Halo-Rt4) and H. almeriensis (Halo-Rt5). Results revealed that both gamma irradiation and bioactive metabolites significantly reduced the virulence factors of the tested MDR strains. The bioactive metabolites showed a maximum efficiency for inhibiting biofilm formation and rhamnolipids production whereas the gamma irradiation succeeded in decreasing other virulence factors to lower levels in comparison to control. Quantitative-PCR results showed that AHL-mediated quorum sensing systems (las/rhl) in P. aeruginosa strains were downregulated either by halo-bacterial metabolites or gamma irradiation in all treatments except the upregulation of both lasI internal gene and rhlR intact gene in P. aeruginosa NCR-RT3 and both rhlI internal gene and rhlR intact gene in P. aeruginosa U3 by nearly two folds or more upon exposure to gamma irradiation. The most potent result was observed in the expression of lasI internal gene that was downregulated by more than ninety folds in P. aeruginosa NCR-RT2 after treatment with metabolites of S. terrae (Halo-Rt4). Analyzing metabolites recovered from H. cupida (Halo-Rt1) and H. elongate (Halo-Rt2) using LC–ESI–MS/MS revealed many chemical compounds that have quorum quenching properties including glabrol, 5,8-dimethoxyquinoline-2-carbaldehyde, linoleoyl ethanolamide, agelasine, penigequinolones derivatives, berberine, tetracosanoic acid, and liquidambaric lactone in the former halophile and phloretin, lycoctonine, fucoxanthin, and crassicauline A in the latter one.

Conclusion
QS inhibitors can significantly reduce the pathogenicity of MDR P. aeruginosa strains; and thus can be an effective and successful strategy for treating antibiotic resistant traits.
Clinical manifestations, antimicrobial resistance and genomic feature analysis of multidrug-resistant Elizabethkingia strains
Authors: Wu Chongyang , Xiong Li , Liao Quanfeng , Zhang Weili , Xiao Yuling , Xie Yi 
Published: April 2024

Abstract
Background
Elizabethkingia is emerging as an opportunistic pathogen in humans. The aim of this study was to investigate the clinical epidemiology, antimicrobial susceptibility, virulence factors, and genome features of Elizabethkingia spp.

Methods
Clinical data from 71 patients who were diagnosed with Elizabethkingia-induced pneumonia and bacteremia between August 2019 and September 2021 were analyzed. Whole-genome sequencing was performed on seven isolates, and the results were compared with a dataset of 83 available Elizabethkingia genomes. Genomic features, Kyoto Encyclopedia of Genes and Genomes (KEGG) results and clusters of orthologous groups (COGs) were analyzed.

Results
The mean age of the patients was 56.9 ± 20.7 years, and the in-hospital mortality rate was 29.6% (21/71). Elizabethkingia strains were obtained mainly from intensive care units (36.6%, 26/71) and emergency departments (32.4%, 23/71). The majority of the strains were isolated from respiratory tract specimens (85.9%, 61/71). All patients had a history of broad-spectrum antimicrobial exposure. Hospitalization for invasive mechanical ventilation or catheter insertion was found to be a risk factor for infection. The isolates displayed a high rate of resistance to cephalosporins and carbapenems, but all were susceptible to minocycline and colistin. Genomic analysis identified five β-lactamase genes (blaGOB, blaBlaB, blaCME, blaOXA, and blaTEM) responsible for β-lactam resistance and virulence genes involved in stress adaptation (ureB/G, katA/B, and clpP), adherence (groEL, tufA, and htpB) and immune modulation (gmd, tviB, cps4J, wbtIL, cap8E/D/G, and rfbC). Functional analysis of the COGs revealed that “metabolism” constituted the largest category within the core genome, while “information storage and processing” was predominant in both the accessory and unique genomes. The unique genes in our 7 strains were mostly enriched in KEGG pathways related to microRNAs in cancer, drug resistance (β-lactam and vancomycin), ABC transporters, biological metabolism and biosynthesis, and nucleotide excision repair mechanisms.

Conclusion
The Elizabethkingia genus exhibits multidrug resistance and carries carbapenemase genes. This study presents a comparative genomic analysis of Elizabethkingia, providing knowledge that facilitates a better understanding of this microorganism.
Agomir-122-loaded nanoparticles coated with cell membrane of activated fibroblasts to treat frozen shoulder based on homologous targeting
Authors: Peng Zhen , Qi Beijie , Luo Zhiwen , Sun Yaying , Zhang Xingyu , Lin Jinrong , Pang Jinhui , Zhang Peng , Zhao Zhihu , Wang Xianwen , Chen Jiwu 
Published: April 2024

AbstractAs a common musculoskeletal disorder, frozen shoulder is characterized by thickened joint capsule and limited range of motion, affecting 2–5% of the general population and more than 20% of patients with diabetes mellitus. Pathologically, joint capsule fibrosis resulting from fibroblast activation is the key event. The activated fibroblasts are proliferative and contractive, producing excessive collagen. Albeit high prevalence, effective anti-fibrosis modalities, especially fibroblast-targeting therapies, are still lacking. In this study, microRNA-122 was first identified from sequencing data as a potential therapeutic agent to antagonize fibroblast activation. Then, Agomir-122, an analog of microRNA-122, was loaded into poly(lactic-co-glycolic acid) (PLGA) nanoparticles (Agomir-122@NP), a carrier with excellent biocompatibility for the agent delivery. Moreover, relying on the homologous targeting effect, we coated Agomir-122@NP with the cell membrane derived from activated fibroblasts (Agomir-122@MNP), with an attempt to inhibit the proliferation, contraction, and collagen production of abnormally activated fibroblasts. After confirming the targeting effect of Agomir-122@MNP on activated fibroblasts in vitro, we proved that Agomir-122@MNP effectively curtailed fibroblasts activation, ameliorated joint capsule fibrosis, and restored range of motion in mouse models both prophylactically and therapeutically. Overall, an effective targeted delivery method was developed with promising translational value against frozen shoulder.
Graphical Abstract
Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV
Authors: Tolentino Jarel Elgin , Lytras Spyros , Ito Jumpei , Sato Kei 
Published: April 2024

Abstract
Background
PlMERS-CoV is a coronavirus known to cause severe disease in humans, taxonomically classified under the subgenus Merbecovirus. Recent findings showed that the close relatives of MERS-CoV infecting vespertillionid bats (family Vespertillionidae), named NeoCoV and PDF-2180, use their hosts’ ACE2 as their entry receptor, unlike the DPP4 receptor usage of MERS-CoV. Previous research suggests that this difference in receptor usage between these related viruses is a result of recombination. However, the precise location of the recombination breakpoints and the details of the recombination event leading to the change of receptor usage remain unclear.

Methods
We used maximum likelihood-based phylogenetics and genetic similarity comparisons to characterise the evolutionary history of all complete Merbecovirus genome sequences. Recombination events were detected by multiple computational methods implemented in the recombination detection program. To verify the influence of recombination, we inferred the phylogenetic relation of the merbecovirus genomes excluding recombinant segments and that of the viruses’ receptor binding domains and examined the level of congruency between the phylogenies. Finally, the geographic distribution of the genomes was inspected to identify the possible location where the recombination event occurred.

Results
Similarity plot analysis and the recombination-partitioned phylogenetic inference showed that MERS-CoV is highly similar to NeoCoV (and PDF-2180) across its whole genome except for the spike-encoding region. This is confirmed to be due to recombination by confidently detecting a recombination event between the proximal ancestor of MERS-CoV and a currently unsampled merbecovirus clade. Notably, the upstream recombination breakpoint was detected in the N-terminal domain and the downstream breakpoint at the S2 subunit of spike, indicating that the acquired recombined fragment includes the receptor-binding domain. A tanglegram comparison further confirmed that the receptor binding domain-encoding region of MERS-CoV was acquired via recombination. Geographic mapping analysis on sampling sites suggests the possibility that the recombination event occurred in Africa.

Conclusion
Together, our results suggest that recombination can lead to receptor switching of merbecoviruses during circulation in bats. These results are useful for future epidemiological assessments and surveillance to understand the spillover risk of bat coronaviruses to the human population.
Transcarotid vascular access for transcatheter aortic valve implantation: is choosing the left side always right?
Authors: Salihu Adil , Rotzinger David C. , Fahrni Guillaume , Nowacka Anna , Antiochos Panagiotis , Fournier Stephane , Muller Olivier , Kirsch Matthias , Lu Henri 
Published: April 2024

Abstract
Background
The transcarotid (TC) vascular access for transcatheter aortic valve implantation (TAVI) has emerged as the first-choice alternative to the transfemoral access, in patients unsuitable for the latter. The use of both the left and right common carotid arteries (CCAs) for TC-TAVI has been described, but the optimal side is subject to debate. We conducted this pilot study to compare the level of vessel tortuosity and plaque burden from either the left CCA to the aortic annulus, or the right CCA to the aortic annulus, considering them as surrogates for technical and procedural complexity.

Methods
Consecutive patients who underwent TC-TAVI between 2018 and 2021 in our institution were included. Using three-dimensional reconstruction, pre-TAVI neck and chest computed tomography angiography exams were reviewed to assess the tortuosity index (TI), sum of angles metric, as well as plaque burden, between each CCA and the aortic annulus.

Results
We included 46 patients who underwent TC-TAVI. No significant difference regarding the mean TIs between the left and right sides (respectively 1.20 and 1.19, p = 0.82), the mean sum of angles (left side: 396°, right side: 384°, p = 0.27), and arterial plaque burden (arterial plaque found in 30% of left CCAs and 45% of right CCAs, p = 0.19) was found.

Conclusions
We found no convincing data favoring the use of one particular access side over the other one. The choice of the CCA side in TC-TAVI should to be made on a case-by-case basis, in a multidisciplinary fashion, and may also depend on the operators’ experience.
Usability and preliminary effectiveness of an app-based physical activity and education program for people with hip or knee osteoarthritis – a pilot randomized controlled trial
Authors: Weber F. , Kloek C. , Stuhrmann S. , Blum Y. , Grüneberg C. , Veenhof C. 
Published: April 2024

Abstract
Background
Hip and knee osteoarthritis (OA) are highly prevalent worldwide. The guidelines recommend physical activity and education as the core treatments for osteoarthritis. Digital health has the potential to engage people in physical activity and disease management. Therefore, we conducted a pilot trial to assess the usability and preliminary effectiveness of an app-based physical activity and education program (Join2Move) compared to usual care for people with hip and/or knee OA in Germany.

Methods
A randomized controlled pilot study was conducted. Individuals with diagnosed or self-reported knee and hip OA were included. Allocation to the intervention or control group was randomized. The intervention group received the Join2Move program. The Join2Move program was previously developed as a website and evaluated in the Netherlands. For the current study, the program was translated and adapted to the German context and adjusted from a website to an app. The control group received usual care. The primary outcomes were usability and preliminary effectiveness (pain and physical functioning). Measurements were taken at baseline and at twelve weeks. The data analysis was performed using SPSS (IBM SPSS Statistics 29.0).

Results
Sixty participants, with a mean age of 61.9 (SD ± 7.2) years, were allocated to the intervention (n = 32) or the control group (n = 28) and included in the analysis. The majority of participants had knee OA (68%), and 12% had hip and knee OA. The dropout rate was n = 11 (18%). No adverse events were reported. Usability was rated as acceptable (mean System Usability Scale = 71.3/100) with a wide range (32.5 to 100). Statistically significant between-group differences were found only for pain (mean difference 8.52 (95% CI 1.01 to 16.04), p = 0.027).

Conclusions
Join2Move demonstrated acceptable usability. The preliminary results of the pilot trial indicate the potential of a stand-alone app for the treatment of patients with hip or knee OA. However, the acceptable usability of Join2Move limits its recommendation for everyone. There appears to be room for improvement in app usability and in identifying patients for whom the app is suitable and the right time to use a stand-alone app.

Trial registration
German Clinical Trials Register DRKS00027164.
An integrated toolkit for human microglia functional genomics
Authors: Haq Imdadul , Ngo Jason C. , Roy Nainika , Pan Richard L. , Nawsheen Nadiya , Chiu Rebecca , Zhang Ya , Fujita Masashi , Soni Rajesh K. , Wu Xuebing , Bennett David A. , Menon Vilas , Olah Marta , Sher Falak 
Published: April 2024

Summary
Background
Microglia, the brain’s resident immune cells, play vital roles in brain development, and disorders like Alzheimer’s disease (AD). Human iPSC-derived microglia (iMG) provide a promising model to study these processes. However, existing iMG generation protocols face challenges, such as prolonged differentiation time, lack of detailed characterization, and limited gene function investigation via CRISPR-Cas9.

Methods
Our integrated toolkit for in-vitro microglia functional genomics optimizes iPSC differentiation into iMG through a streamlined two-step, 20-day process, producing iMG with a normal karyotype. We confirmed the iMG’s authenticity and quality through single-cell RNA sequencing, chromatin accessibility profiles (ATAC-Seq), proteomics and functional tests. The toolkit also incorporates a drug-dependent CRISPR-ON/OFF system for temporally controlled gene expression. Further, we facilitate the use of multi-omic data by providing online searchable platform that compares new iMG profiles to human primary microglia: https://sherlab.shinyapps.io/IPSC-derived-Microglia/.

Results
Our method generates iMG that closely align with human primary microglia in terms of transcriptomic, proteomic, and chromatin accessibility profiles. Functionally, these iMG exhibit Ca2 + transients, cytokine driven migration, immune responses to inflammatory signals, and active phagocytosis of CNS related substrates including synaptosomes, amyloid beta and myelin. Significantly, the toolkit facilitates repeated iMG harvesting, essential for large-scale experiments like CRISPR-Cas9 screens. The standalone ATAC-Seq profiles of our iMG closely resemble primary microglia, positioning them as ideal tools to study AD-associated single nucleotide variants (SNV) especially in the genome regulatory regions.

Conclusions
Our advanced two-step protocol rapidly and efficiently produces authentic iMG. With features like the CRISPR-ON/OFF system and a comprehensive multi-omic data platform, our toolkit equips researchers for robust microglial functional genomic studies. By facilitating detailed SNV investigation and offering a sustainable cell harvest mechanism, the toolkit heralds significant progress in neurodegenerative disease drug research and therapeutic advancement.
New graphical models for sequential data and the improved state estimations by data-conditioned driving noises
Authors: Lee Wonjung 
Published: April 2024

AbstractA prevalent problem in statistical signal processing, applied statistics, and time series analysis arises from the attempt to identify the hidden state of Markov process based on a set of available noisy observations. In the context of sequential data, filtering refers to the probability distribution of the underlying Markovian system given the measurements made at or before the time of the estimated state. In addition to the filtering, the smoothing distribution is obtained from incorporating measurements made after the time of the estimated state into the filtered solution. This work proposes a number of new filters and smoothers that, in contrast to the traditional schemes, systematically make use of the process noises to give rise to enhanced performances in addressing the state estimation problem. In doing so, our approaches for the resolution are characterized by the application of the graphical models; the graph-based framework not only provides a unified perspective on the existing filters and smoothers but leads us to design new algorithms in a consistent and comprehensible manner. Moreover, the graph models facilitate the implementation of the suggested algorithms through message passing on the graph.
The role of university–industry linkages in promoting technology transfer: implementation of triple helix model relations
Authors: Hailu Assefa Tesfaye 
Published: April 2024

AbstractThis study recognized the importance of linking higher education institutions with various industries in a given country to promote technology transfer and sustainable development. However, in one or another way, the linkage was not well-practiced in Ethiopia. The study aims to assess the role of university–industry linkages in technology transfer and identify the barriers and opportunities of the linkage. Universities have institutionalized intermediary organizations such as technology transfer offices, collaborative research centers, incubators, and science parks to enhance university–industry collaboration. The collaboration between academia and industry is understood as the transactions between universities and firms that involve the exchange of knowledge, skills, resources, and capabilities. The study uses the concept of the triple helix model and proposes the establishment of the Higher Education Institutions–Industry Resource Integration Center as a way forward to solving the problems that Ethiopian industries are facing. A triple helix of university–industry–government relations is emerging as a common format that transcends national boundaries. The integration of these functions is changing the nature of the university and its role in society. The potential for national development in Ethiopia and elsewhere resides in entrepreneurial universities taking the lead in infusing knowledge, innovation, technology, and enterprise into the entire society.
Dietary eubiotics of microbial muramidase and glycan improve intestinal villi, ileum microbiota composition and production trait of broiler
Authors: Cho Sungbo , Kumar Shanmugam Suresh , Ramirez Santiago , Valientes Rolando , Kim In Ho 
Published: April 2024

Abstract
Background
Optimal gut health is important to maximize growth performance and feed efficiency in broiler chickens. A total of 1,365 one-day-old male Ross 308 broiler chickens were randomly divided into 5 treatments groups with 21 replicates, 13 birds per replicate. The present research investigated effects of microbial muramidase or a precision glycan alone or in combination on growth performance, apparent total tract digestibility, total blood carotenoid content, intestinal villus length, meat quality and gut microbiota in broiler chickens. Treatments included: NC: negative control (basal diet group); PC: positive control (basal diet + 0.02% probiotics); MR: basal diet + 0.035% microbial muramidase; PG: basal diet + 0.1% precision glycan; and MRPG: basal diet + 0.025% MR + 0.1% PG, respectively.

Results
MRPG group increased the body weight gain and feed intake (P < 0.05) compared with NC group. Moreover, it significantly increased total serum carotenoid (P < 0.05) and MRPG altered the microbial diversity in ileum contents. The MRPG treatment group increased the abundance of the phylum Firmicutes, and family Lachnospiraceae, Ruminococcaceae, Oscillospiraceae, Lactobacillaceae, Peptostreptococcaceae and decreased the abundance of the phylum Campilobacterota, Bacteroidota and family Bacteroidaceae. Compared with the NC group, the chickens fed MRPG showed significantly increased in duodenum villus length at end the trial.

Conclusion
In this study, overall results showed that the synergetic effects of MR and PG showed enhancing growth performance, total serum carotenoid level and altering gut microbiota composition of broilers. The current research indicates that co-supplementation of MR and PG in broiler diets enhances intestinal health, consequently leading to an increased broiler production.