bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial efficacy of direct air gas soft jet plasma for the in vitro reduction of oral bacterial biofilms
Authors: Puca Valentina , Marinacci Beatrice , Pinti Morena , Di Cintio Federica , Sinjari Bruna , Di Marcantonio Maria Carmela , Mincione Gabriella , Acharya Tirtha Raj , Kaushik Nagendra Kumar , Choi Eun Ha , Sallese Michele , Guarnieri Simone , Grande Rossella , Perrotti Vittoria 
Published: May 2024

AbstractThe aim of this study was to evaluate the antimicrobial efficacy of an air gas soft jet CAP for its potential use in removing oral biofilms, given that plasma-based technologies have emerged as promising methods in periodontology. Two types of biofilms were developed, one byStreptococcus mutansUA 159 bacterial strain and the other by a complex mixture of saliva microorganisms isolated from a patient with periodontitis. This latter biofilm was characterized via Next Generation Sequencing to determine the main bacterial phyla. The CAP source was applied at a distance of 6 mm for different time points. A statistically significant reduction of both CFU count and XTT was already detected after 60 s of CAP treatment. CLSM analysis supported CAP effectiveness in killing the microorganisms inside the biofilm and in reducing the thickness of the biofilm matrix. Cytotoxicity tests demonstrated the possible use of CAP without important side effects towards human gingival fibroblasts cell line. The current study showed that CAP treatment was able to significantly reduce preformed biofilms developed by bothS. mutansand microorganisms isolated by a saliva sample. Further studies should be conducted on biofilms developed by additional saliva donors to support the potential of this innovative strategy to counteract oral pathogens responsible for periodontal diseases.
Epitaxial growth of high-quality GaN with a high growth rate at low temperatures by radical-enhanced metalorganic chemical vapor deposition
Authors: Dhasiyan Arun Kumar , Amalraj Frank Wilson , Jayaprasad Swathy , Shimizu Naohiro , Oda Osamu , Ishikawa Kenji , Hori Masaru 
Published: May 2024

AbstractUsing our recently developed radical-enhanced metalorganic chemical vapor deposition (REMOCVD) technique, we have grown gallium nitride (GaN) on bulk GaN and GaN on Si templates. Three features make up this system: (1) applying very high-frequency power (60 MHz) to increase the plasma density; (2) introducing H2 and N2 gas in the plasma discharge region to produce active NHx radical species in addition to nitrogen radicals; and (3) supplying radicals under remote plasma arrangement with a Faraday cage to suppress charged ions and photons. Using this new REMOCVD system, it was found that high-quality crystals can be grown at lower temperatures than that of MOCVD but the disadvantage was that the growth rate was smaller as 0.2–0.8 μm/h than that by MOCVD. In the present work, we have used a pBN inner shield to prevent the deactivation of radicals to increase the growth rate. The growth conditions such as the plasma power, trimethylgallium (TMG) source flow rate, N2 + H2 gas mixture flow rate, and the ratio of N2/H2 were optimized and it was found that the growth rate could be increased up to 3.4 μm/h with remarkably high crystalline quality comparable to that of MOCVD. The XRD-FWHM of GaN grown on the GaN/Si template and the bulk GaN substrate were 977 arcsec and 72 arcsec respectively. This work may be very promising to achieve high-power GaN/GaN devices.
Global seroprevalence of scrub typhus: a systematic review and meta-analysis
Authors: Dasgupta Sauvik , Asish Purushothaman Rajamani , Rachel Gladys , Bagepally Bhavani Shankara , Chethrapilly Purushothaman Girish Kumar 
Published: May 2024

AbstractScrub typhus, a neglected disease, is a significant health concern in the Tsutsugamushi triangle of the Asia–Pacific and has raised global concerns due to recent cases occurring outside this region. To estimate the global prevalence of scrub typhus, we conducted a systematic review and meta-analysis. We conducted a systematic search of PubMed, Scopus, and Embase databases for observational studies on scrub typhus. Using a random-effects model, we combined the prevalence estimates with inverse-variance weights while also evaluating heterogeneity and publication bias. Among 3551 reports screened, we identified 181 studies with 1,48,251 samples for inclusion in our synthesis. The overall pooled seroprevalence (95% confidence intervals) of scrub typhus infections was 24.93% (23.27–26.60). Gender-wise pooled prevalence was estimated to be 50.23% (47.05–53.40) for males and 48.84% (45.87–51.80) for females. Eschar prevalence was observed to be 30.34% (22.54–38.15) among the positive cases. One-fourth of all the samples tested positive for scrub typhus and eschar was present in one-third of these total positive cases, encompassing regions beyond the Tsutsugamushi triangle. This estimation underlines the importance of this neglected disease as a public health problem. Strengthening surveillance and implementing disease control measures are needed in the affected regions.
A fluorescently-tagged tick kinin neuropeptide triggers peristalsis and labels tick midgut muscles
Authors: Hernandez Jonathan R. , Xiong Caixing , Pietrantonio Patricia V. 
Published: May 2024

AbstractTicks are blood-feeding arthropods that require heme for their successful reproduction. During feeding they also acquire pathogens that are subsequently transmitted to humans, wildlife and/or livestock. Understanding the regulation of tick midgut is important for blood meal digestion, heme and nutrient absorption processes and for aspects of pathogen biology in the host. We previously demonstrated the activity of tick kinins on the cognate G protein-coupled receptor. Herein we uncovered the physiological role of the kinin receptor in the tick midgut. A fluorescently-labeled kinin peptide with the endogenous kinin 8 sequence (TMR-RK8), identical in the ticks Rhipicephalus microplus and R. sanguineus, activated and labeled the recombinant R. microplus receptor expressed in CHO-K1 cells. When applied to the live midgut the TMR-RK8 labeled the kinin receptor in muscles while the labeled peptide with the scrambled-sequence of kinin 8 (TMR-Scrambled) did not. The unlabeled kinin 8 peptide competed TMR-RK8, decreasing confocal microscopy signal intensity, indicating TMR-RK8 specificity to muscles. TMR-RK8 was active, inducing significant midgut peristalsis that was video-recorded and evaluated with video tracking software. The TMR-Scrambled peptide used as a negative control did not elicit peristalsis. The myotropic function of kinins in eliciting tick midgut peristalsis was established.
CRISPR/Cas9 genome editing of CCR5 combined with C46 HIV-1 fusion inhibitor for cellular resistant to R5 and X4 tropic HIV-1
Authors: Khamaikawin Wannisa , Saisawang Chonticha , Tassaneetrithep Boonrat , Bhukhai Kanit , Phanthong Phetcharat , Borwornpinyo Suparerk , Phuphuakrat Angsana , Pasomsub Ekawat , Chaisavaneeyakorn Sujittra , Anurathapan Usanarat , Apiwattanakul Nopporn , Hongeng Suradej 
Published: May 2024

AbstractHematopoietic stem-cell (HSC) transplantation using a donor with a homozygous mutation in the HIV co-receptor CCR5 (CCR5Δ32/Δ32) holds great promise as a cure for HIV-1. Previously, there were three patients that had been reported to be completely cured from HIV infection by this approach. However, finding a naturally suitable Human Leukocyte Antigen (HLA)-matched homozygous CCR5Δ32 donor is very difficult. The prevalence of this allele is only 1% in the Caucasian population. Therefore, additional sources of CCR5Δ32/Δ32 HSCs are required. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is one method to mediate CCR5 knockout in HSCs that has been successfully employed as a gene editing tool in clinical trials. Additional anti-HIV-1 strategies are still required for broad-spectrum inhibition of HIV-1 replication. Here in this study, we combined an additional anti-HIV-1 therapy, which is C46, a cell membrane-anchored HIV-1 fusion inhibitor with the CRISPR/Cas9 mediated knockout CCR5. The combined HIV-1 therapeutic genes were investigated for the potential prevention of both CCR5 (R5)- and CXCR4 (X4)-tropic HIV-1 infections in the MT4CCR5 cell line. The combinatorial CRISPR/Cas9 therapies were superior compared to single method therapy for achieving the HIV-1 cure strategy and shows potential for future applications.
Deep-learning survival analysis for patients with calcific aortic valve disease undergoing valve replacement
Authors: Mohammadyari Parvin , Vieceli Dalla Sega Francesco , Fortini Francesca , Minghini Giada , Rizzo Paola , Cimaglia Paolo , Mikus Elisa , Tremoli Elena , Campo Gianluca , Calore Enrico , Schifano Sebastiano Fabio , Zambelli Cristian 
Published: May 2024

AbstractCalcification of the aortic valve (CAVDS) is a major cause of aortic stenosis (AS) leading to loss of valve function which requires the substitution by surgical aortic valve replacement (SAVR) or transcatheter aortic valve intervention (TAVI). These procedures are associated with high post-intervention mortality, then the corresponding risk assessment is relevant from a clinical standpoint. This study compares the traditional Cox Proportional Hazard (CPH) against Machine Learning (ML) based methods, such as Deep Learning Survival (DeepSurv) and Random Survival Forest (RSF), to identify variables able to estimate the risk of death one year after the intervention, in patients undergoing either to SAVR or TAVI. We found that with all three approaches the combination of six variables, named albumin, age, BMI, glucose, hypertension, and clonal hemopoiesis of indeterminate potential (CHIP), allows for predicting mortality with a c-index of approximately$$80\%$$80%. Importantly, we found that the ML models have a better prediction capability, making them as effective for statistical analysis in medicine as most state-of-the-art approaches, with the additional advantage that they may expose non-linear relationships. This study aims to improve the early identification of patients at higher risk of death, who could then benefit from a more appropriate therapeutic intervention.
Facile fabrication of next-generation sustainable brick and mortar through geopolymerization of construction debris
Authors: Rahimpour Hamed , Amini Alireza Babaeian , Sharifi Fatemeh , Fahmi Ahmad , Zinatloo-Ajabshir Sahar 
Published: May 2024

AbstractWaste from construction and demolition (also known as CDW) is one of the most harmful environmental issues. This study's primary goal is to produce new mortar and brick materials from recycled concrete powder (RCP) and recycled brick powder (RBP), two of the most popular CDW. Geopolymeric mortar and brick samples were produced by passing RCP and RBP through sieve No. 50 (with sand filler if necessary) and combining them with an alkaline solution made of water glass (WG) and NaOH. In this study, the mixture was then cured for three days at 80 °C in an oven. The effects of filler, RBP amount, WG amount, and the concentration of NaOH alkaline solution on the samples’ strength were examined. Additionally, XRF and SEM/XRD tests were performed to verify the materials' composition and microstructure. The mechanical strength of the samples showed an increase with the increase of RCP values, so the brick sample with filler showed the highest compressive strength, measuring 59.53 MPa. The study's samples exhibited strong mechanical properties. Additionally, all of the bricks' water absorption fell within the standard range. In summary, according to different standards, both waste concrete and waste brick can be used to produce geopolymer materials especially bricks for construction and paving purposes.
Amyloid-beta antibody binding to cerebral amyloid angiopathy fibrils and risk for amyloid-related imaging abnormalities
Authors: Söderberg Linda , Johannesson Malin , Gkanatsiou Eleni , Nygren Patrik , Fritz Nicolas , Zachrisson Olof , Rachalski Adeline , Svensson Anne-Sophie , Button Emily , Dentoni Giacomo , Osswald Gunilla , Lannfelt Lars , Möller Christer 
Published: May 2024

AbstractTherapeutic antibodies have been developed to target amyloid-beta (Aβ), and some of these slow the progression of Alzheimer’s disease (AD). However, they can also cause adverse events known as amyloid-related imaging abnormalities with edema (ARIA-E). We investigated therapeutic Aβ antibody binding to cerebral amyloid angiopathy (CAA) fibrils isolated from human leptomeningeal tissue to study whether this related to the ARIA-E frequencies previously reported by clinical trials. The binding of Aβ antibodies to CAA Aβ fibrils was evaluated in vitro using immunoprecipitation, surface plasmon resonance, and direct binding assay. Marked differences in Aβ antibody binding to CAA fibrils were observed. Solanezumab and crenezumab showed negligible CAA fibril binding and these antibodies have no reported ARIA-E cases. Lecanemab showed a low binding to CAA fibrils, consistent with its relatively low ARIA-E frequency of 12.6%, while aducanumab, bapineuzumab, and gantenerumab all showed higher binding to CAA fibrils and substantially higher ARIA-E frequencies (25–35%). An ARIA-E frequency of 24% was reported for donanemab, and its binding to CAA fibrils correlated with the amount of pyroglutamate-modified Aβ present. The findings of this study support the proposal that Aβ antibody-CAA interactions may relate to the ARIA-E frequency observed in patients treated with Aβ-based immunotherapies.
Genomic properties of a Bartonella quintana strain from Japanese macaque (Macaca fuscata) revealed by genome comparison with human and rhesus macaque strains
Authors: Sato Shingo , Nishioka Emu , Kabeya Hidenori , Maruyama Soichi 
Published: May 2024

AbstractBartonella quintana, the causative agent of trench fever, is an intracellular bacterium that infects human erythrocytes and vascular endothelial cells. For many years, humans were considered the only natural hosts for B. quintana; however, it was recently discovered that wild Japanese macaques (Macaca fuscata) also serve as hosts for B. quintana. To elucidate the genetic characteristics of the B. quintana strain MF1-1 isolated from a Japanese macaque, we determined the complete genome sequence of the strain and compared it with those of strain Toulouse from a human and strain RM-11 from a rhesus macaque. General genomic features and orthologous gene cluster profiles are similar among the three strains, and strain MF1-1 is genetically closer to strain RM-11 than strain Toulouse based on the average nucleotide identity values; however, a significant inversion of approximately 0.68 Mb was detected in the chromosome of strain MF1-1. Moreover, the Japanese macaque strains lacked the bepA gene, which is responsible for anti-apoptotic function, and the trwL2, trwL4, and trwL6 genes, which may be involved in adhesion to erythrocytes of rhesus macaque and human. These features likely represent the genomic traits acquired by Japanese macaque strains in their host-associated evolution.
Metabolism-driven in vitro/in vivo disconnect of an oral ERɑ VHL-PROTAC
Authors: Hayhow Thomas G. , Williamson Beth , Lawson Mandy , Cureton Natalie , Braybrooke Erin L. , Campbell Andrew , Carbajo Rodrigo J. , Cheraghchi-Bashi Azadeh , Chiarparin Elisabetta , Diène Coura R. , Fallan Charlene , Fisher David I. , Goldberg Frederick W. , Hopcroft Lorna , Hopcroft Philip , Jackson Anne , Kettle Jason G. , Klinowska Teresa , Künzel Ulrike , Lamont Gillian , Lewis Hilary J. , Maglennon Gareth , Martin Scott , Gutierrez Pablo Morentin , Morrow Christopher J. , Nikolaou Myria , Nissink J. Willem M. , O’Shea Patrick , Polanski Radoslaw , Schade Markus , Scott James S. , Smith Aaron , Weber Judith , Wilson Joanne , Yang Bin , Crafter Claire 
Published: May 2024

AbstractTargeting the estrogen receptor alpha (ERα) pathway is validated in the clinic as an effective means to treat ER+ breast cancers. Here we present the development of a VHL-targeting and orally bioavailable proteolysis-targeting chimera (PROTAC) degrader of ERα. In vitro studies with this PROTAC demonstrate excellent ERα degradation and ER antagonism in ER+ breast cancer cell lines. However, upon dosing the compound in vivo we observe an in vitro-in vivo disconnect. ERα degradation is lower in vivo than expected based on the in vitro data. Investigation into potential causes for the reduced maximal degradation reveals that metabolic instability of the PROTAC linker generates metabolites that compete for binding to ERα with the full PROTAC, limiting degradation. This observation highlights the requirement for metabolically stable PROTACs to ensure maximal efficacy and thus optimisation of the linker should be a key consideration when designing PROTACs.
Soil microbiota and herbivory drive the assembly of tomato plant-associated microbial communities through different mechanisms
Authors: Malacrinò Antonino , Bennett Alison E. 
Published: May 2024

AbstractPlant-associated microbial communities are key to shaping many aspects of plant biology. In this study, we tested whether soil microbial communities and herbivory influence the bacterial community of tomato plants and whether their influence in different plant compartments is driven by microbial spillover between compartments or whether plants are involved in mediating this effect. We grew our plants in soils hosting three different microbial communities and covered (or not) the soil surface to prevent (or allow) passive microbial spillover between compartments, and we exposed them (or not) to herbivory by Manduca sexta. Here we show that the soil-driven effect on aboveground compartments is consistently detected regardless of soil coverage, whereas soil cover influences the herbivore-driven effect on belowground microbiota. Together, our results suggest that the soil microbiota influences aboveground plant and insect microbial communities via changes in plant metabolism and physiology or by sharing microorganisms via xylem sap. In contrast, herbivores influence the belowground plant microbiota via a combination of microbial spillover and changes in plant metabolism. These results demonstrate the important role of plants in linking aboveground and belowground microbiota, and can foster further research on soil microbiota manipulation for sustainable pest management.
Structural annotation of unknown molecules in a miniaturized mass spectrometer based on a transformer enabled fragment tree method
Authors: Yang Yiming , Sun Shuang , Yang Shuyuan , Yang Qin , Lu Xinqiong , Wang Xiaohao , Yu Quan , Huo Xinming , Qian Xiang 
Published: May 2024

AbstractStructural annotation of small molecules in tandem mass spectrometry has always been a central challenge in mass spectrometry analysis, especially using a miniaturized mass spectrometer for on-site testing. Here, we propose the Transformer enabled Fragment Tree (TeFT) method, which combines various types of fragmentation tree models and a deep learning Transformer module. It is aimed to generate the specific structure of molecules de novo solely from mass spectrometry spectra. The evaluation results on different open-source databases indicated that the proposed model achieved remarkable results in that the majority of molecular structures of compounds in the test can be successfully recognized. Also, the TeFT has been validated on a miniaturized mass spectrometer with low-resolution spectra for 16 flavonoid alcohols, achieving complete structure prediction for 8 substances. Finally, TeFT confirmed the structure of the compound contained in a Chinese medicine substance called the Anweiyang capsule. These results indicate that the TeFT method is suitable for annotating fragmentation peaks with clear fragmentation rules, particularly when applied to on-site mass spectrometry with lower mass resolution.
Dual-comb spectroscopy of ammonia formation in non-thermal plasmas
Authors: Sadiek Ibrahim , Fleisher Adam J. , Hayden Jakob , Huang Xinyi , Hugi Andreas , Engeln Richard , Lang Norbert , van Helden Jean-Pierre H. 
Published: May 2024

AbstractPlasma-activated chemical transformations promise the efficient synthesis of salient chemical products. However, the reaction pathways that lead to desirable products are often unknown, and key quantum-state-resolved information regarding the involved molecular species is lacking. Here we use quantum cascade laser dual-comb spectroscopy (QCL-DCS) to probe plasma-activated NH3 generation with rotational and vibrational state resolution, quantifying state-specific number densities via broadband spectral analysis. The measurements reveal unique translational, rotational and vibrational temperatures for NH3 products, indicative of a highly reactive, non-thermal environment. Ultimately, we postulate on the energy transfer mechanisms that explain trends in temperatures and number densities observed for NH3 generated in low-pressure nitrogen-hydrogen (N2–H2) plasmas.
Multi-purpose RNA language modelling with motif-aware pretraining and type-guided fine-tuning
Authors: Wang Ning , Bian Jiang , Li Yuchen , Li Xuhong , Mumtaz Shahid , Kong Linghe , Xiong Haoyi 
Published: May 2024

AbstractPretrained language models have shown promise in analysing nucleotide sequences, yet a versatile model excelling across diverse tasks with a single pretrained weight set remains elusive. Here we introduce RNAErnie, an RNA-focused pretrained model built upon the transformer architecture, employing two simple yet effective strategies. First, RNAErnie enhances pretraining by incorporating RNA motifs as biological priors and introducing motif-level random masking in addition to masked language modelling at base/subsequence levels. It also tokenizes RNA types (for example, miRNA, lnRNA) as stop words, appending them to sequences during pretraining. Second, subject to out-of-distribution tasks with RNA sequences not seen during the pretraining phase, RNAErnie proposes a type-guided fine-tuning strategy that first predicts possible RNA types using an RNA sequence and then appends the predicted type to the tail of sequence to refine feature embedding in a post hoc way. Our extensive evaluation across seven datasets and five tasks demonstrates the superiority of RNAErnie in both supervised and unsupervised learning. It surpasses baselines with up to 1.8% higher accuracy in classification, 2.2% greater accuracy in interaction prediction and 3.3% improved F1 score in structure prediction, showcasing its robustness and adaptability with a unified pretrained foundation.