bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resistance of Nile tilapia fed with Padina boergesenii extract to Pseudomonas putida infection
Authors: Bakry Karima A. , Nasr Mahmoud , Al-Amgad Zeinab , kondos Ereen , Kondos Malak K. N. , Mehanny Pierre E. , Alghamdi Abdullah A. A. , Khormi Mohsen A. , Abd-ElHafeez Hanan H. , Emeish Walaa F.A. 
Published: July 2024

AbstractThe aim of this research was to estimate the immunopotentiation effect of brown algae Padina boergesenii water extract on Nile tilapia, Oreochromis niloticus through resistance to Pseudomonas putida infection. Gas Chromatography Mass Spectrometry was utilized to characterize the seaweed phytoconstituents. One hundred and twenty-six fish were divided in triplicates into two equal groups corresponding to two diet variants that used to feed Nile tilapia for 20 successive days: a basal (control), and P. boergesenii water extract supplemented group. Fish samples were collected at 10-days intervals throughout the experiment. Serum biochemical constituents, total antioxidant capacity (TAC), and some immune related genes expression of the spleen and intestinal tissues of experimental fish were studied, as well as histological examination of fish immune tissues. Moreover, following 20 days of feeding, the susceptibility of Nile tilapia to P. putida infection was evaluated to assess the protective effect of the used extract. The findings indicated that the studied parameters were significantly increased, and the best immune response profiles were observed in fish fed P. boergesenii water extract for 20 successive days. A bacterial challenge experiment using P. putida resulted in higher survival within the supplemented fish group than the control. Thus, the lowered post-challenge mortality of the fish may be related to the protection provided by the stimulation of the innate immune system, reduced oxidative stress by higher activity of TAC, and elevated levels of expression of iterleukin-1beta (IL-1β), beta-defensin (β-defensin), and natural killer-lysin (NKl). Moreover, the constituents of the extract used showed potential protective activity for histological features of the supplemented fish group when compared to the control. Collectively, this study presents a great insight on the protective role of P. boergesenii water extract as an additive in Nile tilapia feed which suggests its potential for improving the immune response against P. putida infection.
Thonzonium bromide inhibits progression of malignant pleural mesothelioma through regulation of ERK1/2 and p38 pathways and mitochondrial uncoupling
Authors: Dell’Anno Irene , Morani Federica , Patergnani Simone , Daga Antonio , Pinton Paolo , Giorgi Carlotta , Mutti Luciano , Gemignani Federica , Landi Stefano 
Published: July 2024

Abstract
Background
Malignant Pleural Mesothelioma (MPM) is a rare malignancy with a poor prognosis. Current therapies are unsatisfactory and novel cures are urgently needed. In a previous drug screening, we identified thonzonium bromide (TB) as one of the most active compounds against MPM cells. Since the biological effects of TB are poorly known, in this work we departed from some hints of previous studies and investigated several hypotheses. Moreover, we evaluated the efficacy of TB in an in vivo xenograft rodent model.

Methods
In vitro assessment was made on five MPM (Mero-14, Mero-25, Ren, NCI-H28, MSTO-211H) and one SV40-immortalized mesothelial cell line (MeT-5A). We evaluated TB ability to affect proliferation, apoptosis, mitochondrial functions and metabolism, and the mevalonate pathway. In vivo assay was carried out on MPM-xenograft NOD-SCID mice (4 mg/kg delivered intraperitoneally, twice a week for 4 weeks) and the overall survival was analysed with Kaplan-Meier curves.

Results
After TB treatment, we observed the suppression of ERK 1/2 phosphorylation, the increase of BAX expression and p38 phosphorylation. TB affected Ca2+ homeostasis in both mitochondrial and cytosolic compartments, it regulated the mitochondrial functioning, respiration, and ATP production as well as the mevalonate pathway. The in vivo study showed an increased overall survival for TB treated group vs. vehicle control group (P = 0.0076).

Conclusions
Both in vitro and in vivo results confirmed the effect of TB on MPM and unravelled novel targets with translational potential.
Spatial distribution pattern of immune cells is associated with patient prognosis in colorectal cancer
Authors: Shen Rongfang , Huang Ying , Kong Deyang , Ma Wenhui , Liu Jie , Zhang Haizeng , Cheng Shujun , Feng Lin 
Published: July 2024

Abstract
Background
The spatial context of tumor-infiltrating immune cells (TIICs) is important in predicting colorectal cancer (CRC) patients’ clinical outcomes. However, the prognostic value of the TIIC spatial distribution is unknown. Thus, we aimed to investigate the association between TIICs in situ and patient prognosis in a large CRC sample.

Methods
We implemented multiplex immunohistochemistry staining technology in 190 CRC samples to quantify 14 TIIC subgroups in situ. To delineate the spatial relationship of TIICs to tumor cells, tissue slides were segmented into tumor cell and microenvironment compartments based on image recognition technology, and the distance between immune and tumor cells was calculated by implementing the computational pipeline phenoptr.

Results
MPO+ neutrophils and CD68+IDO1+ tumor-associated macrophages (TAMs) were enriched in the epithelial compartment, and myeloid lineage cells were located nearest to tumor cells. Except for CD68+CD163+ TAMs, other cells were all positively associated with favorable prognosis. The prognostic predictive power of TIICs was highly related to their distance to tumor cells. Unsupervised clustering analysis divided colorectal cancer into three subtypes with distinct prognostic outcomes, and correlation analysis revealed the synergy among B cells, CD68+IDO1+TAMs, and T lineage cells in producing an effective immune response.

Conclusions
Our study suggests that the integration of spatial localization with TIIC abundance is important for comprehensive prognostic assessment.
Advancing targeted combination chemotherapy in triple negative breast cancer: nucleolin aptamer-mediated controlled drug release
Authors: Ma Yuan , Xie Duoli , Chen Zefeng , Shen Xinyang , Wu Xiaoqiu , Ding Feng , Ding Shijian , Pan Yufei , Li Fangfei , Lu Aiping , Zhang Ge 
Published: July 2024

Abstract
Background
Triple-negative breast cancer (TNBC) is a recurrent, heterogeneous, and invasive form of breast cancer. The treatment of TNBC patients with paclitaxel and fluorouracil in a sequential manner has shown promising outcomes. However, it is challenging to deliver these chemotherapeutic agents sequentially to TNBC tumors. We aim to explore a precision therapy strategy for TNBC through the sequential delivery of paclitaxel and fluorouracil.

Methods
We developed a dual chemo-loaded aptamer with redox-sensitive caged paclitaxel for rapid release and non-cleavable caged fluorouracil for slow release. The binding affinity to the target protein was validated using Enzyme-linked oligonucleotide assays and Surface plasmon resonance assays. The targeting and internalization abilities into tumors were confirmed using Flow cytometry assays and Confocal microscopy assays. The inhibitory effects on TNBC progression were evaluated by pharmacological studies in vitro and in vivo.

Results
Various redox-responsive aptamer-paclitaxel conjugates were synthesized. Among them, AS1411-paclitaxel conjugate with a thioether linker (ASP) exhibited high anti-proliferation ability against TNBC cells, and its targeting ability was further improved through fluorouracil modification. The fluorouracil modified AS1411-paclitaxel conjugate with a thioether linker (FASP) exhibited effective targeting of TNBC cells and significantly improved the inhibitory effects on TNBC progression in vitro and in vivo.

Conclusions
This study successfully developed fluorouracil-modified AS1411-paclitaxel conjugates with a thioether linker for targeted combination chemotherapy in TNBC. These conjugates demonstrated efficient recognition of TNBC cells, enabling targeted delivery and controlled release of paclitaxel and fluorouracil. This approach resulted in synergistic antitumor effects and reduced toxicity in vivo. However, challenges related to stability, immunogenicity, and scalability need to be further investigated for future translational applications.
Correlation between circulating advanced glycation end products and thioredoxin-interacting protein levels and renal fat content in type 2 diabetes mellitus patients
Authors: Hua Yulin , Yin Zaifei , Li Mingming , Sun Hong , Shi Bimin 
Published: July 2024

Abstract
Background
This study sought to explore the clinical relevance of the associations of serum levels of advanced glycation end products (AGEs), soluble receptor for AGEs (sRAGE), and thioredoxin-interacting protein (TXNIP) with the renal fat fraction (RFF) in individuals with type 2 diabetes mellitus (T2DM).

Methods
A total of 133 patients with T2DM were enrolled in the study. RFF, which represents the renal fat level, was determined utilizing Dixon magnetic resonance imaging (MRI). Serum levels of AGEs, sRAGE, TXNIP, and other biochemical parameters were measured in patients who fasted.

Results
RFF in T2DM patients was positively correlated with the fasting levels of C-peptide (CP), triglycerides (TG), AGEs, TXNIP, and sRAGE (P < 0.05) and negatively correlated with the high-density lipoprotein cholesterol (HDL-c) level (P < 0.05). Pearson’s correlation analysis indicated that the serum levels of AGEs, sRAGE, and TXNIP were interrelated and positively correlated (P < 0.05). Then, all patients were assigned to four groups according to the RFF quartile. The HC, CP, TG, AGEs, sRAGE, TXNIP, and DKD percentages tended to increase as the RFF quartiles increased, while the HDL-c level tended to decrease (p for trend < 0.05). Next, multiple linear regression analysis was performed using RFF as the dependent variable. After controlling for covariates related to RFF, the results showed that the serum levels of AGEs and TXNIP were still significantly correlated with RFF.

Conclusion
These results suggest that circulating AGEs and TXNIP levels may be associated with ectopic fat accumulation in the kidneys of T2DM patients and may serve as indicators of the severity of renal fat deposition.
Epigenetic scores derived in saliva are associated with gestational age at birth
Authors: Mckinnon Katie , Conole Eleanor L. S. , Vaher Kadi , Hillary Robert F. , Gadd Danni A. , Binkowska Justyna , Sullivan Gemma , Stevenson Anna J. , Corrigan Amy , Murphy Lee , Whalley Heather C. , Richardson Hilary , Marioni Riccardo E. , Cox Simon R. , Boardman James P. 
Published: July 2024

Abstract
Background
Epigenetic scores (EpiScores), reflecting DNA methylation (DNAm)-based surrogates for complex traits, have been developed for multiple circulating proteins. EpiScores for pro-inflammatory proteins, such as C-reactive protein (DNAm CRP), are associated with brain health and cognition in adults and with inflammatory comorbidities of preterm birth in neonates. Social disadvantage can become embedded in child development through inflammation, and deprivation is overrepresented in preterm infants. We tested the hypotheses that preterm birth and socioeconomic status (SES) are associated with alterations in a set of EpiScores enriched for inflammation-associated proteins.

Results
In total, 104 protein EpiScores were derived from saliva samples of 332 neonates born at gestational age (GA) 22.14 to 42.14 weeks. Saliva sampling was between 36.57 and 47.14 weeks. Forty-three (41%) EpiScores were associated with low GA at birth (standardised estimates |0.14 to 0.88|, Bonferroni-adjusted p-value < 8.3 × 10−3). These included EpiScores for chemokines, growth factors, proteins involved in neurogenesis and vascular development, cell membrane proteins and receptors, and other immune proteins. Three EpiScores were associated with SES, or the interaction between birth GA and SES: afamin, intercellular adhesion molecule 5, and hepatocyte growth factor-like protein (standardised estimates |0.06 to 0.13|, Bonferroni-adjusted p-value < 8.3 × 10−3). In a preterm subgroup (n = 217, median [range] GA 29.29 weeks [22.14 to 33.0 weeks]), SES–EpiScore associations did not remain statistically significant after adjustment for sepsis, bronchopulmonary dysplasia, necrotising enterocolitis, and histological chorioamnionitis.

Conclusions
Low birth GA is substantially associated with a set of EpiScores. The set was enriched for inflammatory proteins, providing new insights into immune dysregulation in preterm infants. SES had fewer associations with EpiScores; these tended to have small effect sizes and were not statistically significant after adjusting for inflammatory comorbidities. This suggests that inflammation is unlikely to be the primary axis through which SES becomes embedded in the development of preterm infants in the neonatal period.

Graphical abstract
CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets
Authors: Koci Orges , Russell Richard K. , Shaikh M. Guftar , Edwards Christine , Gerasimidis Konstantinos , Ijaz Umer Zeeshan 
Published: July 2024

Abstract
Background
Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration.

Results
In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case–control relationships.

Conclusions
CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn’s disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential.
Enhanced prediction of thermomechanical systems using machine learning, PCA, and finite element simulation
Authors: Schneider Thomas , Bedrikow Alexandre Beiderwellen , Stahl Karsten 
Published: July 2024

AbstractThis research paper presents a comprehensive methodology for analyzing wet clutches, focusing on their intricate thermomechanical behavior. The study combines advanced encoding techniques, such as Principal Component Analysis (PCA), with metamodeling, to efficiently predict pressure and temperature distributions on friction surfaces. By parametrically varying input parameters and utilizing Finite Element Method (FEM) simulations, we generate a dataset comprising 200 simulations, divided into training and testing sets. Our findings indicate that PCA encoding effectively reduces data dimensionality while preserving essential information. Notably, the study reveals that only a few PCA components are required for accurate encoding: two components for temperature distribution and pressure, and three components for heat flux density. We compare various metamodeling techniques, including Linear Regression, Decision Trees, Random Forest, Support Vector Regression, Gaussian Processes, and Neural Networks. The results underscore the varying performance of these techniques, with Random Forest excelling in mechanical metamodeling and Neural Networks demonstrating superiority in thermal metamodeling.
Beyond skills: reflections on the tacit knowledge-brain-cognition nexus on heritage conservators
Authors: Otero Jorge 
Published: July 2024

Abstract
The conventional perception of heritage conservators’ knowledge has primarily focused on their explicit knowledge rooted between science and humanities. However, this perspective on their knowledge is imprecise and often overlooks other intangible dimensions, particularly their accumulated practical (hands-on) tacit knowledge, which extends beyond the traditional view and is often reduced to a mere skill. This comment/perspective article challenges this traditional view and aims to explore the significance of this ineffable knowledge and the possible implications of repetitive practical sensorimotor motions on the conservator's brain, embodied cognition, intuition, and decision-making. This new vision aims to reflect on how we understand the scope of knowledge of worldwide heritage conservators and to open new doors for research and interdisciplinary collaborations.
Development and implementation of an injury and illness surveillance system for team USA
Authors: Post Eric G. , Anderson Travis , Samson Olivia , Gidley Alexis D. , Triplett Ashley N. , Donaldson Amber T. , Finnoff Jonathan T. , Adams William M. 
Published: July 2024

Abstract
Background
The purpose of this report is to provide insight and details regarding the development and implementation of an injury and illness surveillance (IIS) system for the United States Olympic and Paralympic Committee (USOPC).

Methods
The development and deployment of the IIS employed a multiphase approach. First, researchers determined variables to include in the IIS using the recommendations from the 2020 IOC consensus statement for reporting sport epidemiological data. Second, the hosting and deployment platforms were comprehensively evaluated for their suitability, ease of use, flexibility, and backend data structure (for both capture and aggregation). Third, focus groups consisting of the Sports Medicine department leadership and clinicians piloted the IIS system and revisions were made based on their feedback. Pilot testing of the IIS and follow-up focus groups were then conducted among all departmental clinicians to solicit additional feedback and drive further revisions. Finally, the IIS system was piloted among providers working during the 2023 Pan American and Parapan American Games to refine the system for future Games. After reviewing all potential software platform options (electronic medical record [EMR] system, athlete management systems, secure data collection platforms), Qualtrics (Qualtrics, Provo, UT, USA) was selected to host the IIS system. This choice was made due to the inability of the EMR and athlete-management systems to make frequent updates, modify existing questions, and provide the necessary form logic for the variety of scenarios in which the IIS system would be deployed. Feedback from the department’s leadership and clinicians resulted in a number of changes, most notably being the ability to enter multiple diagnoses for a single injury event. Additionally, clinician feedback resulted in the creation of additional diagnostic codes not currently present in the OSIICS v14.0 diagnostic coding system, adding “non-sport” as an additional variable for injury setting, and developing a system for reporting return-to-sport date for time-loss injuries.

Discussion
A multi-stage process of extensive planning, stakeholder feedback, and ongoing updates is required in order to successfully develop and implement an IIS system within a National Olympic and Paralynpic Committee. This process can be used to inform the development and implementation of IIS systems in other sporting organizations.
Keratectasia severity staging and progression assessment based on the biomechanical E-staging
Authors: Flockerzi Elias , Seitz Berthold 
Published: July 2024

AbstractUntil recently, corneal topography has been the gold standard in detecting keratectasia and monitoring its progression. The recently introduced ABCD tomographic keratoconus staging system focuses on anterior (“A”) and posterior (“B”) radius of curvature, thinnest corneal thickness (“C”), best-corrected visual acuity with spectacles (“D”) and is supplemented with the introduction of the biomechanical E-staging (BEST, “E”). The need for biomechanical staging arose from the fact of altered biomechanical characteristics of keratectasia in comparison to healthy corneas. Ectatic corneas usually exhibit a biomechanical weakening and greater deformation than healthy corneas when exposed to a biomechanical stressor such as a standardized air puff indentation as provided by the Corvis ST® (CST, Oculus, Wetzlar, Germany). The BEST is based on the linear term of the Corvis Biomechanical Index (CBI) and provides a biomechanical keratoconus severity staging and progression assessment within the CST software. This review traces the development of the BEST as an addition to the tomographic ABCD staging system and highlights its strengths and limitations when applied in daily practice for the detection, monitoring and progression assessment in keratectasia.
The exercise world of otaku: extended body techniques, alternative body projects, and controllable social architecture
Authors: Zhou Jiangwei , Zhao Yu 
Published: July 2024

AbstractWhy do some people opt for exergames like Ring Fit Adventure (RFA) over traditional exercise venues such as gyms? Focusing on the case of RFA, this study examines the social factors that contribute to this preference and explores the potential of video games to create alternative social contexts of physical exercise. Our findings indicate that that RFA constructs a distinct social context that aligns more closely with the body conceptions of the players, assisting them in partially breaking away from dominant norms of body presentation. Notably, RFA acknowledges and extends players’ body techniques related to video games, allowing them to acquire various exercise skills and helping them form alternative body projects and exercise practices through narrative design and game mechanics. The players’ utilization of multiple social media tools constructs a more controllable and individual-centric social architecture that enhances the autonomy of their body presentations.