bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis of Rhipicephalus microplus hemocytes from female ticks infected with Babesia bovis or Babesia bigemina
Authors: Vimonish Rubikah , Capelli-Peixoto Janaina , Johnson Wendell , Kappmeyer Lowell , Saelao Perot , Taus Naomi , Chung Chungwon , Ueti Massaro 
Published: February 2025

Abstract

Background
Tick hemolymph is a sterile fluid that carries nutrients to maintain tick health. The hemolymph creates a hostile environment for invaders including the destruction of microorganisms by its circulating hemocytes. However, Babesia parasites escape and disseminate to other organs through the hemolymph to continue their transmission life cycle. Still, it is unknown how tick hemocytes respond to B. bovis or B. bigemina infection. In this study, we conducted a transcriptomic analysis of hemocytes from female Rhipicephalus microplus ticks infected with Babesia parasites to understand how gene expression changes during parasite infection.

Methods
During Babesia acute infection, female R. microplus ticks were fed on bovines to acquire parasites. Engorged females were collected and incubated to develop Babesia kinetes in tick hemolymph. The hemolymph was examined to identify ticks that were highly infected with Babesia kinetes. Hemocyte cells were collected from replete female ticks infected with Babesia bovis or Babesia bigemina to perform high-throughput RNA-sequencing (RNA-Seq) analysis.

Results
This study identified major changes in the gene profile of tick hemocytes during Babesia infection. The main groups of hemocyte genes that were altered during Babesia infection were associated with metabolism, immunity, and cytoskeletal rearrangement. Upregulated genes were mainly involved in defense mechanisms, while downregulated genes were related to cell proliferation and apoptosis. However, the expression of hemocyte genes varied among Babesia species’ infections, and it reflected the changes that occurred in the tick’s physiology, including growth, reproduction, and skeletal muscle development.

Conclusions
The differential gene expression of R. microplus hemocytes revealed that genes highly regulated upon Babesia infection were related to metabolism, tick immunity, cell growth, apoptosis, development, metabolism, and reproduction. Additional research is necessary to further define the genes that exhibited varying expression levels in hemocytes during the infection. The findings of this study will enhance our understanding on how Babesia parasites survive in the hostile environment of ticks and perpetuate their transmission cycle, ultimately contributing to the spread of bovine babesiosis.

Graphical Abstract
AxiWorm: a new tool using YOLOv5 to test antiparasitic drugs against Trichinella spiralis
Authors: Sánchez-Montejo Javier , Marín Miguel , Villamizar-Monsalve María Alejandra , Vieira María del Carmen , Vicente Belén , Peláez Rafael , López-Abán Julio , Muro Antonio 
Published: February 2025

Abstract

Background-Objective

Trichinella spiralis drug development and control need an objective high throughput system to assess first stage larvae (L1) viability. YOLOv5 is an image recognition tool easily trained to count muscular first stage larvae (L1) and recognize morphological differences. Here we developed a semi-automated system based on YOLOv5 to capture photographs of 96 well microplates and use them for L1 count and morphological damage evaluation after experimental drug treatments.

Material and methods
Morphological properties were used to distinguish L1 from debris after pepsin muscle digestion and distinguish healthy (serpentine) or damaged (coiled) L1s after 72 h untreated or treated with albendazole or mebendazole cultures. An AxiDraw robotic arm with a smartphone was used to scan 96 well microplates and store photographs. Images of L1 were manually annotated, and augmented based on exposure, bounding, blur, noise, and mosaicism.

Results
A total of 1309 photographs were obtained that after L1 labeling and data augmentation gave 27478 images. The final dataset of 12571 healthy and 14907 affected L1s was used for training, testing, and validating in a ratio of 70/20/10 respectively. A correlation of 92% was found in a blinded comparison with bare-eye assessment by experienced technicians.

Conclusion
YOLOv5 is capable of accurately counting and distinguishing between healthy and affected L1s, thus improving the performance of the assessment of meat inspection and potential new drugs.

Graphical Abstract
Long-read 16S rRNA amplicon sequencing reveals microbial characteristics in patients with colorectal adenomas and carcinoma lesions in Egypt
Authors: El Leithy Asmaa A. , Youssef Amira Salah El-Din , Nassar Auhood , Aziz Ramy K. , Khaled Nadin M. , Mahrous Mina T. , Farahat Ghobrial N. , Mohamed Aya H. , Bakr Yasser Mabrouk 
Published: February 2025

Abstract

Background
Colorectal cancer (CRC) is among the five leading causes of cancer incidence and mortality. During the past decade, the role of the gut microbiota and its dysbiosis in colorectal tumorigenesis has been emphasized. Metagenomics and amplicon-based microbiome profiling provided insights into the potential role of microbial dysbiosis in the development of CRC.

Aim
To address the scarcity of information on differential microbiome composition of tumor tissue in comparison to adenomas and the lack of such data from Egyptian patients with CRC.

Materials and methods
Long-read nanopore sequencing of 16S rRNA amplicons was used to profile the colonic microbiota from fresh colonoscopic biopsy samples of Egyptian patients with CRC and patients with colonic polyps.

Results
Species richness of CRC lesions was significantly higher than that in colonic polyps (p-value = 0.0078), while evenness of the CRC group was significantly lower than the colonic polyps group (p-value = 0.0055). Both species richness and Shannon diversity index of the late onset CRC samples were significantly higher than those of the early onset ones. The Firmicutes-to-Bacteroidetes (F/B) ratio was significantly higher in the CRC group than in the colonic polyps group (p-value = 0.0054), and significantly higher in samples from early-onset CRC. The Enterococcus spp. were significantly overabundant in patients with rectal cancer and early-onset CRC, while Staphylococcus spp. were significantly higher in patients with sigmoid cancer and late-onset CRC. In addition, the relative abundance of Fusobacterium nucleatum was significantly higher in CRC patients.

Conclusion
Differentiating trends were identified at phylum, genus, and species levels, despite the inter-individual differences. In summary, this study addressed the microbial dysbiosis associated with CRC and colonic polyps groups, paving the way for a better understanding of the pathogenesis of early and late-onset CRC in Egyptian patients.
Sex and gender differences in the molecular etiology of Parkinson’s disease: considerations for study design and data analysis
Authors: Schaffner Samantha L. , Tosefsky Kira N. , Inskter Amy M. , Appel-Cresswell Silke , Schulze-Hentrich Julia M. 
Published: February 2025

Abstract
Parkinson’s disease (PD) is more prevalent in men than women, and presents with different clinical features in each sex. Despite widespread recognition of these differences, females are under-represented in clinical and experimental studies of PD, and much remains to be elucidated regarding the biological underpinnings of sex differences in PD. In this review, we summarize known contributors to sex differences in PD etiology across the life course, with a focus on neurological development and gene regulation. Sex differences that are established at conception and heightened during adolescence and midlife may partially embed future PD risk, due to the complex interactions between gonadal hormones, gene regulation, lifestyle factors, and aging. While the neuroprotective properties of estrogen are strongly implicated in reduced prevalence of PD in women, interactions with genotype and gender-biased lifestyle factors are incompletely understood. Consideration of sex and gender-related factors in study design, data analysis, and interpretation have the power to expedite our knowledge of the etiology of PD in men and in women, and to inform prevention and therapeutic strategies tailored to each sex.
Establishing a radiomics model using contrast-enhanced ultrasound for preoperative prediction of neoplastic gallbladder polyps exceeding 10 mm
Authors: Jiang Dong , Qian Yi , Gu Yijun , Wang Ru , Yu Hua , Wang Zhenmeng , Dong Hui , Chen Dongyu , Chen Yan , Jiang Haozheng , Li Yiran 
Published: February 2025

Abstract

Background
A key challenge in the medical field is managing gallbladder polyps (GBP) > 10 mm, especially when their nature is uncertain. GBP with a diameter exceeding 10 mm are associated with an increased risk of gallbladder cancer, making the key to their management the differentiation between benign and malignant types. The current practice, due to the inability to predict accurately, leads to excessive surgeries and ineffective follow-ups, increasing patient risks and medical burdens.

Purpose
This study aims to establish an imaging radiomics model using clinical data and contrast-enhanced ultrasound (CEUS) to predict neoplastic GBP exceeding 10 mm in diameter preoperatively.

Materials and methods
Data from 119 patients with GBP > 10 mm of unknown origin were analyzed. A total of 1197 features were extracted from the GBP area using conventional ultrasound (US) and CEUS. Significant features were identified using the Mann–Whitney U test and further refined with a least absolute shrinkage and selection operator (LASSO) regression model to construct radiomic features. By integrating clinical characteristics, a radiomics nomogram was developed. The diagnostic efficacy of the preoperative logistic regression (LR) model was validated using receiver operating characteristic (ROC) curves, calibration plots, and the Hosmer–Lemeshow test. CEUS is an examination based on conventional ultrasound, and conventional two-dimensional ultrasound still poses significant challenges in differential diagnosis. CEUS has a high accuracy rate in diagnosing the benign or malignant nature of gallbladder space-occupying lesions, which can significantly reduce the preoperative waiting time for related examinations and provide more reliable diagnostic information for clinical practice.

Results
Feature selection via Lasso led to a final LR model incorporating high-density lipoprotein, smoking status, basal width, and Rad_Signature. This model, derived from machine learning frameworks including Support Vector Machine (SVM), Logistic Regression (LR), Multilayer Perceptron (MLP), k-Nearest Neighbors (KNN), and eXtreme Gradient Boosting (XGBoost) with fivefold cross-validation, showed AUCs of 0.95 (95% CI: 0.90–0.99) and 0.87 (95% CI: 0.72–1.0) in internal validation. The model exhibited excellent calibration, confirmed by calibration graphs and the Hosmer–Lemeshow test (P = 0.551 and 0.544).

Conclusion
The LR model accurately predicts neoplastic GBP > 10 mm preoperatively. Radiomics with CEUS is a powerful tool for analysis of GBP > 10 mm. The model not only improves diagnostic accuracy and reduces healthcare costs but also optimizes patient management through personalized treatment plans, enhancing clinical outcomes and ensuring resources are more precisely allocated to patients who need surgery.
Exploring single cell microbial protein as a sustainable fishmeal alternative in yellowtail kingfish (Seriola lalandi) diets: impacts on health and gut microbiome
Authors: Pilmer Luke , Woolley Lindsey , Lymbery Alan , Dam Chinh , Elizur Abigail , Foysal Md Javed , Partridge Gavin 
Published: February 2025

Abstract

Background
With the global expansion of aquaculture and the increasing demand for fish meal, identifying appropriate and sustainable alternative protein sources for aquafeeds has become essential. Single-cell protein (SCP), derived from methanotrophic bacteria, presents a promising alternative by converting methane into protein, potentially addressing both the need for alternative protein sources and reducing industrial greenhouse gas emissions. This study aimed to evaluate the effects of different levels of SCP inclusion (0%, 25%, 50%, and 75% fish meal replacement) on the health, gene expression, and gut microbiome of yellowtail kingfish (YTK, Seriola lalandi) following a 35-day growth trial.

Results
The study found that SCP inclusion at the highest level of fishmeal replacement (75%) induced a mild inflammatory response in the hindgut of the fish. However, micromorphological assessments of the hindgut, serum biochemistry, and gene expression analyses revealed no significant detrimental effects from SCP replacement. Notably, there were indications of improved lipid digestibility with SCP. Furthermore, SCP inclusion significantly enhanced microbial richness and altered the composition of the gut microbiome, introducing beneficial bacterial taxa that may contribute to improved gut health and resilience.

Conclusions
This study highlights SCP as a viable and sustainable alternative to fish meal in YTK diets. The findings suggest that SCP can be included in YTK diets without adverse health effects at moderate levels and may even offer benefits in terms of lipid digestibility and gut microbiome diversity. These results contribute to the advancement of more sustainable aquaculture practices.
Real-world study of phakic refractive lens for correction of high myopia
Authors: Pan An-Peng , Shao Xu , Li Yi-Ke , Li Zi-Yue , Yan Qiong , Sun Wei-Yang , Yu A-Yong 
Published: February 2025

Abstract

Background
To assess the safety and efficacy of phakic refractive lens (PRL) implantation for correcting high myopia, as well as an ophthalmic viscosurgical device-free (OVD-free) method for PRL implantation.

Methods
In this real-world prospective study, consecutive patients implanted with PRL in one or both eyes were enrolled. Based on the surgical techniques used, the eyes were divided into the OVD-free method group and the conventional method group. The patients were examined 2 h after surgery and were scheduled for follow-up at 1 day, 1 week, 1 month, 3 months, 6 months, and 12 months. The corrected distance visual acuity (CDVA), uncorrected distance visual acuity (UDVA), the manifest refraction spherical equivalent (MRSE), intraocular pressure (IOP) and lens vault were assessed postoperatively. Corneal endothelial cell density (ECD) was measured at the 3- and 12-month postoperative visits.

Results
Fifty-seven consecutive patients (108 eyes) were enrolled. At the 3-month postoperative visit, both mean UDVA and CDVA were significantly improved after PRL implantation (0.19 ± 0.21 and 0.01 ± 0.14 logMAR) with efficacy index and safety index of 0.92 and 1.30, respectively. None of the eyes had any loss of CDVA. The percentage of eyes within ± 0.50 D and ± 1.00 D of target refraction was 58% and 83%, respectively. Mean MRSE changed from − 14.49 ± 4.22 D, preoperatively, to − 1.22 ± 1.26 D at 1 day (P < 0.001) and remained stable thereafter. Mean endothelial cell loss was 11.3%, 9.6%, respectively, at 3 and 12 months, with no significant difference between the two follow-ups (P = 0.395). Fifty-nine eyes received the OVD-free method, and 49 eyes received the conventional method. The OVD-free method demonstrated a significant reduction in the incidence of early acute IOP elevations (28.8% vs. 53.1%, P = 0.022) compared to the conventional method. The difference of initial endothelial cell loss (9.4 ± 14.2% vs. 13.6 ± 14.6%) between the two groups trended toward significance (P = 0.056). In both groups, no other major complications were observed up to 12-month follow-up.

Conclusions
PRL implantation was a safe, efficient, predictable and stable method for correcting high myopia. The potential of lower incidence of early acute IOP elevations makes the OVD-free method a promising alternative to the conventional method.

Trail registration: Chinese Clinical Trial Registry, ChiCTR2100043600. Registered on 23 February 2021, https://www.chictr.org.cn/showproj.html?proj=122229
Influence of preoperative variables on the 3-month functional outcomes of the Vivity extended depth-of-focus intraocular lens: a prospective case series
Authors: Savini Giacomo , Galzignato Alice , Coutinho Catarina P. , Huang Jinhai , Wu Yue , Barboni Piero , Mendanha Dias João , Ribeiro Filomena J. , Schiano-Lomoriello Domenico 
Published: February 2025

Abstract

Background
To investigate the functional results of the AcrySof IQ Vivity (Alcon, Fort Worth, TX) extended depth-of-focus intraocular lens (EDoF-IOL) and explore correlations between the preoperative biometric parameters and the postoperative functional outcomes.

Methods
In a prospective, single-center, non-randomized study, axial length, keratometry, anterior chamber depth, scotopic and photopic pupil diameters, pupil decentration, corneal asphericity, corneal higher-order aberrations (HOAs), coma and spherical aberration were measured preoperatively. The EDoF-IOL was implanted bilaterally. Three months postoperatively, manifest refraction, monocular and binocular uncorrected and corrected visual acuity at 4 m, 66 cm and 40 cm, binocular defocus curve, binocular contrast sensitivity, halometry and Strehl ratio were measured. Visual disturbances and spectacle independence were assessed with McAlinden and IOLSAT questionnaires, respectively. Assuming a minimum Pearson r correlation coefficient between variables of 0.5 with a power of 80% and a P value less than 0.05, a minimum sample size of 29 (58 eyes) cases was required.

Results
Forty-three patients were enrolled. Binocular distance corrected visual acuity was lower than 0.1 logMAR for a defocus between + 1.0 and − 1.5 D. The mean values at 66 cm and 40 cm were − 0.07 ± 0.06 and 0.19 ± 0.13 logMAR, respectively. McAlinden’s questionnaire revealed mean scores close to zero for all questions. The IOLSAT questionnaire showed that spectacles were never used for distance and intermediate vision. Regression analysis did not disclose any significant correlation between the preoperatively measured variables and the postoperative outcomes, with a few exceptions: preoperative higher order corneal aberrations were correlated to halometry area (r2 = 0.2592, P = 0.0006) and the Q value to contrast sensitivity (r2 = 0.1717, P = 0.00574) under photopic conditions with glare at a spatial frequency of 18 cpd and without glare for all spatial frequencies (P < 0.01); it was also correlated to contrast sensitivity under mesopic conditions without glare at a spatial frequency of 12 cpd (r2 = 0.2311, P = 0.0011).

Conclusions
In healthy unoperated eyes, the visual outcomes for this EDoF-IOL are independent of most of the patients’ preoperative parameters. Attention should be paid to preoperative corneal aberrations and asphericity, which did not lead to visual disturbances, but may be potential sources of halo and reduced contrast sensitivity.
Factors influencing academic staff satisfaction and continuous usage of generative artificial intelligence (GenAI) in higher education
Authors: Baig Maria Ijaz , Yadegaridehkordi Elaheh 
Published: February 2025

Abstract
Generative Artificial Intelligence (GenAI) tools hold significant promises for enhancing teaching and learning outcomes in higher education. However, continues usage behavior and satisfaction of educators with GenAI systems are still less explored. Therefore, this study aims to identify factors influencing academic staff satisfaction and continuous GenAI usage in higher education, employing a survey method and analyzing data using Partial Least Squares Structural Equation Modeling (PLS-SEM). This research utilized the Unified Theory of Acceptance and Use of Technology (UTAUT) and the Expectation Confirmation Model (ECM) as its theoretical foundations, while also integrating ethical concerns as a significant factor. Data was collected from a sample of 127 university academic staff through an online survey questionnaire. The study found a positive correlation between effort expectancy, ethical consideration, expectation confirmation, and academic staff satisfaction. However, performance expectancy did not show a positive correlation with satisfaction. Performance expectancy was positively related to the intention to use GenAI tools, while academic staff satisfaction positively influenced the intention to use GenAI. The social influence did not correlate positively with the use of GenAI. Security and privacy were positively associated with staff satisfaction. Facilitation conditions also positively influenced the intention to use GenAI. The findings of this study provide valuable insights for academia and policymakers, guiding the responsible integration of GenAI tools in education while emphasizing factors for policy considerations and developers of GenAI tools.
Collagen peptide protects Saccharomyces cerevisiae from furfural stress for enhancing bioethanol synthesis
Authors: Yang Ming , Li Xia , Wang Bo , Liu Xian , Zhang Bo , Liao Xue-Pin 
Published: February 2025

Abstract
The efficient biosynthesis is important for the sustainable development of lignocellulosic ethanol industry, but it is limited by furfural stress produced with cellulose pretreatment. Collagen peptide (CP), as an affluent protein resource, considerably improved the tolerance of Saccharomyces cerevisiae against furfural stress. When the furfural concentration was 2 g/L, the residual sugar concentration was reduced from 122.39 to 8.90 g/L, and the final ethanol yield increased from 30.69 to 87.27 g/L in the presence of CP. In addition, the ethanol yield in CP containing media was higher than those in other peptides. Transcriptome analysis showed CP can improve the expression of genes (FBA1, PDC1, PDC6, and ENO1) associated with glycolysis to promote sugar utilization, and enhance ethanol biosynthesis under furfural stress, which were further verified by quantitative real-time PCR. These results indicated that CP is a promising protectant and accelerator for bioethanol biosynthesis.

Graphical abstract
Zebrafish as a model for human epithelial pathology
Authors: Abu-Siniyeh Ahmed , Khataibeh Moayad , Al-Zyoud Walid , Al Holi Majed 
Published: February 2025

Abstract
Zebrafish (Danio rerio) have emerged as an influential model for studying human epithelial pathology, particularly because of their genetic similarity to humans and their unique physiological traits. This review explores the structural and functional homology between zebrafish and human epithelial tissues in organs, such as the gastrointestinal system, liver, and kidneys. Zebrafish possess significant cellular and functional homology with mammals, which facilitates the investigation of various diseases, including inflammatory bowel disease, nonalcoholic fatty liver disease, and polycystic kidney disease. The advantages of using zebrafish as a model organism include rapid external development, ease of genetic manipulation, and advanced imaging capabilities, allowing for the real-time observation of disease processes. However, limitations exist, particularly concerning the lack of organs in zebrafish and the potential for incomplete phenocopy of human conditions. Despite these challenges, ongoing research in adult zebrafish promises to enhance our understanding of the disease mechanisms and regenerative processes. By revealing the similarities and differences in epithelial cell function and disease pathways, this review highlights the value of zebrafish as a translational model for advancing our knowledge of human health and developing targeted therapies.