bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accelerated atherosclerosis in patients with systemic lupus erythematosus (SLE): a case–control study
Authors: Niakan Zahrasadat. , Abdolahi Nafiseh. , Mohammadi Mohaddeseh. , Behnampour Naser. , Hosseini Fatemeh. 
Published: May 2024

Abstract

Introduction: Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that can lead to cardiovascular disease (CVD) and increased mortality. Identifying accelerated atherosclerosis, preventing risk factor propagation, and intervening during the preclinical stage of atherogenesis is crucial. This study aimed to evaluate accelerated atherosclerosis in SLE patients and explore related factors. Methods: This study included 86 patients and 45 age- and sex–matched individuals in the control group. The intima-media thickness (IMT) of the common carotid arteries (CCA) and internal carotid arteries (ICA) was measured using color Doppler ultrasound. The following laboratory parameters, were evaluated: CBC, total cholesterol, HDL, LDL, Cr, ESR, CRP, anti-DNA, and urine. The patients completed a questionnaire that included the Lupus Disease Activity Index (SLEDAI) and demographic information. Results: The average IMT in both the CCA and ICA was significantly greater in patients with lupus (CCA: 0.57 ± 0.09 mm, ICA: 0.49 ± 0.11 mm) than in controls (CCA: 0.37 ± 0.06 mm, ICA: 0.27 ± 0.07 mm); (P < 0.0001). A significant and positive correlation was found between the IMT of the ICA and CCA and age, disease duration, and ESR in the SLE group. Conclusion: The IMT of the CCA and ICA can predict the risk of accelerated atherosclerosis in SLE patients; and is correlated with age, disease duration, and the ESR.
Selection signatures associated with adaptation in South African Drakensberger, Nguni, and Tuli beef breeds
Authors: Gomo Maxman , Marle-Köster Este van , Lashmar Simon Fredrick , Visser Carina 
Published: May 2024

Abstract

Climate change is an important consideration for sustainable beef production systems. Sanga cattle (Bos taurus africanus) are a unique genetic resource known for their adaptability to diverse climates. Genomic technologies have allowed opportunities to investigate indigenous cattle at the deoxyribonucleic acid (DNA) and genome level for insight into variation associated with adaptive traits. 1709 cattle, including 1118 Drakensberger (DRB), 377 Nguni (NGI), and 214 Tuli (TUL), were genotyped using the GeneSeek® Genomic Profiler™ 150K bovine SNP panel. 122632 quality-filtered SNPs was used to assess runs of homozygosity (ROH) and runs of heterozygosity (ROHet) within the three cattle populations using the detectRUNS R package (Biscarini et al., 2018) and PLINK v1.90 (Purcell et al., 2007). The study identified selection signatures associated with adaptation within-and-between three breeds based on ROH, ROHet, and FST-based differentiation of SNPs. The mean number of ROH per animal varied across breeds ranging from 36.09 ± 12.82 (NGI) to 51.82 ± 21.01 (DRB), and the mean ROH length per breed ranged between 2.31Mb (NGI) and 3.90Mb (DRB). The smallest length categories i.e., ROH < 4Mb and ROHet < 0.25Mb were most frequent, indicating predominantly historic inbreeding effects for all breeds. The ROH based inbreeding coefficients (FROH) ranged between 0.033 ± 0.024 (NGI) and 0.081 ± 0.046 (DRB). Genes mapped to candidate regions were associated with immunity (ADAMTS12, CYSTM1, WDPCP) and adaptation (LMAN2, TUBB3) in cattle as well as genes previously only reported for immunity in mice and human (EXOC3L1, MYO1G). This study contributes to the understanding of the mechanisms of adaptation, providing information for functional genomic studies and application in genetic evaluation and selection programs.
Nicotiana benthamiana-derived dupilumab-scFv reaches deep into the cultured human nasal epithelial cells and inhibits CCL26 expression
Authors: Kwon Beom Jun , Cho Na Hyun , Ahn Taeyoung , Kim Geunah , Diệu Nguyễn Thị Xuân , Kim Woo Taek , Cho Hyung-Ju , Seo Dong Hye , Kim Joo Young 
Published: May 2024

Abstract

Plants offer a cost-effective and scalable pharmaceutical platform devoid of host-derived contamination risks. However, their medical application is complicated by the potential for acute allergic reactions to external proteins. Developing plant-based protein therapeutics for localized diseases with non-invasive treatment modalities may capitalize on the benefits of plant proteins while avoiding their inherent risks. Dupilumab, which is effective against a variety of allergic and autoimmune diseases but has systemic responses and injection-related side effects, may be more beneficial if delivered locally using a small biological form. In this study, we engineered a single-chain variable fragment (scFv) of dupilumab, termed Dup-scFv produced by Nicotiana benthamiana, and evaluated its tissue permeability and anti-inflammatory efficacy in air-liquid interface cultured human nasal epithelial cells. Despite showing 3.67- and 17-fold lower binding affinity for IL-4Ra in surface plasmon resonance assays and cell binding assays, respectively, Dup-scFv retained most of the affinity of dupilumab, which was originally high, with a dissociation constant (KD) of 4.76 pM. In human nasal epithelial cells cultured at the air-liquid interface, Dup-scFv administered on the air side inhibited the inflammatory marker CCL26 in hard-to-reach basal cells more effectively than dupilumab. In addition, Dup-scFv had an overall permeability of 0.8% across cell layers compared to undetectable levels of dupilumab. These findings suggest that plant-produced Dup-scFv can be delivered non-invasively to cultured human nasal epithelial cells to alleviate inflammatory signaling, providing a practical approach to utilize plant-based proteins for topical therapeutic applications.
Investigation of the Anti-Cancer of Photodynamic Therapy Effects by Using the Novel Schiff-Base Ligand Complex on Human Breast Cancer Cell Line
Authors: Demirbağ Burcu , Ballı Ebru , Yildirim Metin , Ünver Hakan , Temel Gülhan , Yılmaz Mustafa Kemal , Değirmenci Evren , Kibar Deniz 
Published: May 2024

Abstract

Chemotherapy plays a role in many cancer therapies, including breast cancer, but due to its significant side effects, alternate treatment approaches have been investigated. One such alternative is Photodynamic Therapy (PDT), which employs a combination of oxygen, a photosensitizer (PS), and light of a specific wavelength. Transition metal complexes and SBL have gained interest in PDT. In this study aimed to assess the potential antitumor activity and underlying mechanism of a newly synthesized Schiff Base Ligand (SBL)-mediated PDT on MCF-7 cells, comparing its efficacy to cisplatin. We synthesized and characterized two novel Pd-conjugated SBL compounds (complex-1 and 2). Following the treatment of MCF-7 cells with these compounds, a Light-Emitting Diode (LED) was utilized to deliver a light dose of 14.8 J/cm2. In MCF-7 cells, we also looked at cytotoxicity, cell death rates, and ROS levels. Results indicated a significant increase in cytotoxicity and ROS levels in the group treated with complex-1 mediated PDT. The apoptotic and necrotic cell death also rose significantly. In conclusion, our study suggests that the complex-1 compound may serve as a promising candidate for anticancer agents in PDT for MCF-7 cells. In contrast, complex-2 mediated PDT did not demonstrate any observable anticancer activity.
Deciphering the Impact of PROM1 Alternative Splicing on Human Photoreceptor Development and Maturation
Authors: Lako Majlinda , Molina Marina Moya , Dorgau Birthe , Flood Emily , Letteboer Stef , Lorentzen Esben , Coxhead Jonathan , Smith Graham , Roepman Ronald , Nagaraja-Grellscheid Sushma , Armstrong Lyle 
Published: May 2024

Abstract

Conclusions: Importantly, the use of retinal organoids provides a valuable platform to study AS and unravel disease mechanisms in a more physiologically relevant context, opening avenues for further research and potential therapeutic interventions. Together our data indicate that cones may be more sensitive to PROM1 exon 4 skipping, corroborating the pathogenesis of late-onset mild maculopathy.
Introduction: Alternative splicing (AS) is a crucial mechanism contributing to proteomic diversity, which is highly regulated in tissue- and development-specific patterns. Retinal tissue exhibits one of the highest levels of AS. In particular, photoreceptors have a distinctive AS pattern involving the inclusion of microexons not found in other cell types. PROM1 whose encoded protein Prominin-1 is located in photoreceptor outer segments (OSs), undergoes exon 4 inclusion from the 12th post-conception week of human development through adulthood. Exon 4 skipping in PROM1 is associated with late-onset mild maculopathy, however its role in photoreceptor maturation and function is unknown.
Methods: In this study retinal organoids, a valuable model system, were employed in combination with phosphorodiamidate morpholino oligos (PMOs) to assess the role of exon 4 AS in the development of human retina. Retinal organoids were treated with the PMOs for four weeks after which RT-PCR, western blotting and immunofluorescence analysis were performed to assess exon 4 exclusion and its impact on photoreceptors. The transcriptome of treated ROs was studied by bulk RNA-Seq.
Results: Our data demonstrate that 55% skipping of PROM1 exon 4 resulted in decreased Prominin-1 expression by 40%, abnormal accumulation of cones in the basal side of the retinal organoids as well as detectable cone photoreceptor cilium defects. Transcriptomic and western blot analyses revealed decreased expression of cone, inner segment and connecting cilium basal body markers, increased expression of genes associated with stress response and the ubiquitin-proteasome system and downregulation of autophagy.
Higher Basic Teachers’ Perspective on Integrating Code Programming Nigerian Basic Education to Propel National Technological Advancement
Authors: Eke Eke Ogbu 
Published: May 2024

Abstract

This descriptive survey examines the perception of male and female higher Basic teachers on the integration of coding programming into the Nigerian basic education curriculum to propel national technological advancement. The population comprises 281(91 male and 190 females) public higher Basic education teachers in Owerri Municipal Council of Imo State. The population also serves as the sample size. Researcher’s made attitude questionnaire titled” Higher Basic Educational Teachers Questionnaire on Integrating Coding Programming in Basic Education for National Technological Advancement. (BETQICNTA) was used for data collection. It had reliability coefficient of 0.83 determined using Cronbach Alpha. The findings showed that higher Basic school teachers have positive perception on the integration of coding programming into the Nigerian basic education curriculum to propel national technological advancement. It was recommended among others that educational policymakers should prioritize the integration of coding programming into the Nigerian basic education curriculum. This integration should be comprehensive, ensuring that coding education is accessible to all students, regardless of their background or socioeconomic status.
A Gene Selection Algorithm for Microarray Cancer Classification Using an improved Particle Swarm Optimization
Authors: Nagra Arfan Ali , Khan Ali Haider , Abubakar Muhammad , Faheem Muhammad , Rasool Adil , Masood Khalid , Hussain Muzammil 
Published: May 2024

Abstract

Gene selection is an essential step for the classification of microarray cancer data. Gene expression cancer data (DNA microarray) facilitates computing the robust and concurrent expression of various genes. Particle swarm optimization (PSO) requires simple operators and less number of parameters for tuning the model in gene selection. The selection of a prognostic gene with small redundancy is a great challenge for the researcher as there are a few complications in PSO based selection method. In this research, a new variant of PSO (Self-inertia weight adaptive PSO) has been proposed. In the proposed algorithm, SIW-APSO-ELM is explored to achieve gene selection prediction accuracies. This novel algorithm establishes a balance between the exploitation and exploration capabilities of the improved inertia weight adaptive particle swarm optimization. The self-inertia weight adaptive particle swarm optimization (SIW-APSO) algorithm is employed for solution explorations. Each particle in the SIW-APSO increases its position and velocity iteratively through an evolutionary process. The extreme learning machine (ELM) has been designed for the selection procedure. The proposed method has been to identify several genes in the cancer dataset. The classification algorithm contains ELM, K- centroid nearest neighbor (KCNN), and support vector machine (SVM) to attain high forecast accuracy as compared to the start-of-the-art methods on microarray cancer datasets that show the effectiveness of the proposed method.
Fault diagnosis method for rolling bearings based on BICNN under complex operating conditions
Authors: Duan Xiaoyan , Shi Jiashuo , Lei ChunLi , Zhao Zhengtian 
Published: May 2024

Abstract

To address the issues of poor noise resistance and insufficient generalization performance in traditional fault diagnosis methods, an end-to-end rolling bearing fault diagnosis method based on Bidirectional Interactive Convolutional Neural Network (BICNN) is proposed. Firstly, the bearing vibration signal is directly input into the wide convolutional kernel for rapid feature extraction, reducing the interference of high-frequency noise. Secondly, a modified Rectified Linear Unit (M-ReLU) activation function is designed to solve the problem of "neuron death" in the ReLU activation function. Then, a bidirectional interactive feature extraction module is constructed, and the features extracted are input into the bidirectional interactive feature extraction module to capture the channel and spatial feature information simultaneously. Next, the extracted information is imported the presented feature enhancement module to achieve more valuable information transmission and accumulation. Finally, a small convolutional kernel is applied to further extract feature information, and a global average pooling layer is used to replace the fully connected layer, reducing the number of parameters while avoiding the problem of model overfitting. The Softmax is utilized to classify the types of bearing faults. Two different datasets are adopted to validate the fault diagnosis performance of the proposed model under − 4dB signal-to-noise ratio and variable working conditions. Experimental results show that compared with other fault diagnosis methods, the proposed model has higher fault diagnosis accuracy, stronger noise resistance, and generalization ability.
Incorporation of residual lime can ameliorate subsoil acidity promptly and improve crop performance on sandy soils of the semi-arid regions of Western Australia
Authors: Azam Gaus , Rahman Md Shahinur 
Published: May 2024

Abstract

Background and Aims
Repeated surface application of lime to acidic soil improves farm productivity but cannot manage subsoil acidity promptly. Lime accumulation in topsoil prompted this study to evaluate the role of strategic tillage as a method to swiftly improve subsoil acidity, crop root growth, and yield without additional lime.
Methods
We measured residual lime (carbonate concentration), pH and exchangeable aluminium concentration (EAC) in 2-cm layers in the top 10 cm of soils from three long-term lime experiments at Wongan Hills (WH), Northam (NO) and Merredin (ME). We then incorporated topsoil from 0–4 cm (containing the highest amount of residual lime) at eight incorporation rates with the most acidic subsoil from 20–30 cm depth of the same profile and incubated for six weeks before re-measuring pH and EAC and growing wheat and barley to assess the impact on root growth. In addition, we conducted a field experiment at WH by rotary hoeing both limed and untreated control plots to 25 cm depth in 2018 and grew wheat, canola and barley in 2018, 2019 and 2020, respectively, to measure the impact on soil parameters and crop performance.
Results
A significant amount of residual lime was concentrated in the top 4 cm of soil at all three sites. We measured a total of 1.7, 1.8 and 1.3 t/ha of residual lime in the topsoil (0–10 cm) for the limed plots at WH, NO and ME, respectively. The incorporation of 5%, 10% and 25% topsoil containing residual lime from NO, WH and ME, respectively, with the acidic subsoil was enough to increase soil pH to the target level and to decrease soil EAC significantly and hence improved wheat and barley root length by up to 2 and 13-fold. In the field experiment at WH, the incorporation of residual lime significantly increased subsoil pH by up to 0.7 units, decreased EAC and improved canola yield and water use efficiency.
Conclusion
We concluded that with a good surface liming history, the incorporation of topsoil containing sufficient residual lime with the acidic subsoil may offer a quick amelioration of subsoil acidity without further lime application.
The molecular mechanism investigation of HBP-A slows down meniscus hypertrophy and mineralization by the damage mechanical model
Authors: Yang Zongrui , Feng Yuanyuan , Zhang Mingcai , Liu Yongming , Xiong Yizhe , Wang Xiang , Shi Ying , Chen Bo , Wang Zhengming , Ge Haiya , Zhan Hongsheng , Shen Zhibi , Du Guoqing 
Published: May 2024

Abstract

Objective
This study aimed to determine if HBP-A slows down meniscus hypertrophy and mineralization due to abnormal mechanical damage and if the therapeutic effects of HBP-A are mediated through p38-MAPK signaling pathways.
Methods In vivo guinea pig study:
Male Hartley guinea pigs underwent anterior cruciate ligament transection (ACLT) on the right knee; the left knee served as the control. Three days after molding, high, medium, and low doses of HBP-A were injected into the right knee cavity. The injections were given twice a week for 10 weeks. The width of the medial and lateral meniscus is measured separately using a ruler to assess its hypertrophy. The intensity and area of meniscal calcification were evaluated by Alizarin red and Von Kossa staining. Safranin O/Fast Green staining and OA menisci or cartilage damage scores rated to evaluate degeneration of meniscus and cartilage. Meniscal hypertrophy and calcification-related markers, mtrix metalloproteinase 13 (MMP13), runt-related transcription factor 2 (Runx2), Indian hedgehog (Ihh), alkaline phosphatase (ALP), and ankylosis homolog (ANKH), were detected by immunohistochemistry and RT-qPCR. In vitro rat PMFs study: In vitro isolation and identification of the phenotype of rat primary meniscus fibrochondrocytes (PMFs). 10% stretch force was applied to the isolated PMFs for 24 hours, followed by intervention with 0.3 mg/ml of HBP-A. PMFs proliferation, apoptosis, calcification, and hypertrophy were detected by CCK-8, flow cytometry, Alizarin red, and Toluidine blue staining, respectively. Western Blot and RT-qPCR determine meniscal hypertrophy and calcification related markers with p38 MAPK signaling pathway-related target markers.
Results In vivo guinea pig study:
Guinea pig's meniscus the width, as well as the area and intensity of meniscus calcification and meniscus and articular cartilage injury score were significantly reduced in the HBP-A intervention group compared to the ACLT group. The expression levels of MMP13, Runx2, Ihh, ALP, and ANKH at the protein and gene level significantly decreased in the HBP-A intervention group compared to the ACLT group. In vitro rat PMFs study: Apoptosis, hypertrophy, and calcification of rat PMFs after 10% stretch force for 24h were significantly improved with 0.3mg/ml HBP-A. Western blot and RT-qPCR showed that hypertrophy, calcification, and p38 MAPK signaling pathway-related markers of PMFs were incredibly depressed in the HBP-A intervention group compared to the 10% stretch force group.
Conclusion
HBP-A can slow down meniscus hypertrophy and mineralization induced by abnormal mechanical loading, and its mechanism of action may be through the p38-MAPK signaling pathway.
Evaluation of different irrigation activation techniques for the removal of various medicaments from a simulated internal resorption cavity
Authors: SARIYILMAZ Öznur , USLU Gülşah , SARIYILMAZ Evren , KESKİN Neslihan Büşra 
Published: May 2024

Abstract

Objectives: This study aimed to assess different activation techniques’ efficacy in the removing calcium hydroxide (Ultracal XS), Ledermix and Bio-C Temp from simulated internal root resorption (IRR) cavities.
Materials and Methods: 108 single-rooted maxillary incisors were prepared using Reciproc R50 files. Simulated IRR cavities, 2 mm in diameter and 8 mm from the apex, were created. Ultracal XS, Ledermix, and Bio-C Temp were applied to the samples, grouped by irrigation activation techniques: Standard Needle Irrigation (SNI), EDDY, Passive Ultrasonic Irrigation (PUI), and XP-endo Finisher (XPF). Medicament removal efficacy was evaluated using a standardized scoring system. Statistical analysis was performed using the Kruskal-Wallis test.
Results: XPF and PUI were more effective than SNI in medicament removal across the groups, with no significant difference between them. EDDY showed no a significant difference compared to other groups. Ledermix was more effectively removed in all activation groups compared to Bio-C Temp. The XPF was superior in removing Ultracal XS compared to Bio-C Temp. However, none of the groups achieved complete medicament removal.
Conclusions:XPF and PUI techniques enhance medicament removal efficacy. Bio-C Temp was more difficult to remove from the IRR cavities than other medicaments.
Clinical Relevance: Bio-C Temp is a novel bioceramic intracanal medicament recommended for root resorptions. This study compared its removability from internal resorption cavities to various medicaments using different irrigation activation methods
Exploring the potential of Candida sp. as probiotic for enhancing water quality in aquaculture
Authors: Cheng Ann-Chang , Li Jie-Ying , Balantyne Rolissa , Chiu Shieh-Tsung , Liu Chun-Hung 
Published: May 2024

Abstract

Aquaculture is an important industry that provides a significant amount of seafood globally. However, the industry faces challenges such as water quality management. The objective of the study was to isolate and identify bacteria with the capacity to eliminate nitrite in water from shrimp ponds and evaluate their potential as probiotics to improve water quality. Additionally, the study also determines the ideal conditions for the probiotic to effectively reduce nitrite-N and ammonia-N. Water samples were collected from four shrimp ponds (SW1', SW2', SW3', SW4') and isolates were obtained. Among all the samples, SW4 was the most effective in reducing concentration of nitrite-N. Upon further isolation of SW4, the strain SW4-W6 showed significant nitrite-N reduction capability compared to 19 other isolates tested. Through morphological, genetic (ITS sequence), and phylogenetic analyses, strain SW4-6 was identified. Candida sp. SW4-6 showed superior nitrite-N and ammonia-N reduction capabilities with sucrose as the carbon source, with complete reduction observed at a C/N ratio of 15–20. Gene expression analysis revealed up-regulation of nitrite reductase in SW4-6 after inoculation, with significantly higher expression observed with sucrose as the carbon source. Salinity and temperature significantly influenced nitrite-N and ammonia-N reduction by SW4-6, with higher temperatures (30°C) and 0% NaCl favoring faster reduction rates. Candida sp. SW4-6 emerges as a promising probiotic candidate for aquaculture water quality management due to its efficient nitrite-N and ammonia-N reduction capabilities under optimal conditions. Its safety profile and ability to thrive across various salinity and temperature conditions further support its potential applicability in aquaculture.