bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specification for Light Rare Earth Concentrates Prepared from Egyptian Crude Monazite Spectrophotometrically
Authors: Shehata SH. B. , El-Ghany M. S. Abd , Helaly O. S. , Abo-Aly M. M. 
Published: February 2024

Abstract
Determination of several light and medium REEs individually such as lanthanum, neodymium, praseodymium, samarium and gadolinium in high-grade concentrates prepared from Egyptian crude Monazite are achieved. These concentrates were firstly specified using SCAN-EDX analysis to identify the constituents of the analyzed rare earth elements. Complex formation study was carried out spectrophotometrically between disodium ethylene diaminetetraacetic acid (EDTA) and these trivalent rare earth elements “REEs” as Ln-EDTA for light and middle REEs. Different factors have been investigated including, EDTA-REEs molar ratio, pH of the LREEs / EDTA medium; time required for complex formation and initial concentrations of rare earth elements.
Subtractive Genome mining in Xanthomonas citri pv. Citri strain 306 for identifying novel drug target proteins coupled with in-depth protein-protein interaction and coevolution analysis - A leap towards prospective drug design
Authors: Mahato Tumpa , Mandal Jayanta , Chatterjee Eilita , Bhattacharya Satyabrata , Sinha Sangram 
Published: February 2024

Abstract
Citrus canker (CC) poses a serious threat to a highly significant citrus fruit crop, this disease caused by one of the most destructive bacterial plant pathogens Xanthomonas citri pv. citri. Bacterial plant diseases cause substantial global losses in crop production. Reducing crop yield losses is necessary to meet growing global food demands with a rising population. High rates of antibiotic resistance to conventional pesticides and antibiotics among Xanthomonas citri pv. citri (XCC) strains the effectiveness of current control methods is diminishing, have rendered treatment management more challenging and highlighted the need for novel therapeutic targets or new approaches to combat the rising antimicrobial resistance trend. Utilizing OMICS data offers an appealing alternative to experimental methods, propelling drug discovery and reducing the risk of later-stage drug failures. Using an innovative hierarchical computational method, the goal of this present study was to identify and characterize potential drug targets against the pathogen XCC strain 306. The study involved retrieving the XAC proteome from the UniProt database, eliminating paralogous proteins using CD-HIT (80% identity cutoff), and selecting nonhomologous proteins through BLASTp (e-value < 0.005). Essential proteins were identified using BLAST against the DEG (e-value cutoff 0.00001). Subsequent analyses included metabolic pathway assessment, subcellular localization prediction, and druggability analysis. Protein network analysis, coevolution analysis (CoeViz server), protein active site identification (CastP 3.0), and centrality betweenness graph plotting (ProsNex) were performed. In conclusion, this study identified eight drug targets (GlmU, CheA, RmlD, GspE, FleQ, RpoN, Shk, SecB), highlighting RpoN, FleQ, and SecB as unprecedented targets for XCC. These findings may contribute to the development of novel antimicrobial agents in the future that can efficiently control citrus canker disease.
Stress boundary layers for the Phan-Thien–Tanner fluid at the static contact line in extrudate swell
Authors: Evans Jonathan D. , Evans Morgan L. 
Published: February 2024

Abstract

The method of matched asymptotic expansions is used to examine the behaviour of the Phan-Thien–Tanner (PTT) fluid in the neighbourhood of the contact line singularity in extrudate swell. The solution structure for this shear-thinning viscoelastic fluid model, has solvent stresses that dominate the polymer stresses, but requires stress boundary layers to fully resolve the solution at the die wall and free surface. The sizes and mechanism of the boundary layers at the two surfaces are different. We derive and present a similarity solution for the boundary layer at the die wall and an exact solution for the boundary layer at the free-surface. An expression for the local behaviour of the free-surface is also derived. The results for the boundary layers completes the preliminary asymptotic results for the PTT model presented in previous work.
Utility of an untargeted metabolomics approach using a 2D GC-GC‒MS platform to distinguish relapsing and progressive multiple sclerosis
Authors: Datta Indrani , Zahoor Insha , Ata Nasar , Rashid Faraz , Cerghet Mirela , Rattan Ramandeep , Pisson Laila M , Giri Shailendra 
Published: February 2024

Abstract

Introduction:
Multiple sclerosis (MS) is the most common inflammatory neurodegenerative disease of the central nervous system (CNS) in young adults and results in progressive neurological defects. The relapsing-remitting phenotype (RRMS) is the most common disease course in MS and may progress to the progressive form (PPMS).
Objectives
There is a gap in knowledge regarding whether the relapsing form can be distinguished from the progressive course or healthy subjects (HS) based on an altered serum metabolite profile. In this study, we performed global untargeted metabolomics with the 2D GCxGC-MS platform to identify altered metabolites between RRMS, PPMS, and HS.
Methods
We profiled 235 metabolites in the serum of patients with RRMS (n = 41), PPMS (n = 31), and HS (n = 91). A comparison of RRMS and HS patients revealed 22 significantly altered metabolites at p < 0.05 (false discovery rate [FDR] = 0.3). The PPMS and HS comparisons revealed 28 altered metabolites at p < 0.05 (FDR = 0.2).
Results
Pathway analysis using MetaboAnalyst revealed enrichment of four metabolic pathways in both RRMS and PPMS (hypergeometric test p < 0.05): 1) galactose metabolism; 2) amino sugar and nucleotide sugar metabolism; 3) phenylalanine, tyrosine, and tryptophan biosynthesis; and 4) aminoacyl-tRNA biosynthesis. The Qiagen IPA enrichment test identified the sulfatase 2 (SULF2) (p = 0.0033) and integrin subunit beta 1 binding protein 1 (ITGB1BP1) (p = 0.0067) genes as upstream regulators of altered metabolites in the RRMS vs. HS groups. However, in the PPMS vs. HS comparison, valine was enriched in the neurodegeneration of brain cells (p = 0.05), and heptadecanoic acid, alpha-ketoisocaproic acid, and glycerol participated in inflammation in the CNS (p = 0.03).
Conclusion
Overall, our study suggested that RRMS and PPMS may contribute metabolic fingerprints in the form of unique altered metabolites for discriminating MS disease from HS, with the potential for the construction of a metabolite panel for progressive autoimmune diseases such as MS.
COVID-related Constrictive Pericarditis Requiring Pericardiectomy: A Case Report
Authors: Boyles Rachel , Lu Joseph , Yoo Joseph , Samuels Louis 
Published: February 2024

Abstract

Background
The COVID-19 pandemic was primarily considered a respiratory malady in the early phases of the outbreak. However, as more patients suffer from this illness, a myriad of symptoms emerge in organ systems separate from the lungs. Among those patients with cardiac involvement, myocarditis, pericarditis, myocardial infarction, and arrhythmia were among the most common manifestations. Pericarditis with pericardial effusion requiring medical or interventional treatments has been previously reported in the acute setting. Notably, chronic pericarditis with pericardial thickening resulting in constriction requiring sternotomy and pericardiectomy has not been published to date.
Case Presentation
A patient with COVID-19-associated constrictive pericarditis three years after viral infection requiring pericardiectomy was reported. The COVID-19 infection originally manifested as anosmia and ageusia. Subsequently, the patient developed dyspnea, fatigue, right-sided chest pressure, bilateral leg edema, and abdominal fullness. Following recurrent right pleural effusions and a negative autoimmune work-up, the patient was referred for cardiothoracic surgery for pericardiectomy when radiographic imaging and hemodynamic assessment were consistent with constrictive pericarditis. Upon median sternotomy, the patient’s pericardium was measured to be 8 mm thick. Descriptions of the clinical, diagnostic, and therapeutic features are provided. Within the first week after the operation, the patient’s dyspnea resolved; one month later, leg edema and abdominal bloating were relieved.
Conclusions
Although an association between COVID-19 and cardiac complications has been established, this case adds another element of virus severity and chronic manifestations. The need for sternotomy and pericardiectomy to treat COVID-19-related constrictive pericarditis is believed to be the first reported diagnosis.
Integrative analysis of genomic and epigenomic regulation reveals microRNA regulatory network mediated tumor heterogeneity and immune evasion in lower grade glioma
Authors: Yang Zhen , Liu Xiaocen , Xu Hao , Teschendorff Andrew E. , Xu Lingjie , Li Jingyi , Fu Minjie , Liu Jun , Zhou Hanyu , Wang Yingying , Zhang Licheng , He Yungang , Lv Kun , Yang Hui 
Published: February 2024

Abstract
Background
Lower grade glioma (LGG) is the most frequent primary tumors of the central nervous system and has been a major healthcare burden, however, the specific molecular mechanism underlying its initiation and progression remains to be elucidated. Although it is known that microRNAs (miRNAs) are widely involved in the regulation of malignant phenotypes of glioma, the underling mechanism for miRNA dysregulation remains largely unanswered.
Methods
In the present work, we developed a novel strategy to obtain the genome wide copy number variation (CNV) and promoter DNA methylation (DNAm) data of miRNAs and performed a systematic integrative study for the multi-omics data to identify mechanisms underlying miRNA dysregulation molecular subtyping in LGG. The relationship between LGG subtypes, prognosis, molecular features, tumor immune microenvironment and response to immune therapy was further analyzed. We also developed a prognostic model based on immune-related miRNAs that were differentially expressed between LGG samples. Then, the influence of the prognostic model on the immune microenvironment in LGG was comprehensively analyzed.
Results
We identify 719 miRNAs whose expression was associated with alterations of copy number variation or promoter methylation. Integrative multi-omics analysis of the copy number and methylation related miRNAs revealed four subtypes with differing prognoses, which were validated with independent cohort data. These glioma subtypes exhibited distinct immune-related characteristics as well as clinical and genetic features. We further screened immune-related miRNAs through investigation of their correlation with immune cell infiltrations and immune microenvironment. By construction of a miRNA regulatory network, we identified candidate miRNAs associated with immune evasion and response to glioma immunotherapy. We finally evaluated the associations between prognosis related miRNAs and immune regulation. Among them, miR-155-5p, miR-196a-5p, miR-196b-5p, miR-200a-3p, miR-503-5p, and miR-15b-5p were validated as immunoevasive biomarkers and to promote cell migration, invasion and proliferation for glioma through in vitro experiments.
Conclusions
Our study systematically reveals the crosstalk among DNA methylation, copy number variation and miRNA expression for immune regulation in glioma, and could have important implications for patient stratification and development of novel biomarkers for immunotherapy approaches.
KDM6B enhances anti-PD-L1 immunotherapy efficacy by increasing CD8+ T-cell infiltration in colorectal cancer
Authors: Xun Jing , Liu Zehan , Liu Bin , Jiang Xiaolin , Liu Jinjin , Wang Botao , Gao Ruifang , Zhang Aimin , Wu Xueliang , Wang Ximo , Yu Xiangyang , Zhang Qi 
Published: February 2024

Abstract

Background: CD8+ T cells in the tumor microenvironment are crucial for antitumor effects. Boosting their infiltration can significantly enhance the efficacy of antitumor immunotherapy. However, the precise contribution of the epigenetic regulator lysine-specific demethylase 6B (KDM6B) to colorectal cancer (CRC) immunity remains elusive.
Methods: KDM6B expression was detected in adjacent and CRC tissues or normal and cancer cells. Mouse models of CRC were established to assess the impact of KDM6B on tumor progression. The infiltration of CD8+ T cells was detected by IHC and a transwell assay. RT-qPCR, western blotting or flow cytometry were used to detect the effect of KDM6B on PD-L1, CD8+ T-cell-attracting chemokines and p-STAT3 expression. ChIP-qPCR was performed to determine the H3K27me3 enrichment in the promoter regions of target genes PD-L1 and CD8+ T-cell-attracting chemokines. Finally, paricalcitol was combined with anti-PD-L1 antibodies to evaluate their anti-CRC effects.
Results: KDM6B was downregulated in CRC tissues and cells, but its overexpression successfully hindered CRC growth and liver metastasis. Mechanistically, the activation of demethylase activity and STAT3 signaling, leading to increased expression of CD8+ T-cell-attracting chemokines CCL5, CXCL9, and CXCL10, as well as enhanced PD-L1 expression in CRC cells. This ultimately resulted in increased infiltration of CD8+ T cells. Paricalcitol and anti-PD-L1 antibody therapy work together to achieve superior tumor elimination efficiency. Paricalcitol, combined with anti-PD-L1 antibodies, offered superior tumor elimination efficiency.
Conclusion: These findings suggest that KDM6B plays a positive role in regulating the immune microenvironment in CRC, potentially offering a theoretical basis for CRC immunotherapy.
Generalized Coupled Matrix Tensor Factorization Method Based on Normalized Mutual Information for Simultaneous EEG-fMRI Data Analysis
Authors: Rabiei Zahra , Kordy H. Montazery 
Published: February 2024

Abstract

Through the fusion of electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) data, the complementary properties of both modalities can be exploited. Thus, joint analysis of both modalities can be utilized in brain studies to estimate their shared and unshared components in brain activities. In this study, a comprehensive approach was proposed to jointly analyze EEG and fMRI datasets based on the advanced coupled matrix tensor factorization (ACMTF) method. The similarity of the components based on normalized mutual information (NMI) was defined to overcome the restrictive equality assumption of shared components in the common dimension of the ACMTF method. Because the mutual information (MI) measure is capable of identifying both linear and nonlinear relationships between the components, the proposed method can be viewed as a generalization of the ACMTF method; thus, it is called the generalized coupled matrix tensor factorization (GCMTF). The proposed GCMTF method was applied to simulated data, in which there was a nonlinear relationship between the components. The results demonstrate that the average match score increased by 23.46% compared to the ACMTF model, even with different noise levels. Furthermore, by applying this method to real data from an auditory oddball paradigm, it was demonstrated that three shared components with frequency responses in the alpha and theta bands were identified. The proposed MI-based method is not only capable of extracting shared components with any nonlinear or linear relationship but it is also able to identify more active brain areas corresponding to an auditory oddball paradigm compared to the ACMTF and other similar methods.
Genetic variability in Iranian sainfoin (Onobrychis viciifolia Scop.) landraces by morphological characteristics
Authors: Sabaghnia Naser , Ahadnezhad Amin , Moayed Farid Normand , Janmohammdi Mohsen 
Published: February 2024

Abstract
The sainfoin (Onobrychis viciifolia Scop.) is an ancient fodder crop traditionally cultivated in Mediterranean climates, yet its cultivation has dwindled in favor of other forage options across many regions. We investigated the diversity among 32 sainfoin landraces sourced from various parts of Iran, analyzing 18 distinct traits over two seasons (2022 and 2023) using a randomized complete block scheme. Notable variations were observed across the majority of measured characteristics, whereas the coefficient of variation ranged from 10.5–6.8% (for days to seed filling initiation) to as high as 63.2% and 70.8% (for inflorescence dry weight) in the first and second years, respectively. Principal Component Analysis (PCA) highlighted significant variability, with the first four components explaining 83% of the variance in 2022 and 78% in 2023. When plotting PCA1 against PCA2 for both years, distinct groups emerged, revealing three discernible groups of sainfoin landraces. Notably, certain landraces consistently grouped together across both years, including G1 (Bonab), G3 (Marand), and G11 (Urmia) from the northwest, G23 (Khomeyn), G24 (Arak), and G30 (Khansar) from the central region, and G26 (Asadabad) from the western, alongside G28 (Damavand) from the north. These landraces, originating from diverse geographical locations, were identified as particularly promising due to their distinct traits. Our findings underscore the rich morphological diversity present in current sainfoin landraces, suggesting ample opportunities for genetic improvement initiatives. These insights hold relevance for future breeding efforts aimed at enhancing specific traits through strategic crossbreeding of parent plants.
Factors Affecting Student Learning Experience: The Case of Arabic Calligraphy and Morphology Subjects in MSU KFCIAAS During Online Modality
Authors: Mama Jasmin Jeanette C. , Vistal Jogie A. , Maruhom Jenan Shahri A. 
Published: February 2024

Abstract
During the pandemic, educational institutions worldwide were forced to shift to online modalities for safety reasons, affecting not only English subjects but also Arabic subjects. This shift posed challenges for Arabic subjects, as the standard online learning infrastructure often did not adequately support these specialized courses. Students found it more difficult to adjust compared to traditional face-to-face classes. Hence, this study aims to investigate the factors influencing students’ learning experiences in Arabic subjects during online modality using Structural Equation Modelling. Key elements were identified as influential on students’ learning outcomes on these subjects, such as self-regulation, technology literacy and competency, technological sufficiency, technology complexity, and learning resources. On the other hand, the study explores the factors contributing to students’ successful completion of Arabic Calligraphy and Morphology subjects during online learning such as imitating, consolidation, deep mastery, tamrin, and ijazah. The study was conducted on a sample size of 100 students who were enrolled in Arabic Calligraphy and Arabic Morphology subjects during the online modality. The instrument comprised 52 questions designed to collect data on the factors affecting students’ learning experiences during the online modality. The findings shed light on the implications of teaching and learning Arabic subjects within online education.
Binding predictions and molecular docking as a computational approach to identify human T CD4 epitopes from Leishmania proteins
Authors: Martínez Magda Melissa Flórez , Larios Dariannis , Martínez Wilson David , Rojas Karel , Uribe Yajaira , Torres Francy Elaine 
Published: February 2024

Abstract

Leishmaniasis is an important public health problem caused by a protozoan parasite and distributed in 98 countries worldwide. Leishmania can causes from skin ulcers to complex visceral involvement, and treatment options available for humans have high toxicity and prolonged application schemes, therefore low treatment adhesion. So far there are not licensed vaccines for humans so is necessary to develop a strategy that can improve treatment options or that can prevent the onset of the disease. To eliminate intracellular Leishmania amastigotes inside macrophage, a cellular immune response of CD4+ Th1 profile is essential, therefore the identification of sequences that binds strong to HLA class II pockets are good candidates to induce a protective immune response against Leishmania spp.
The aim of this study was to identify T CD4+ epitopes from immunogenic Leishmania proteins.
Methodology: First, three prediction tools were used as screening comparing the 15mer sequences along the complete protein sequence against 25 HLA-DR alleles employing NH, SMT, CPA, CPB, and CPC proteins. Second, molecular docking was run for the best candidates.
Results: 6 peptides were identified as HLA-DR strong binders simultaneously from the three bioinformatic prediction tools: NH69-83, SMT133-148, CPA39-54, CPA301-316, CPB42-57, and CPC37-52. After alignment and molecular docking analysis, the most promising sequences were SMT113-148 and CPA39-54.
Conclusion: This bioinformatic strategy allowed a sequential screening from 1 857 possible peptides to 2 promising candidates, raising the probability of these sequences being natural T CD4+ Leishmania spp. epitopes in humans, therefore good candidates to be evaluated in further studies.
Subcision with and without suction for acne scars: A split-faced, rater-blinded randomized control trial
Authors: Shi Victoria J. , Ma Melissa S. , Koza Eric , Haq Misha , Ahmed Areeba , Yi Michael D. , Dirr McKenzie A. , Anvery Noor , Christensen Rachel E. , Pagdhal Kapila , Geisler Amelia , Nodzenski Michael , Roongpisuthipong Wanjarus , Brieva Joaquin C. , Cahn Brian A. , Yoo Simon S. , Lucas Jennifer , Poon Emily , West Dennis P. , Fife Douglas , Alam Murad 
Published: February 2024

Abstract

Objectives: Therapeutic options for acne scars include subcision and suction with microdermabrasion, but these treatment modalities have not been studied in conjunction.
To compare effectiveness of subcision alone versus subcision with suction for the treatment of facial acne scars.
Methods: Randomized, split-faced, evaluator-blinded control trial. Participants underwent one subcision treatment on both sides of the face followed by 10 sessions of suction to one side. Photographs at baseline, 1-month, and 4-months were assessed. Primary outcome measures were the validated Acne Scar Severity Scale (ASSS) (0=no acne scarring, 4=severe), Acne Scar Improvement Grading Scale (ASIGS) (-100% to 100%), and modified Quantitative Global Scarring Grades (QGSG) (point-based questionnaire instrument), as well as subject preference.
Results: Twenty-eight treatment areas and 154 treatments were analyzed. Dermatologist raters found no differences between subcision alone and subcision-suction at 1-month or 4-months. Mean subject-assessed percent improvement for subcision-suction was higher than that for subcision alone at 1-month (37% versus 24%, p=0.04) but not at 4-months (p=0.37). Subjects preferred combination therapy to monotherapy at 1 month (50% vs 21%) and 4 months (43%, 21%).
Conclusions: While blinded raters did not detect significant differences, subjects perceived combination treatment as working more quickly than monotherapy, and preferred combination treatment at all time points.
Clinical trial registration: NCT01696513 on Clinicaltrials.gov