bluuebunny/crossref_metadata_2025_split huggingface dataset:
The color of Philosophicalism among a group of contemporary Shia commentators: A typical applied Study on the interpretation of “The Concepts of the Qur’an”
Authors: Muhammad Arif Ataee  
Published: August 2024

Undoubtedly, for the interpretation of the Qur’an, there are principles and rules that attention for them are mandatory for the interpreter of the Qur’an, among these principles is to follow the method of the Salaf and not mix the interpretation with anything else. This is what the Prophet (PBUH) mentioned: “Whoever interprets the Qur’an based on his own view and opinion, his place is Hell.” For this reason, scholars have prohibited the interpretation of the Qur’an based on the opinions of philosophers and the wonders of their philosophy, and the interpreter should not use philosophers as his guide in the interpretation of the Holy Qur’an. We see that some Shia commentators criticize the Sunnis and claim that the Sunnis have harmed themselves by not taking tafsir from its pure sources, “the Ahl al-Bayt of the Prophet” (as will be explained in this article) but they themselves are in a worse situation than what they criticize others for, and that is abandoning the interpretation of the Sahaba and Tabi‘in and following the views of the philosophers and this category applies exactly to them who say: They see straw in the eyes of others, but they do not see the branch of the tree in their own eyes. This discussion clarifies the extent of the influence of Philosophicalism on the contemporary interpretations of the Shiites through a brief sampling of an important interpretation of their interpretations, that is, the interpretation of “The Concepts of the Qur’an” by Jafar Subhani, who is considered one of the most prominent contemporary scholars and one of the critics of sunnite (as I mentioned in this article) in Iran. Also, this article informs us about the sources of contemporary Shiite interpretations, that is, those who are influenced by them in rationality and theology. From this discussion, it becomes clear to the respected reader, the method of interpretation by opinion in the eyes of contemporary Shia. The results of this discussion show that many contemporary Shiite scholars followed the path of philosophers such as Mulla Sadra, Ibn Sina, Nasir al-Din al-Tusi, Fakhr al-Din al-Razi and others. Not only have they filled their interpretations based on the opinions of these scholars and the opinions of the Mu’tazila sect before these scholars, but, they have considered the opinions of those scientists as an illuminating light for the light of their path In this article, a critical descriptive method is used, and the field of applying and taking examples, the interpretation of “The Concepts of the Qur’an” by Ayatollah Jafar Subhani, is determined.
Inventarisasi Gulma di Beberapa Lahan Perkebunan Rakyat, Jawa Timur
Authors: Tarigan Puji Lestari 
Published: August 2024

Plantation crops are plants that can be cultivated for many years to come. East Java has numerous plantation crops, including apples, guava, oranges, cocoa, moringa, and sugarcane. Wild plants are commonly found around crops in plantation areas. Plantation crops are at risk from biotic disturbances caused by these plants, which requires adequate management. Knowing the dominant weeds in the region allows for effective control. Weed dominance is measured using a species IVI (Importance Value Index). The purpose of this study is to investigate how weeds spread throughout each plantation area. The quadrat technique is used to manage inventories. Three samples are collected from each land and measured according to a formula. The dominant weeds in each plantation land are as follows: apple=Cyperus rotundus, guava=Parietaria judaica, orange=Mikania scandens, cocoa=Persicaria odorata, moringa=Muhlenbergia schreberi, and sugarcane=Dactylotenium aegyptium. Control is based on weed groups, namely broad-leaved (Parietaria judaica, Mikania scandenes, and Persicaria odorata), as well as narrow-leaved (Muhlenbergia schreberi), and nutsedge (Cyperus rotundus). Weeds in the land may threaten crops, thus it must be managed. Controls have to conform to its principles so that they may be carried out properly and efficiently.
Detection of Breast Lumps with Fine Needle Aspiration Cytology: Experience of 50 Cases in Bangladesh
Authors: Quddus Md Abdul , Jahan Nusrat , Syeed-Ul-Alam SM , Jahan Semonty , Moureen Adneen 
Published: August 2024

Background: Detection of breast lump is very crucial.
Objective: This study was carried out to evaluate the effectiveness of FNAC as a diagnostic method for breast lump.
Methodology: This cross sectional study was conducted among 50 women with breast lump at Popular Medical College Hospital, Dhaka, Dhaka Medical College Hospital and Ad-Din Barrister Rafique Ul Huq Hospital, Dhaka during the period of November 2021 to April 2022. This study was conducted using convenient type of non-probability sampling technique. Data were collected by face to face interview, clinical examination and findings of both cytological and histopathological examination.
Results: The study revealed the most benign breast lesion (89.45%) were below the age of 40 years and most of the breast cancer (91.2%) were above the age of 40 years. The study showed that 29 cases (58.0%) were diagnosed as benign clinically but cytologically 30(60.0%) cases were benign. Clinically 14(27.0%) cases were malignant but cytologically 13(26.0%) cases malignant. Clinical diagnosis of 8(7.5%) cases were uncertain, whereas cytologically 2(4.0%) cases were suspicious of malignancy and 1(2.0%) case was atypical. The comparison study between cyological and final histopathological diagnosis showed that out of 28 benign lesions diagnosed cytologically among which only 2 cases were found malignant histologically like false negative 2 (7.20%). 13 malignant cases were diagnosed cytologically which were confirmed histologically like no false positive was found. The study found that sensitivity of FNAC 85.3% of the presence of breast cancer and specificity 100.0% for absence of breast cancer. They also showed that the negative predictive value of FNAC for benign breast lump was 93.5% and positive predictive value for malignant breast lump was 100.0% and the overall diagnostic accuracy was 95.40%.
Conclusion: In conclusion, FNAC can be used as a diagnostic method in the management of breast lump which has reasonable sensitivity and specificity.
Journal of Current and Advance Medical Research, July 2023;10(2):65-69
Global transcriptomic network analysis of the crosstalk between microbiota and cancer-related cells in the oral-gut-lung axis
Authors: Otálora-Otálora Beatriz Andrea , Payán-Gómez César , López-Rivera Juan Javier , Pedroza-Aconcha Natalia Belén , Aristizábal-Guzmán Claudia , Isaza-Ruget Mario Arturo , Álvarez-Moreno Carlos Arturo 
Published: August 2024

BackgroundThe diagnosis and treatment of lung, colon, and gastric cancer through the histologic characteristics and genomic biomarkers have not had a strong impact on the mortality rates of the top three global causes of death by cancer.MethodsTwenty-five transcriptomic analyses (10 lung cancer, 10 gastric cancer, and 5 colon cancer datasets) followed our own bioinformatic pipeline based on the utilization of specialized libraries from the R language and DAVID´s gene enrichment analyses to identify a regulatory metafirm network of transcription factors and target genes common in every type of cancer, with experimental evidence that supports its relationship with the unlocking of cell phenotypic plasticity for the acquisition of the hallmarks of cancer during the tumoral process. The network’s regulatory functional and signaling pathways might depend on the constant crosstalk with the microbiome network established in the oral-gut-lung axis.ResultsThe global transcriptomic network analysis highlighted the impact of transcription factors (SOX4, TCF3, TEAD4, ETV4, and FOXM1) that might be related to stem cell programming and cancer progression through the regulation of the expression of genes, such as cancer-cell membrane receptors, that interact with several microorganisms, including human T-cell leukemia virus 1 (HTLV-1), the human papilloma virus (HPV), the Epstein–Barr virus (EBV), and SARS−CoV−2. These interactions can trigger the MAPK, non-canonical WNT, and IFN signaling pathways, which regulate key transcription factor overexpression during the establishment and progression of lung, colon, and gastric cancer, respectively, along with the formation of the microbiome network.ConclusionThe global transcriptomic network analysis highlights the important interaction between key transcription factors in lung, colon, and gastric cancer, which regulates the expression of cancer-cell membrane receptors for the interaction with the microbiome network during the tumorigenic process.
Hemodynamics in the treatment of pseudoaneurysm caused by extreme constriction of aortic arch with coated stent
Authors: Li Lanlan , Wang Yiwei , Jin Ping , Yang Tingting , Zhu Guangyu , Li Yuxi , Tang Jiayou , Liu Yang , Yang Jian 
Published: August 2024

ObjectivesTo evaluate the changes in distal vascular morphology and hemodynamics in patients with extremely severe aortic coarctation (CoA) after covered palliative (CP) stent dilation with different surgical strategies.Materials and methodsPerioperative computed tomography angiography and digital subtraction angiography were utilized to construct three aortic models with varying stenosis rates and one follow-up model in a patient with extremely severe CoA. The models included: an idealized non-stenosed model (A: 0%), a model post initial stent deployment (B: 28%), a model post balloon expansion (C: 39%), and a model 18 months after post-balloon expansion (D: 39%). Consistent boundary conditions were applied to all models, and hemodynamic simulation was conducted using the pure fluid method.ResultsThe narrowest and distal diameter of the stent increased by 34.71% and 59.29%, respectively, from model B to C. Additionally, the distal diameter of the stent increased by −13.80% and +43.68% compared to the descending aorta diameter, respectively. Furthermore, the ellipticity of the maximum cross-section of the aneurysm region in model A to D continued to increase. The oscillatory shear index at the stenosis to the region of the aneurysm were found to be higher in Models A and B, and lower in Models C and D. At the moment of maximum flow velocity, the blood flow distribution in models A and B was more uniform in the widest section of the blood vessels at the distal end of the stenosis, whereas models C and D exhibited disturbed blood flow with more than 2 eddy currents. The time-averaged wall shear stress (TAWSS) decreased in the distal and basal aneurysms, while it significantly increased at the step position. The aneurysmal region exhibited an endothelial cell activation potential value lower than 0.4 Pa−1.ConclusionIn patients with extremely severe CoA, it is crucial to ensure that the expanded diameter at both ends of the CP stent does not exceed the native vascular diameter during deployment. Our simulation results demonstrate that overdilation leads to a decrease in the TAWSS above the injured vessel, creating an abnormal hemodynamic environment that may contribute to the development and enlargement of false aneurysms in the early postoperative period.
Clinical Trial RegistrationClinicalTrials.gov, (NCT02917980).
Severe mitochondrial encephalomyopathy caused by de novo variants in OPA1 gene
Authors: Di Nottia Michela , Rizza Teresa , Baruffini Enrico , Nesti Claudia , Torraco Alessandra , Diodato Daria , Martinelli Diego , Dal Canto Flavio , Gilea Alexandru Ionut , Zoccola Martina , Siri Barbara , Dionisi-Vici Carlo , Bertini Enrico , Santorelli Filippo Maria , Goffrini Paola , Carrozzo Rosalba 
Published: August 2024

BackgroundMitochondria adjust their shape in response to the different energetic and metabolic requirements of the cell, through extremely dynamic fusion and fission events. Several highly conserved dynamin-like GTPases are involved in these processes and, among those, the OPA1 protein is a key player in the fusion of inner mitochondrial membranes. Hundreds of monoallelic or biallelic pathogenic gene variants have been described in OPA1, all associated with a plethora of clinical phenotypes without a straightforward genotype-phenotype correlation.MethodsHere we report two patients harboring novel de novo variants in OPA1. DNA of two patients was analyzed using NGS technology and the pathogenicity has been evaluated through biochemical and morphological studies in patient’s derived fibroblasts and in yeast model.ResultsThe two patients here reported manifest with neurological signs resembling Leigh syndrome, thus further expanding the clinical spectrum associated with variants in OPA1. In cultured skin fibroblasts we observed a reduced amount of mitochondrial DNA (mtDNA) and altered mitochondrial network characterized by more fragmented mitochondria. Modeling in yeast allowed to define the deleterious mechanism and the pathogenicity of the identified gene mutations.ConclusionWe have described two novel-single OPA1 mutations in two patients characterized by early-onset neurological signs, never documented, thus expanding the clinical spectrum of this complex syndrome. Moreover, both yeast model and patients derived fibroblasts showed mitochondrial defects, including decreased mtDNA maintenance, correlating with patients’ clinical phenotypes.
Development and characterization of dendritic cell internalization and activation assays contributing to the immunogenicity risk evaluation of biotherapeutics
Authors: Siegel Michel , Padamsey Aman , Bolender Anna-Lena , Hargreaves Patrick , Fraidling Johannes , Ducret Axel , Hartman Katharina , Looney Cary M. , Bertinetti-Lapatki Cristina , Rohr Olivier , Hickling Timothy P. , Kraft Thomas E. , Marban-Doran Céline 
Published: August 2024

IntroductionImmunogenicity refers to the ability of a substance, such as a therapeutic drug, to elicit an immune response. While beneficial in vaccine development, undesirable immunogenicity can compromise the safety and efficacy of therapeutic proteins by inducing anti-drug antibodies (ADAs). These ADAs can reduce drug bioavailability and alter pharmacokinetics, necessitating comprehensive immunogenicity risk assessments starting at early stages of drug development. Given the complexity of immunogenicity, an integrated approach is essential, as no single assay can universally recapitulate the immune response leading to the formation of anti-drug antibodies.MethodsTo better understand the Dendritic Cell (DC) contribution to immunogenicity, we developed two flow cytometry-based assays: the DC internalization assay and the DC activation assay. Monocyte-derived dendritic cells (moDCs) were generated from peripheral blood mononuclear cells (PBMCs) and differentiated over a five-day period. The internalization assay measured the accumulation rate of therapeutic antibodies within moDCs, while the activation assay assessed the expression of DC activation markers such as CD40, CD80, CD86, CD83, and DC-SIGN (CD209). To characterize these two assays further, we used a set of marketed therapeutic antibodies.ResultsThe study highlights that moDCs differentiated for 5 days from freshly isolated monocytes were more prone to respond to external stimuli. The internalization assay has been shown to be highly sensitive to the molecule tested, allowing the use of only 4 donors to detect small but significant differences. We also demonstrated that therapeutic antibodies were efficiently taken up by moDCs, with a strong correlation with their peptide presentation on MHC-II. On the other hand, by monitoring DC activation through a limited set of activation markers including CD40, CD83, and DC-SIGN, the DC activation assay has the potential to compare a series of compounds. These two assays provide a more comprehensive understanding of DC function in the context of immunogenicity, highlighting the importance of both internalization and activation processes in ADA development.DiscussionThe DC internalization and activation assays described here address key gaps in existing immunogenicity assessment methods by providing specific and reliable measures of DC function. The assays enhance our ability to pre-clinically evaluate the immunogenic potential of biotherapeutics, thereby improving their safety and efficacy. Future work should focus on further validating these assays and integrating them into a holistic immunogenicity risk assessment framework.
IL6 receptor inhibitors: exploring the therapeutic potential across multiple diseases through drug target Mendelian randomization
Authors: Fu Chong , Wang Longquan , Cai Wenjiao 
Published: August 2024

BackgroundHigh interleukin-6 levels correlate with diseases like cancer, autoimmune disorders, and infections. IL-6 receptor inhibitors (IL-6Ri), used for rheumatoid arthritis and COVID-19, may have wider uses. We apply drug-target Mendelian Randomization (MR) to study IL-6Ri’s effects.MethodTo simulate the effects of genetically blocking the IL-6R, we selected single nucleotide polymorphisms (SNPs) within or near the IL6R gene that show significant genome-wide associations with C-reactive protein. Using rheumatoid arthritis and COVID-19 as positive controls, our primary research outcomes included the risk of asthma, asthmatic pneumonia, cor pulmonale, non-small cell lung cancer, small cell lung cancer, Parkinson’s disease, Alzheimer’s disease, ulcerative colitis, Crohn’s disease, systemic lupus erythematosus, type 1 diabetes, and type 2 diabetes. The Inverse Variance Weighted (IVW) method served as our principal analytical approach, with the hypotheses of MR being evaluated through sensitivity and colocalization analyses. Additionally, we conducted Bayesian Mendelian Randomization analyses to minimize confounding and reverse causation biases to the greatest extent possible.ResultsIL-6 inhibitors significantly reduced the risk of idiopathic pulmonary fibrosis (OR= 0.278, 95% [CI], 0.138–0.558; P &lt;0.001), Parkinson’s disease (OR = 0.354, 95% CI, 0.215–0.582; P &lt;0.001), and positively influenced the causal relationship with Type 2 diabetes (OR = 0.759, 95% CI, 0.637–0.905; P = 0.002). However, these inhibitors increased the risk for asthma (OR = 1.327, 95% CI, 1.118–1.576; P = 0.001) and asthmatic pneumonia (OR = 1.823, 95% CI, 1.246–2.666; P = 0.002). The causal effect estimates obtained via the BWMR method are consistent with those based on the IVW approach. Similarly, sIL-6R also exerts a significant influence on these diseases.Diseases such as Alzheimer’s disease, Crohn’s disease, pulmonary heart disease, systemic lupus erythematosus, Type 1 diabetes, Non-small cell lung cancer and ulcerative colitis showed non-significant associations (p &gt; 0.05) and were excluded from further analysis. Similarly, Small cell lung cancer were excluded due to inconsistent results. Notably, the colocalization evidence for asthmatic pneumonia (coloc.abf-PPH4 = 0.811) robustly supports its association with CRP. The colocalization evidence for Parkinson’s disease (coloc.abf-PPH4 = 0.725) moderately supports its association with CRP.ConclusionIL-6Ri may represent a promising therapeutic avenue for idiopathic pulmonary fibrosis, Parkinson’s disease, and Type 2 diabetes.
Respiratory, cardio-metabolic and neurodevelopmental long-term outcomes of moderate to late preterm birth: not just a near term-population. A follow-up study
Authors: Alonso-Lopez Patricia , Arroyas Maria , Beato Maite , Ruiz-Gonzalez Sara , Olabarrieta Iciar , Garcia-Garcia Maria Luz 
Published: August 2024

IntroductionModerate-to-late preterm infants constitute the majority within the preterm infant population. Most research on preterm infants has focused on very preterm children, often treating moderate-to-late preterm infants as similar to full-term infants. Our objective was to compare clinical, respiratory, cardio-metabolic and neurodevelopmental outcomes in adolescents aged 12–15 years born moderate and late preterm with a control group of the same age born full-term.MethodsObservational cross-sectional study, comparing moderate-to-late preterm (32–36+6 weeks’ gestational age) with full-term adolescents (37–41+6 weeks’ gestational age; 75 each group). Perinatal and neonatal history were collected as well as data on respiratory evolution (ISAAC questionnaire for asthma symptoms for adolescents 13–14 years), anthropometric values, learning difficulties, behavioral test (screening questionnaire for high-performance autism spectrum disorder and evaluation test for attention deficit hyperactivity disorder), skin prick test, pulmonary function test, echocardiogram and blood pressure. A blood test with metabolic profile was conducted.ResultsModerate-to-late preterm adolescents had more current asthma [p = 0.008, OR3 (95% CI 1.26–7.14)] and longer duration of combined treatments to control asthma (inhaled corticosteroids and anti-leukotrienes; p = 0.048). Forced vital capacity &lt;80% was detected more often in moderate-to-late preterm patients (p = 0.013). When assessing right ventricle, moderate-to-late preterm adolescents showed better tricuspid annular plane systolic excursion z-score (p = 0.003), shortening fraction (p &lt; 0.001) and E/A ratio z-score (p = 0.002). Regarding left ventricular assessment, moderate-to-late preterm group had smaller ventricle diastolic diameter (p = 0.04) and lower posterior wall z-score values (p = 0.037). They also showed a better S’wave z-score (p = 0.027), E wave (p = 0.005), E/A ratio (p = 0.003) and a higher septal myocardial performance index z-score (p = 0.025). Moderate-to-late preterm adolescents presented lower weight z-score (p = 0.039), body mass index z-score (p = 0.013), Waterlow weight index (p = 0.006) and higher undernutrition index [p = 0.04; OR 1.4 (95% CI 1–1.9)]. Although there were no differences in neurodevelopmental survey or behavioral tests.ConclusionOur findings underscore the importance of extended follow-up for this predominant group of premature infants to identify potential respiratory, cardiac and anthropometric issues that may emerge in the future.