bluuebunny/crossref_metadata_2025_split huggingface dataset:
Injection of antioxidant trace minerals/vitamins into peripartum crossbred cows improves the nutritional and immunological properties of colostrum/milk and the health of their calves under heat stress conditions
Authors: Yadav Dhawal Kant , Somagond Yallappa M. , Lathwal Surender Singh , Kamboj Aarti , Alhussien Mohanned Naif , Dang Ajay Kumar 
Published: September 2023

Abstract
Multimineral and vitamin injections can provide better nutrient availability at the cellular level, which is essential for mitigating transition period stress and improving the well being and productivity of dairy cows. The present study was conducted to assess the colostrum quality and calf health after intramuscular injection of multi-minerals (MM) and multi-vitamins (MV) to peripartum cows during winter (THI = 60.29) and summer (THI = 81.05) months. In each season, twenty-four pregnant crossbred Karan Fries cows were grouped into four, each consisting of six cows. Group I, referred to as the Control, received solely the basal diet, without any additional supplements. Groups II, III, and IV were administered additional MM (T1), MV (T2), and a combined MM and MV (T3) along with their basal diet, starting 30 days before calving and continuing for 30 days after calving. Blood samples were collected from the calves, while colostrum/milk samples were obtained from the cows on days 1, 3, 7, and 15 after calving. The somatic cell counts (SCC) in the milk were determined using a cell counter. Cortisol, IgG, IGF1 and total immunoglobulins (IgG) in whey and plasma from cow colostrum/milk or calf blood samples were estimated by ELISA. Cows that calved in the summer exhibited notably reduced levels (P<0.05) of IgG, milk, and plasma IGF1, along with lower calf body weights, in comparison to those calving in the winter season. Furthermore, the summer months saw significant increases (P<0.05) in plasma and milk cortisol levels, as well as total somatic cell counts (SCC) in both colostrum and milk samples. Maximum beneficial effect was observed in T3 group. Results indicate that injections to peripartum cows could be an important strategy for improving colostrum quality and calf health during the summer seasons.
Fibroblast Matrix Implants - A Better Alternative for Incisional Hernia Repair?
Authors: Hendrawan Siufui , Lheman Jennifer , Weber Ursula , Oberkofler Christian Eugen , Eryani Astheria , Vonlanthen René , Baer Hans Ulrich 
Published: September 2023

Abstract

Background: The standard surgical procedure for abdominal hernia repair with conventional prosthetic mesh still results in a high recurrence rate. In the present study, we propose a Fibroblast Matrix Implant (FMI), which is a Poly-L-lactic acid (PLLA) scaffold coated with three-dimensional (3D) collagen (matrix) and seeded with fibroblasts, as an alternative to conventional prosthetic mesh for hernia repair.
Methods: The matrix was seeded with fibroblasts (cellularized) and treated with a Conditioned Medium (CM) of human Umbilical Cord Mesenchymal Stem Cells (hUC-MSC). Fibroblast proliferation and collagen secretion were assessed and compared between the treated group and the untreated group (without CM hUC-MSC) 24 hours after seeding onto the matrix (n=3). To study the matrices in vivo, male Sprague Dawley rats were used as hernia models. The hernia was surgically created and repaired with four different grafts (n=3), including a commercial mesh (mesh group), a matrix without cells (cell-free group), a matrix seeded with fibroblasts (FMI group), and a matrix seeded with fibroblasts and cultured in medium enriched with 1 % CM hUC-MSC (FMI-CM group).
Results: In vitro examination showed that the fibroblasts’ proliferation on the matrices (treated group) did not differ significantly compared to the untreated group. CM hUC-MSC was able to promote the collagen synthesis of the fibroblasts, resulting in a higher collagen concentration compared to the control group. Furthermore, the in vivo study showed that the matrices allowed fibroblast growth and supported cell functionality for at least 1 month after implantation. The highest number of fibroblasts was observed in the FMI group at the 14-day endpoint, but at the 28-day endpoint, the FMI-CM group had the highest. Collagen production and neovascularization were observed in all groups without any significant difference between the groups.
Conclusions: FMI combined with CM hUC-MSC may serve as a better option for hernia repair, providing adequate reinforcement and promoting greater scar formation, which in turn should reduce hernia recurrence.
A multistep in silico approach identifies potential glioblastoma drug candidates via inclusive molecular targeting of glioblastoma stem cells
Authors: Dogra Nilambra , Singh Parminder , Kumar Ashok 
Published: September 2023

Abstract
Aims

Glioblastoma (GBM) is the highest-grade of glioma for which no effective therapy is currently available. Despite extensive research in diagnosis and therapy there has been no significant improvement in GBM outcomes, with a median overall survival continuing at a dismal 15–18 months. In recent times, glioblastoma stem cells (GSCs) have been identified as crucial drivers of treatment resistance and tumor recurrence; and GBM therapies targeting GSCs are expected to improve patient outcomes. We used a multistep screening strategy to identify repurposed candidate drugs against therapeutic molecular targets in GBM with potential to concomitantly target GSCs.

Main methods

Common differentially expressed genes (DEGs) were identified through analysis of multiple GBM and GSC datasets from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). For identification of target genes, we further selected the genes with most significant effect on overall patient survival. The relative mRNA and protein expression of the selected genes in TCGA control versus GBM samples was also validated and their cancer dependency scores were assessed. Drugs targeting these genes and their corresponding proteins were identified from LINCS database using Connectivity Map (CMap) portal, and by in silico molecular docking against each individual target using FDA approved drugs library from DrugBank database, respectively. The molecules thus obtained were further evaluated for their ability to cross blood brain barrier (BBB) and their likelihood of resulting in drug resistance by acting as p-glycoprotein (p-Gp) substrates. The effect of these final shortlisted compounds on a panel of GBM cell lines was examined and compared with temozolomide through the drug sensitivity EC50 values and AUC from the PRISM Repurposing Secondary Screen, and IC50 values obtained from GDSC portal.

Key findings

We identified RPA3, PSMA2, PSMC2, BLVRA and HUS1 as molecular targets in GBM including GSCs with significant impact on patient survival. Our results show GSK-2126458, linifanib, drospirenone, eltrombopag, nilotinib and PD198306 as candidate drugs which can be further evaluated for their anti-tumor potential against GBM.

Significance

Through this work we identified repurposed candidate therapeutics against GBM utilizing a GSC inclusive targeting approach, which demonstrated high in vitro efficacy. These drugs have the potential to be developed as individual or combination therapy to improve GBM outcomes.
Discovery of specific activity of 2-HPA acting on the membrane progestin receptor alpha (paqr7) by purification of natural products from the marine algae Padina
Authors: Amin Mohammad Tohidul , Acharjee Mrityunjoy , Jyoti Md. Maisum , Rezanujjaman Md. , Hassan Md. Maksudul , Hossain Md. Forhad , Ahamed Saokat , Kodani Shinya , Tokumoto Toshinobu 
Published: September 2023

Abstract
Membrane progestin receptors (mPRs) are members of the progestin and adipoQ (PAQR) receptor family that are stimulated by endogenous steroids to initiate rapid intracellular signalling through a nongenomic pathway. Previously, water-soluble compounds with mPRα-binding activity from the marine algae Padina arborescens were fractionated by HPLC steps. In this study, the structure of one of the major compounds in the fraction was identified as 2-hydroxypentanoic acid (2-HPA) using Nuclear Magnetic Resonance spectroscopy. 2-HPA showed a substantial competitive binding affinity for hmPRα in the GQD-hmPRα binding assay. In contrast, synthetic structural analogues of 2-HPA showed no competitive binding activity. The physiological activity of 2-HPA and its analogues was then investigated using in vitro goldfish and in vivo zebrafish oocyte maturation and ovulation assays. As with the hmPRα binding assay, only 2-HPA showed inhibitory activity on oocyte maturation and ovulation of fish oocytes. Furthermore, the inhibitory activity of 2-HPA was compared between S- and R-type 2-HPA. The results showed that both types had the same level of activity. These results indicate that 2-HPA, found as a secreted compound from Padina arborescens, is a novel mPRα antagonist and its chemical structure is highly restricted to show its activity.
Comparative Analysis of Host Responses Between Sepsis and COVID-19: A Prospective Observational Study of Whole Blood Transcriptome
Authors: Muratsu Arisa , Onishi Shinya , Yoshimura Jumpei , Matsumoto Hisatake , Togami Yuki , Mitsuyama Yumi , Ito Hiroshi , Oda Sayaka , Okuzaki Daisuke , Ogura Hiroshi , Oda Jun 
Published: September 2023

Abstract
OBJECTIVES: This study aimed to comprehensively compare host responses to sepsis and COVID-19 by analyzing messenger RNA (mRNA) and microRNA (miRNA) profiles to shed light on their distinct pathophysiological mechanisms.
DESIGN: Prospective observational study
SETTING: Whole blood RNA sequencing was used to analyze mRNA and miRNA profiles of patients diagnosed as having sepsis or COVID-19 at the Department of Trauma and Emergency Medicine, Osaka University Graduate School of Medicine.
PATIENTS: Twenty-two sepsis patients, 35 COVID-19 patients, and 15 healthy subjects admitted to the department were included. We diagnosed sepsis patients according to the Sepsis-3 criterion that the Sequential Organ Failure Assessment score must increase to 2 points or more among patients with suspected infections. COVID-19 patients were diagnosed using SARS-CoV-2 RT-PCR testing, and presence of pneumonia was assessed through chest computed tomography scans.
INTERVENTIONS: None.
MEASUREMENTS AND MAIN RESULTS: For RNA sequencing, 14,500 mRNAs, 1121 miRNAs, and 2556 miRNA-targeted mRNAs were available for analysis in sepsis patients. Numbers of genes showing upregulated:downregulated gene expression (false discovery rate <0.05, |log2 fold change| >1.5) were 256:2887 for mRNA, 53:5 for miRNA, and 49:2507 for miRNA-targeted mRNA. Similarly, in COVID-19 patients, 14,500 mRNAs, 1121 miRNAs, and 327 miRNA-targeted mRNAs were analyzed, with numbers of genes exhibiting upregulated:downregulated gene expression of 672:1147 for mRNA, 3:4 for miRNA, and 165:162 for miRNA-targeted mRNA. This analysis revealed significant differences in the numbers of upregulated and downregulated genes expressed and pathways between the sepsis and COVID-19 patients. Sepsis patients showed activation of the PD-1 and PD-L1 cancer immunotherapy signaling pathway and concurrent suppression of Th1 signaling.
CONCLUSION: Our study illuminated distinct molecular variances between sepsis and COVID-19. Sepsis patients had a greater number of upregulated and downregulated genes and pathways compared to COVID-19 patients, indicating a dynamic change in gene expression and pathway activation in sepsis.
A mathematical Theory of Elasticity for Photoelastic Experimental Hybrid Method
Authors: Mose Bruno R. , Shin Dong-Kil , Nam Jeong Hwan , Alunda B. O. 
Published: September 2023

Abstract
In this paper, the mathematical theory of elasticity that enables the construction of representative stress functions for photoelastic experimental hybrid method (PEHM) is revisited and reviewed. PEHM has been shown as an important and powerful tool used by experimental stress analysts to predict the stress state in complex engineering structures. To demonstrate the utility of stress functions from the mathematical theory of elasticity in real engineering applications the contact problem of a mechanical seal with a rectangular cross-section as well as a plate with a central hole are considered. It was found that when the stress functions are applied to the contact problem of a mechanical seal with rectangular cross section, the contact stresses on the upper side were larger compared to those on the front side. On the front side, the highest stresses were concentrated in the region around the extrusion gap. When a comparison between theoretical and experimental stress concentration factors was done, it was found that there was remarkable agreement between theoretical and experimental results. Therefore, the mathematical theory of elasticity from this study shows that it can provide stress functions that serve as an invaluable input tool to predict the SCF using the photoelastic experimental hybrid method
Fluorocarbon-driven pore size reduction in polyurethane foams: an effect of improved bubble entrainment
Authors: Hamann Martin , Cotte-Carluer Guillaume , Andrieux Sébastien , Telkemeyer Daniel , Ranft Meik , Schütte Markus , Drenckhan Wiebke 
Published: September 2023

Abstract
Polyurethane (PU) foams are created via the chemical reactions arising after the blending of two initially liquid components (polyols and isocyanates). They are widely used for thermal insulation, for which a small pore size is required. Some of the most efficient pore size-reducing agents have proven to be per- and polyfluorinated carbons (FCs) which are simply added in small quantities to the initially liquid mixture. However, despite their long-standing use, their modes of action have only recently begun to be studied in detail. One widely accepted explanation of their action is that they supposedly suppress diffusional gas exchange between bubbles in the liquid-foam-state of the nascent PU foam (foam coarsening). However, using a new double-syringe mixing technique, we show that FCs act at a much earlier state of the process: they facilitate the entrainment of tiny air bubbles into PU foam systems during the initial blending processing. These bubbles serve as sites for heterogeneous nucleation during the foaming process, and their large number leads to a significant reduction of the characteristic pore size. More importantly, we also demonstrate that the same overall relation is found between the air bubble density and the final pore size for systems with- and without FC. Combined with a detailed analysis of the pore size distribution, we argue that the main pore size reducing effect of FCs is to facilitate air entrainment and that foam aging-related effects only play a minor role.
iLEC-DNA: Identifying Long Extra-chromosomal Circular DNA by Fusing Sequence-derived Features of Physicochemical Properties and Nucleotide Distribution Patterns
Authors: Abbasi Ahtisham Fazeel , Asim Muhammad Nabeel , Dengel Andreas , Ahmed Sheraz 
Published: September 2023

Abstract
Long extrachromosomal circular DNA (leccDNA) regulates several biological processes such as genomic instability, gene amplification, and oncogenesis. The identification of leccDNA holds significant importance to investigate its potential associations with cancer, autoimmune, cardiovascular, and neurological diseases. In addition, understanding these associations can provide valuable insights about disease mechanisms and potential therapeutic approaches. Conventionally , wet lab-based methods are utilized to identify leccDNA, which are hindered by the need for prior knowledge, and resource-intensive processes, potentially limiting their broader applicability. To empower the process of leccDNA identification across multiple species, the paper in hand presents the very first computational predictor. The proposed iLEC-DNA predictor makes use of SVM classifier along with sequence-derived nucleotide distribution patterns and physico-chemical properties-based features. In addition, the study introduces a set of 12 benchmark leccDNA datasets related to three species, namely Homo sapiens (HM), Arabidopsis Thaliana (AT), and Saccharomyces cerevisiae (SC/YS). It performs large-scale experimentation across 12 benchmark datasets under different experimental settings using the proposed predictor and more than 140 baseline predictors. The proposed predictor outperforms baseline predictors across diverse leccDNA datasets by producing average performance values of 80.699%, 61.45% and 80.7% in terms of ACC, MCC and AUC-ROC across all the datasets. The source code of the proposed and baseline predictors is available at https://github.com/FAhtisham/Extrachrosmosomal-DNA-Prediction. To facilitate the scientific community, a web application for leccDNA identification is available at https://sds_genetic_analysis.opendfki.de/iLEC_DNA//.
Immune Correlates of Hyperglycemia and Vaccination in a Non-human Primate Model of Long-COVID
Authors: Palmer Clovis , Perdios Chrysostomos , Abdel-Mohsen Mohamed , Mudd Joseph , Datta Prasun , Maness Nicholas , Lehmicke Gabrielle , Golden Nadia , Hellmers Linh , Coyne Carol , Green Kristyn Moore , Midkiff Cecily , Williams Kelsey , Tiburcio Rafael , Fahlberg Marissa , Boykin Kyndal , Kenway Carys , Russell-Lodrigue Kasi , Bohm Rudolf , Blair Robert , Dufour Jason , Fischer Tracy , Saied Ahmad , Rappaport Jay 
Published: September 2023

Abstract

Hyperglycemia, and exacerbation of pre-existing deficits in glucose metabolism, are major manifestations of the post-acute sequelae of SARS-CoV-2 (PASC). Our understanding of lasting glucometabolic disruptions after acute COVID-19 remains unclear due to the lack of animal models for metabolic PASC. Here, we report a non-human primate model of metabolic PASC using SARS-CoV-2 infected African green monkeys (AGMs). Using this model, we have identified a dysregulated chemokine signature and hypersensitive T cell population during acute COVID-19 that correlates with elevated and persistent hyperglycemia four months post-infection. This persistent hyperglycemia correlates with elevated hepatic glycogen, but there was no evidence of long-term SARS-CoV-2 replication in the liver and pancreas. Finally, we report a favorable glycemic effect of the SARS-CoV-2 mRNA vaccine, administered on day 4 post-infection. Together, these data suggest that the AGM metabolic PASC model exhibits important similarities to human metabolic PASC and can be utilized to assess therapeutic candidates to combat this syndrome.
Exploratory machine-learning based proteomic analysis to improve the diagnostic accuracy in patients with occlusion myocardial infarction
Authors: Knoery Charles , McGilligan Victoria , Iftikhar Aleeha , Rjoob Khaled , Bond Raymond , Peace Aaron , McShane Anne , Leslie Stephen J 
Published: September 2023

Abstract
Background: Prompt recognition and treatment of occlusion myocardial infarction (OMI) is essential, yet current pathways miss a proportion of patients who have OMI as not all have electrocardiogram changes. This exploratory study aimed to determine if proteomic analysis combined with clinical factors could improve diagnostic accuracy in OMI patients.
Methods: In this case-controlled exploratory study 368 proteins were analysed from patients having a myocardial infarction and controls with stable angina. Angiographic and clinical features were recorded. Proteins were analysed using a proximity extension assay. Machine-learning techniques of hybrid and forward feature selection algorithms followed by comparing decision tree and logistical regression analysis were used to indicate the optimal classifier of proteins and clinical factors to increase diagnostic sensitivity in OMI.
Results: Plasma samples were obtained from 130 patients, 41 (31.5%) had a non-OMI and 16 (12.3%) had OMI. The other 73 (56.2%) had stable angina with no evidence of myocardial infarction. A combination of 19 clinical features and 87 biomarkers for OMI gave a detection of AUC=0.90 which was higher than identification of OMI by clinical features alone (AUC=0.84) although similar to biomarkers alone (AUC=0.91). The decision tree classifier that included combination of biomarkers and clinical factors reached statistical significance for detection for OMI (p<0.001) compared to the logistical regression tree classifier.
Conclusion: In this study we created a classifier for the diagnosis of OMI through a combination of clinical factors and proteins following proteomic analysis. Further refinement with larger cohorts and focused prior feature selection are required for validation.
Conversion in Land Use Change Soil Physiochemical Properties in the Highland of Western Ethiopia
Authors: Regasa Abu 
Published: September 2023

Abstract

Information on the effects of various land-use types on selected soil physicochemical properties is critical for the sustainable use of soil resources. As a result, this study was carried out to assess the effects of land use types on Soil Physiochemical Properties in the Sayo District of Western Highland of Ethiopia. The main aim of this study is to evaluate the effects of different land use types and soil depth on soil's physical and chemical properties. A total of 45 composite soil samples were collected from forest, grass, eucalyptus tree plantations, cultivating, and grazing lands using three soil depths (0-15cm, 15–30 and 30–45 cm) and three replications. Analysis of variance was used to test the mean differences in soil physicochemical properties. Sand and clay mean values were highest in grazing and forest, respectively. The mean bulk density of the soils ranged between 1.10 and 1.61gcm− 3, and the mean total porosity ranged between 39.37 and 58.49%, indicating lower soil compaction. The mean field capacity ranged from 34.21 to 42.93% whereas the permanent wilting point ranged from 19.79 to 27.87% and the mean water holding capacity ranged between 14.07 and 16.21%. The mean pH ranged from 4.92 to 5.55, with mean OM values ranging from 0.64 to 5.91% while the mean values of total N ranged from 0.04 to 0.31%. The mean value of available P ranged from 2.10 to 7.26mg kg− 1. Conversion of land use types harms soil properties, particularly overgrazing, eucalyptus plantation and cultivation of deforested land. Therefore, the deteriorated physiochemical properties of the soils should be amended with the application of different sources of nutrients and sustainable management practices.