Miracle-dz/UniFAR-FTUs huggingface dataset:
Dosage of Dual-Protein Nutrition Differentially Impacts the Formation of Atherosclerosis in ApoE−/− Mice

Atherosclerosis (AS) is recognized as the original cause of most cardiovascular and cerebrovascular diseases. The dual-protein (DP) nutrition that consists of soy protein and whey protein is reported to be associated with a reduction in AS; however, the relationship between DP and AS remains ambiguous. Therefore, this study aimed to verify the effect of DP on AS and explore the optimal DP intake to improve AS. ApoE−/− mice were administrated with low- (LDP), middle- (MDP), and high-dose (HDP) DP. The MDP group exhibited significant improvements in AS. In terms of lipid metabolism, the levels of plasma total triglyceride and LDL-C and the mRNA expression levels of Cyp7a1 and PCSK9 were markedly tuned in the MDP group. In addition, the MDP treatment group had a substantially lower inflammatory response and better intestinal barrier function than LDP and HDP groups. The species richness demonstrated by the Chao1 index was distinctly increased in the MDP group, and the relative abundance of intestinal-permeability-protective microbes Blautia and Akkermansia was significantly elevated. In summary, an adequate intake of DP was able to counteract atherosclerosis development in ApoE−/− mice, and this study provides a scientific theoretical basis for the application of DP in the food and pharmaceutical fields.
Cereulide and Deoxynivalenol Increase LC3 Protein Levels in HepG2 Liver Cells

Abstract Food contaminants of bacterial or fungal origin frequently contaminate staple foods to various extents. Among others, the bacterial toxin cereulide (CER) and the mycotoxin deoxynivalenol (DON) co-occur in a mixed diet and are absorbed by the human body. Both toxins exert dis-tinctive mitotoxic potential. As damaged mitochondria are removed via autophagy, mitochondrial and lysosomal toxicity were assessed by applying low doses of single and combined toxins (CER 0.1–50 ng/mL; DON 0.01–5 µg/mL) to HepG2 liver cells. In addition to cytotoxicity assays, RT-qPCR was performed to investigate genes involved in lysosomal biogenesis and autophagy. CER and DON caused significant cytotoxicity on HepG2 cells after 5 and 24 h over a broad concentration range. CER, alone and in combination with DON, increased the transcription of the autophagy related genes coding for the microtubule associated protein 1A/1B light chain 3 (LC3) and sequestome 1 (SQSTM1) as well as LC3 protein expression which was determined using immunocytochemistry. DON increased LC3 protein expression without induction of gene transcription, hence it seems plausible that CER and DON act on different pathways. The results support the hypothesis that CER induces autophagy via the LC3 pathway and damaged mitochondria are therefore eliminated.
Defining Diffuse Large B-Cell Lymphoma Immunotypes by CD8+ T Cells and Natural Killer Cells

Background There is a poor prognosis for diffuse large B-cell lymphoma (DLBCL), one of the most common types of non-Hodgkin lymphoma (NHL). Through gene expression profiles, this study intends to reveal potential subtypes among patients with DLBCL by evaluating their prognostic impact on immune cells. Methods Immune subtypes were developed based on CD8+ T cells and natural killer cells calculated from gene expression profiles. The comparison of prognoses and enriched pathways was made between immune subtypes. Following this validation step, samples from the independent data set were analyzed to determine the correlation between immune subtype and prognosis and immune checkpoint blockade (ICB) response. To provide a model to predict the DLBCL immune subtypes, machine learning methods were used. The virtual screening and molecular docking were adopted to identify small molecules to target the immune subtype biomarkers. Results A training data set containing 432 DLBCL samples from five data sets and a testing dataset containing 420 DLBCL samples from GSE10846 were used to develop and validate immune subtypes. There were two novel immune subtypes identified in this study: an inflamed subtype (IS) and a noninflamed subtype (NIS). When compared with NIS, IS was associated with higher levels of immune cells and a better prognosis for immunotherapy. Based on the random forest algorithm, a robust machine learning model has been established by 12 hub genes, and the area under the curve (AUC) value is 0.948. Three small molecules were selected to target NIS biomarkers, including VGF, RAD54L, and FKBP8. Conclusion This study assessed immune cells as prognostic factors in DLBCL, constructed an immune subtype that could be used to identify patients who would benefit from ICB, and constructed a model to predict the immune subtype.
Healthy Aging and Dietary Patterns

A number of factors contribute to the complex process of aging, which finally define whether someone will or not develop age-associated chronic diseases in late life. These determinants comprise genetic susceptibility as well as various behavioral, environmental, and dietary factors, all of which have been shown to influence specific pathways regulating the aging process and the extension of life, which makes longevity a multidimensional phenomenon. Although a “miraculous elixir” or a “nutrition pill” are not plausible, researchers agree on the notion that nutritional factors have major impact on the risk of age-associated chronic non-communicable diseases and mortality. In recent years nutrition research in relation to health outcomes has considerably changed from focusing exclusively on single nutrients to considering combinations of foods rather than nutrients in isolation. Although research on specific nutrients is scientifically valid providing crucial evidence on the mechanisms by which nutrition impacts health, the recent switch targeting the multifaceted synergistic interplay among nutrients, other dietary constituents, and whole foods, has promoted emerging interest on the actions of total dietary patterns. This narrative review aims to describe some specific dietary patterns with evidence of associations with reduction in the incidence of chronic diseases allowing older adults to live a long-lasting and healthier life, and confirming the powerful impact nutrition can exert on healthy aging.
The Effectiveness of Stone Column Spacing in Reducing the Potential of Liquefaction

ABSTRACTLiquefaction is a liquefied soil phenomenon caused by cyclic load or earthquake. One of the soil liquefaction prevention methods is the installation of stone column. The stone column is a column filled with compacted rock fragments. It has 50 cm in diameter and 5 m deep This method is believed to reduce the excess pore water pressure that occurs during an earthquake. The stone column has been applied in many construction projects which located in high potential of liquefaction area. This research aims to know the effectiveness of stone column in reducing the liquefaction potential. This research conducted by using borelog data and soil laboratory test. This research also runs the numerical simulation of soil liquefaction with stone column stabilization. The variations in column spacing (2 m; 1.5 m; and 1 m) and subsurface review point (1 m; 1.5 m; 2 m; and 2.5 m) will be applied by using Quake/W from Geostudio 2012 software. The results show that the liquefaction potential can be reduced with the closer stone column spacing up to 1.5 m. Reduction of pore water pressure and liquefaction potential only occurs in the initial period of the earthquake before reaching the peak of earthquake acceleration.ABSTRAKLikuefaksi merupakan fenomena pencairan tanah akibat adanya beban siklik atau gempa. Salah satu metode penanganan likuefaksi yaitu dengan melakukan instalasi stone column. Stone column merupakan suatu kolom yang diisi oleh fragmen batuan yang dipadatkan. Umumya kolom berukuran diameter 50 cm dan kedalaman hingga 5 m. Metode ini dipercaya dapat mengurangi tekanan air pori yang terjadi pada tanah saat gempa. Penelitian ini bertujuan untuk mengetahui efektifitas stone collumn dalam mengurangi potensi likuefaksi. Penelitian ini dilakukan dengan menggunakan data bor dan uji laboratorium. Simulasi numeris juga dilakukan berupa permodelan tanah dengan stabilisasi stone column. Variasi pada jarak stone solumn (2m; 1,5m; dan 1m) dan titik tinjau (1m; 1,5m; 2m; dan 2,5m) dilakukan dengan menggunakan perangkat lunak Quake/w dari Geostudio 2012. Hasil menunjukkan bahwa potensi likuefaksi dapat berkurang dengan jarak stone column yang semakin dekat hingga 1,5 m. Pengurangan tekanan air pori dan potensi likuefaksi hanya terjadi pada periode awal gempa sebelum mencapai puncak percepatan gempa.
MOT: a Multi-Omics Transformer for multiclass classification tumour types predictions

Motivation Breakthroughs in high-throughput technologies and machine learning methods have enabled the shift towards multi-omics modelling as the preferred means to understand the mechanisms underlying biological processes. Machine learning enables and improves complex disease prognosis in clinical settings. However, most multi-omic studies primarily use transcriptomics and epigenomics due to their over-representation in databases and their early technical maturity compared to others omics. For complex phenotypes and mechanisms, not leveraging all the omics despite their varying degree of availability can lead to a failure to understand the underlying biological mechanisms and leads to less robust classifications and predictions. Results We proposed MOT (Multi-Omic Transformer), a deep learning based model using the transformer architecture, that discriminates complex phenotypes (herein cancer types) based on five omics data types: transcriptomics (mRNA and miRNA), epigenomics (DNA methylation), copy number variations (CNVs), and proteomics. This model achieves an F1-score of 98.37% among 33 tumour types on a test set without missing omics views and an F1-score of 96.74% on a test set with missing omics views. It also identifies the required omic type for the best prediction for each phenotype and therefore could guide clinical decisionmaking when acquiring data to confirm a diagnostic. The newly introduced model can integrate and analyze five or more omics data types even with missing omics views and can also identify the essential omics data for the tumour multiclass classification tasks. It confirms the importance of each omic view. Combined, omics views allow a better differentiation rate between most cancer diseases. Our study emphasized the importance of multi-omic data to obtain a better multiclass cancer classification. Availability and implementation MOT source code is available at https://github.com/dizam92/multiomic_predictions.
PBDEs Found in House Dust Impact Human Lung Epithelial Cell Homeostasis

The toxicity of eight polybrominated diphenyl ethers (PBDEs) congeners detected in environmental and biological samples (BDE-28, -47, -99, -100, -153, -154, -183, and -209) was evaluated on the epithelial lung cells. Exposure to these PBDEs increased membrane disruption and a release of lactate dehydrogenase, accompanied by oxidative stress in cells through the formation of reactive oxygen species (ROS) and a decrease in mitochondrial membrane potential. Interestingly, some of the tested PBDEs increased apoptotic markers as well. For several congeners, the observed toxicity was time dependent, meaning that even smaller concentrations of these compounds will have negative effects over time. Such time-dependent toxicity was also confirmed for cell treatment with a real house dust sample extract. This could be indicative with regard to the constant exposure to a mixture of PBDE congeners through different pathways in the organism and thereby presenting a risk for human health. As such, our findings point to the importance of further studies on the negative effects of PBDEs to understand their mechanism of action in detail.
Cryopreservation in a Standard Freezer: −28 °C as Alternative Storage Temperature for Amniotic Membrane Transplantation

Human amniotic membrane (hAM) is usually stored at −80 °C. However, in many regions, cryopreservation at −80 °C is not feasible, making hAM unavailable. Therefore, the possibility of cryopreservation at −28 °C (household freezer) was investigated. hAMs (n = 8) were stored at −80 °C or −28 °C for a mean time of 8.2 months. hAM thickness, epithelial integrity and basement membrane were assessed histologically. The collagen content, concentration of hepatocyte growth factor (HGF) and basic fibroblast growth factor (bFGF) were determined. Elastic modulus and tensile strength were measured. The mean thickness of hAM stored at −28 °C was 33.1 ± 21.6 µm (range 9.7–74.9); thickness at −80 °C was 30.8 ± 14.7 µm (range 13.1–50.7; p = 0.72). Mean collagen content, epithelial cell number and integrity score showed no significant difference between samples stored at −28 °C or −80 °C. Basement membrane proteins were well preserved in both groups. Mean tensile strength and elastic modulus were not significantly different. Concentration of bFGF at −28 °C was 1063.2 ± 680.3 pg/g (range 369.2–2534.2), and 1312.1 ± 778.2 pg/g (range 496.2–2442.7) at −80 °C (p = 0.11). HGF was 5322.0 ± 2729.3 pg/g (range 603.3–9149.8) at −28 °C, and 11338.5 ± 6121.8 pg/g (range 4143.5 to 19806.7) at −80 °C (p = 0.02). No microbiological contamination was detected in any sample. The cryopreservation of hAM at −28 °C has no overt disadvantages compared to −80 °C; the essential characteristics of hAM are preserved. This temperature could be used in an alternative storage method whenever storage at −80 °C is unavailable.
Hemodynamics and Wall Shear Stress of Blood Vessels in Aortic Coarctation with Computational Fluid Dynamics Simulation

The purpose of this study was to identify the characteristics of blood flow in aortic coarctation based on stenotic shape structure, stenosis rate, and the distribution of the wall load delivered into the blood vessels and to predict the impact on aneurysm formation and rupture of blood vessels by using a computational fluid dynamics modeling method. It was applied on the blood flow in abdominal aortic blood vessels in which stenosis occurred by using the commercial finite element software ADINA on fluid-solid interactions. The results of modeling, with an increasing stenosis rate and Reynolds number, showed the pressure drop was increased and the velocity was greatly changed. When the stenosis rate was the same, the pressure drop and the velocity change were larger in the stenosis with a symmetric structure than in the stenosis with an asymmetric one. Maximal changes in wall shear stress were observed in the area before stenosis and minimal changes were shown in stenosis areas. The minimal shear stress occurred at different locations depending on the stenosis shape models. With an increasing stenosis rate and Reynolds number, the maximal wall shear stress was increased and the minimal wall shear stress was decreased. Through such studies, it is thought that the characteristics of blood flow in the abdominal aorta where a stenosis is formed will be helpful in understanding the mechanism of growth of atherosclerosis and the occurrence and rupture of the abdominal aortic flow.
Brushing Effect on the Properties of Glass Ionomer Cement Modified by Hydroxyapatite Nanoparticles or by Bioactive Glasses

This study evaluated the physical and mechanical properties of glass ionomer cement (GIC) associated with 5% hydroxyapatite nanoparticles (NPHAps) and 10% bioactive glass (BAG) 45S5 before and after brushing at different storage times. Surface roughness was evaluated using a rugosimeter, Vickers hardness using a microdurometer, and mass variation measured in an analytical balance at 1, 7, 15, 30, and 60 days before and after the brushing test, with the aid of toothbrushing simulator and soft bristle toothbrushes. Nonnormal distribution was observed, and the nonparametric Wilcoxon and Kruskal–Wallis tests followed by Dunn's were performed, with a significance level of 5%. We observed higher values for mass loss on the first day for all groups. The surface roughness was lower in the control and NP groups, 30 days after brushing. Higher values for hardness were found in the control group and lower ones for NP, after brushing. The control and BAG groups presented a decrease in hardness over time. The NP group presented the highest values before brushing, while the control group had the highest values after brushing. The association of NPHPa with the GIC is the most promising combination, since it presented satisfactory values for surface hardness. However, conventional GIC not associated with NPHPa or BAG is still an option, since it is available in the market and the most economically viable option.
Effect of Myostatin Gene Mutation on Slaughtering Performance and Meat Quality in Marchigiana Bulls

Simple Summary The aim of this work was the evaluation of slaughtering performance in a sample of 78 Marchigiana bulls with different allelic situation at the myostatin locus; in addition, the qualitative composition of meat samples collected from Longissimus thoracis muscle was evaluated. At the myostatin gene, 67 homozygotes normal, 11 heterozygotes, and no double-muscled homozygote bulls were detected. Heterozygote bulls showed high values in final live weight and dressing yield; moreover, they were characterized by a low incidence of fat at steak dissection, as well as in meat chemical composition. A better muscular conformation in heterozygote bulls’ carcasses was highlighted, with a higher incidence of their carcasses in class E and evident convexity of round, back, and shoulder muscular masses compared to the carcasses of Marchigiana bulls which were normal at the myostatin gene. Abstract The myostatin gene also called Growth Differentiation Factor 8 gene (GDF8) is one of the most investigated loci that can be responsible for several quantitative and qualitative carcass and meat traits in double-muscled beef cattle. The objective of the study was to bring to light the effect of the myostatin polymorphism on slaughtering performance and meat quality in Marchigiana beef cattle. The experiment was carried out on 78 bulls reared according to the “cow-calf” extensive managing system. At the end of the fattening period, in vivo and carcass data were recorded. From each carcass, a steak of Longissimus thoracis was taken and used to determine the meat’s analytical composition and colorimetric properties. Finally, from each steak a sample of Longissimus thoracis was collected, then used for DNA extraction and genotyping at the myostatin locus. The heterozygous bulls showed slight superiority in the carcass data (e.g., hot carcass weight: 426.09 kg—heterozygotes vs. 405.32 kg—normal) and meat quality parameters, although not always with statistical significance. Only fat and ashes content were significantly affected by the myostatin genotype (heterozygotes: 2.01%, 1.26%; normal: 3.04%, 1.15%). The greater muscularity of heterozygous animals compared to normal ones could be a starting point to improving productive efficiency in Marchigiana beef cattle.
Evaluation of Bi-Lateral Co-Infections and Antibiotic Resistance Rates among COVID-19 Patients

In addition to the pathogenesis of SARS-CoV-2, bacterial co-infection plays an essential role in the incidence and progression of SARS-CoV-2 infections by increasing the severity of infection, as well as increasing disease symptoms, death rate and antimicrobial resistance (AMR). The current study was conducted in a tertiary-care hospital in Lahore, Pakistan, among hospitalized COVID-19 patients to see the prevalence of bacterial co-infections and the AMR rates among different isolated bacteria. Clinical samples for the laboratory diagnosis were collected from 1165 hospitalized COVID-19 patients, of which 423 were found to be positive for various bacterial infections. Most of the isolated bacteria were Gram-negative rods (n = 366), followed by Gram-positive cocci (n = 57). A significant association (p < 0.05) was noted between the hospitalized COVID-19 patients and bacterial co-infections. Staphylococcus aureus (S. aureus) showed high resistance against tetracycline (61.7%), Streptococcus pyogenes against penicillin (100%), E. coli against Amp-clavulanic acid (88.72%), Klebsiella pneumoniae against ampicillin (100%), and Pseudomonas aeruginosa against ciprofloxacin (75.40%). Acinetobacter baumannii was 100% resistant to the majority of tested antibiotics. The prevalence of methicillin-resistant S. aureus (MRSA) was 14.7%. The topmost symptoms of >50% of COVID-19 patients were fever, fatigue, dyspnea and chest pain with a significant association (p < 0.05) in bacterial co-infected patients. The current study results showed a comparatively high prevalence of AMR, which may become a severe health-related issue in the future. Therefore, strict compliance of antibiotic usage and employment of antibiotic stewardship programs at every public or private institutional level are recommended.
AGT May Serve as a Prognostic Biomarker and Correlated with Immune Infiltration in Gastric Cancer

Purpose Angiotensinogen (AGT), as a component of the renin–angiotensin system (RAS), is associated with multiple risk factors for gastric cancer (GC). However, the relationship between AGT and tumor-infiltrating lymphocytes in GC remains elusive. Methods AGT expression was analyzed based on the Cancer Genome Atlas (TCGA) dataset. Kaplan–Meier curve was employed to assess the role of AGT expression in gastric patients’ prognosis. The association between AGT expression and tumor immune infiltration was further evaluated via exploring Tumour Immune Estimation Resource (TIMER) and The Gene Expression Profiling Interactive Analysis (GEPIA). We also used multiple public databases to analyse the aberrant methylation of AGT, construct protein–protein interaction (PPI) and gene ontology (GO) analyses. Results AGT was overexpressed in GC tissues compared with normal gastric tissues (P<0.05). High AGT expression related with poorer overall survival of patients with GC, especially in advanced GC patients. Immune infiltration analysis revealed that AGT was associated with several immune cells (including B cells, CD4+ T cells, macrophages), and AGT expression was also associated with the markers of NK cells, TAMs, Tregs, and so on (all P<0.05). Methylation analysis indicated that hypomethylation may lead to abnormal upregulation of the AGT. GO analysis showed that AGT and its related genes were enriched in systemic arterial blood pressure by hormone, regulation of blood volume by renin-angiotensin, NIK/NF-kappaB signaling, ficolin-1-rich granule and so on. Conclusion AGT could act as a promising biomarker for prognosis and immune infiltration in GC.
The Perimeter of the Home in Old Age: Reflecting on the Sense of Home in a Sheltered Housing Facility During the COVID-19 Pandemic

Abstract This article focuses on the concept of home in old age in the context of a sheltered housing facility. Drawing on regulation theory, we examine how the SARS-CoV-2 pandemic shapes the sense of home in this type of housing. The search for control over one’s daily routine during the lockdown serves as an indicator of the dynamics of expansion and contraction in the perimeter of the home. The way in which sheltered housing tenants comply with stay-at-home recommendations during the lockdown reveals certain aspects of their sense of home. The unusual character of the regulatory measures introduced during confinement increases the importance of perceptions of the meaning of the home among older adults with regard to their self-image and relationship to the surrounding environment.