Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Immune Function-Related Subtypes in Cutaneous Melanoma

Tumour immunotherapy combined with molecular typing is a new therapy to help select patients. However, molecular typing algorithms related to tumour immune function have not been thoroughly explored. We herein proposed a single sample immune signature network (SING) method to identify new immune function-related subtypes of cutaneous melanoma of the skin. A sample-specific network and tumour microenvironment were constructed based on the immune annotation of cutaneous melanoma samples. Then, the differences and heterogeneity of immune function among different subtypes were analysed and verified. A total of 327 cases of cutaneous melanoma were divided into normal and immune classes; the immune class had more immune enrichment characteristics. After further subdividing the 327 cases into three immune-related subtypes, the degree of immune enrichment in the “high immune subtype” was greater than that in other subtypes. Similar results were validated in both tumour samples and cell lines. Sample-specific networks and the tumour microenvironment based on immune annotation contribute to the mining of cutaneous melanoma immune function-related subtypes. Mutations in B2M and PTEN are considered potential therapeutic targets that can improve the immune response. Patients with a high immune subtype can generally obtain a better immune prognosis effect, and the prognosis may be improved when combined with TGF-β inhibitors.
Red Blood Cell Proteasome in Beta-Thalassemia Trait: Topology of Activity and Networking in Blood Bank Conditions

Proteasomes are multi-catalytic complexes with important roles in protein control. Their activity in stored red blood cells (RBCs) is affected by both storage time and the donor’s characteristics. However, apart from their abundancy in the membrane proteome, not much is known about their topology, activity, and networking during the storage of RBCs from beta-thalassemia trait donors (βThal+). For this purpose, RBC units from fourteen βThal+ donors were fractionated and studied for proteasome activity distribution and interactome through fluorometric and correlation analyses against units of sex- and aged-matched controls. In all the samples examined, we observed a time-dependent translocation and/or activation of the proteasome in the membrane and a tight connection of activity with the oxidative burden of cells. Proteasomes were more active in the βThal+ membranes and supernatants, while the early storage networking of 20S core particles and activities showed a higher degree of connectivity with chaperones, calpains, and peroxiredoxins, which were nonetheless present in all interactomes. Moreover, the βThal+ interactomes were specially enriched in kinases, metabolic enzymes, and proteins differentially expressed in βThal+ membrane, including arginase-1, piezo-1, and phospholipid scramblase. Overall, it seems that βThal+ erythrocytes maintain a considerable “proteo-vigilance” during storage, which is closely connected to their distinct antioxidant dynamics and membrane protein profile.
Copy Number Changes and Allele Distribution Patterns of Chromosome 21 in B Cell Precursor Acute Lymphoblastic Leukemia

Simple Summary Array analysis is an efficient method for defining in a single experiment all genome-wide large and fine-scale copy number abnormalities, as well as their corresponding allele patterns. Based on the results of the analysis that we performed in 578 children with acute lymphoblastic leukemia, we provide a comprehensive overview of the genetic subgroup-specific incidence and distribution of all the various types of chromosome 21 copy number alterations in this cohort, most of which are of eminent diagnostic and clinical relevance. By doing so, we also uncovered some unusual and difficult to explain discrepancies between copy number and allele distribution patterns that we investigated and eventually succeeded to resolve with polymorphic short tandem repeat analyses. Abstract Chromosome 21 is the most affected chromosome in childhood acute lymphoblastic leukemia. Many of its numerical and structural abnormalities define diagnostically and clinically important subgroups. To obtain an overview about their types and their approximate genetic subgroup-specific incidence and distribution, we performed cytogenetic, FISH and array analyses in a total of 578 ALL patients (including 26 with a constitutional trisomy 21). The latter is the preferred method to assess genome-wide large and fine-scale copy number abnormalities (CNA) together with their corresponding allele distribution patterns. We identified a total of 258 cases (49%) with chromosome 21-associated CNA, a number that is perhaps lower-than-expected because ETV6-RUNX1-positive cases (11%) were significantly underrepresented in this array-analyzed cohort. Our most interesting observations relate to hyperdiploid leukemias with tetra- and pentasomies of chromosome 21 that develop in constitutionally trisomic patients. Utilizing comparative short tandem repeat analyses, we were able to prove that switches in the array-derived allele patterns are in fact meiotic recombination sites, which only become evident in patients with inborn trisomies that result from a meiosis 1 error. The detailed analysis of such cases may eventually provide important clues about the respective maldistribution mechanisms and the operative relevance of chromosome 21-specific regions in hyperdiploid leukemias.
Gold–Protein Composite Nanoparticles for Enhanced X-ray Interactions: A Potential Formulation for Triggered Release

Drug-delivery vehicles have been used extensively to modulate the biodistribution of drugs for the purpose of maximizing their therapeutic effects while minimizing systemic toxicity. The release characteristics of the vehicle must be balanced with its encapsulation properties to achieve optimal delivery of the drug. An alternative approach is to design a delivery vehicle that preferentially releases its contents under specific endogenous (e.g., tissue pH) or exogenous (e.g., applied temperature) stimuli. In the present manuscript, we report on a novel delivery system with potential for triggered release using external beam radiation. Our group evaluated Zein protein as the basis for the delivery vehicle and used radiation as the exogenous stimulus. Proteins are known to react with free radicals, produced during irradiation in aqueous suspensions, leading to aggregation, fragmentation, amino acid modification, and proteolytic susceptibility. Additionally, we incorporated gold particles into the Zein protein matrix to create hybrid Zein–gold nanoparticles (ZAuNPs). Zein-only nanoparticles (ZNPs) and ZAuNPs were subsequently exposed to kVp radiation (single dose ranging from 2 to 80 Gy; fractionated doses of 2 Gy delivered 10 times) and characterized before and after irradiation. Our data indicated that the presence of gold particles within Zein particles was correlated with significantly higher levels of alterations to the protein, and was associated with higher rates of release of the encapsulated drug compound, Irinotecan. The aggregate results demonstrated a proof-of-principle that radiation can be used with gold nanoparticles to modulate the release rates of protein-based drug-delivery vehicles, such as ZNPs.
Metallothioneins and Megalin Expression Profiling in Premalignant and Malignant Oral Squamous Epithelial Lesions

Simple Summary Interactions of metallothioneins with the multiligand receptor megalin have been found to promote cell survival and proliferation after noxious stimuli in non-malignant tissues. However, the relationship between these proteins and their interaction remains to be addressed in malignancies and premalignant lesions. In this retrospective study, we compared the expression profiles of metallothioneins and megalin in different histological grades of oral squamous cell carcinoma, oral leukoplakia, and oral lichen planus. The data obtained show a gradual increase of both proteins concomitantly with the gaining of more malignant features, as well as their co-expression and direct interaction in carcinomatous tissue. The results point to the pro-oncogenic role of the metallothionein-megalin functional axis, which may impact tumor phenotype and behavior. Abstract This study aimed to assess the relationship and possible interactions between metallothioneins (MTs) and megalin (LRP-2) in different grades of oral squamous cell carcinoma (OSCC) and premalignant lesions of the oral mucosa (oral leukoplakia and oral lichen planus). The study included archived samples of 114 patients and control subjects. Protein expression was examined by immunohistochemistry and immunofluorescence, and staining quantification was performed by ImageJ software. Protein interaction in cancer tissue was tested and visualized by proximity ligation assay. Mann-Whitney and Kruskal-Wallis tests were used to determine the significance of differences between each group, whereas Pearson correlation coefficient was performed to test correlation. Expression of both proteins differed significantly between each group showing the same pattern of gradual increasing from oral lichen planus to poorly differentiated OSCC. Moreover, MTs and megalin were found to co-express and interact in cancer tissue, and their expression positively correlated within the overall study group. Findings of prominent nuclear and chromosomal megalin expression suggest that it undergoes regulated intramembrane proteolysis upon MTs binding, indicating its ability to directly affect gene expression and cellular division in cancer tissue. The data obtained point to the onco-driving potential of MTs-megalin interaction.
The Role of Extracellular HSP70 in the Function of Tumor-Associated Immune Cells

Simple Summary The intracellular heat shock protein 70 (HSP70) is essential for cells to respond to stress, for instance, by refolding damaged proteins or inhibiting apoptosis. However, in cancer, HSP70 is overexpressed and can translocate to the extracellular milieu, where it emerged as an important modulator of tumor-associated immune cells. By targeting the tumor microenvironment (TME) through different mechanisms, extracellular HSP70 can trigger pro- or anti-tumorigenic responses. Therefore, understanding the pathways and their consequences is crucial for therapeutically targeting cancer and its surrounding microenvironment. In this review, we summarize current knowledge on the translocation of extracellular HSP70. We further elucidate its functions within the TME and provide an overview of potential therapeutic options. Abstract Extracellular vesicles released by tumor cells (T-EVs) are known to contain danger-associated molecular patterns (DAMPs), which are released in response to cellular stress to alert the immune system to the dangerous cell. Part of this defense mechanism is the heat shock protein 70 (HSP70), and HSP70-positive T-EVs are known to trigger anti-tumor immune responses. Moreover, extracellular HSP70 acts as an immunogen that contributes to the cross-presentation of major histocompatibility complex (MHC) class I molecules. However, the release of DAMPs, including HSP70, may also induce chronic inflammation or suppress immune cell activity, promoting tumor growth. Here, we summarize the current knowledge on soluble, membrane-bound, and EV-associated HSP70 regarding their functions in regulating tumor-associated immune cells in the tumor microenvironment. The molecular mechanisms involved in the translocation of HSP70 to the plasma membrane of tumor cells and its release via exosomes or soluble proteins are summarized. Furthermore, perspectives for immunotherapies aimed to target HSP70 and its receptors for cancer treatment are discussed and presented.
A Journey on the Skin Microbiome: Pitfalls and Opportunities

The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the “core” and “transient” types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.
Examining the Clinical Prognosis of Critically Ill Patients with COVID-19 Admitted to Intensive Care Units: A Nationwide Saudi Study

Backgroundand Objectives: COVID-19 is a novel infectious disease caused by a single-stranded RNA coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to conduct a nationwide multicenter study to determine the characteristics and the clinical prognostic outcome of critically ill COVID-19 patients admitted to intensive care units (ICUs). Materials and Methods: This is a nationwide cohort retrospective study conducted in twenty Saudi hospitals. Results: An analysis of 1470 critically ill COVID-19 patients demonstrated that the majority of patients were male with a mean age of 55.9 ± 15.1 years. Most of our patients presented with a shortness of breath (SOB) (81.3%), followed by a fever (73.7%) and a cough (65.1%). Diabetes and hypertension were the most common comorbidities in the study (52.4% and 46.0%, respectively). Multiple complications were observed substantially more among non-survivors. The length and frequency of mechanical ventilation use were significantly greater (83%) in the non-survivors compared with the survivors (31%). The mean Sequential Organ Failure Assessment (SOFA) score was 6 ± 5. The overall mortality rate of the cohort associated with patients that had diabetes, hypertension and ischemic heart disease was 41.8%. Conclusion: Age; a pre-existing medical history of hypertension, diabetes and ischemic heart disease; smoking cigarettes; a BMI ≥ 29; a long mechanical ventilation and ICU stay; the need of ventilatory support; a high SOFA score; fungal co-infections and extracorporeal membrane oxygenation (ECMO) use were key clinical characteristics that predicted a high mortality in our population.
Clinical Significance of Pleural Effusion in Mycoplasma pneumoniae Pneumonia in Children

The clinical significance of pleural effusion in Mycoplasma pneumoniae (MP) pneumonia in children has not yet been elucidated. Herein, we investigated the clinical implications of pleural effusion in children with MP pneumonia. Overall, 150 children with MP pneumonia transferred to a tertiary hospital were enrolled in this study. Information on their clinical, laboratory, and radiological features was retrospectively obtained from medical chart reviews. In total, 24 (16.0%) children had pleural effusion at the time of admission. The duration of fever and length of hospitalization were significantly longer in the pleural effusion group than in the non-pleural effusion group. A significantly higher proportion of individuals in the pleural effusion group had a poor response to stepwise treatment for MP pneumonia. The mean C-reactive protein, lactate dehydrogenase, and aspartate aminotransferase levels were significantly higher in the pleural effusion group than in the non-pleural effusion group at admission. The prevalence of severe pneumonia, defined on the basis of the extent of pneumonic lesions on chest radiography, was higher in the pleural effusion group than in the non-pleural effusion group. However, there was no significant intergroup difference in the proportion of macrolide-resistant MP cases or respiratory viral coinfections. The presence of pleural effusion in children with MP pneumonia indicated a more severe clinical course and poor treatment response. The results of the present study would help in the creation of a therapeutic plan and prediction of the clinical course of MP pneumonia in children.
Inferring Excitatory and Inhibitory Connections in Neuronal Networks

The comprehension of neuronal network functioning, from most basic mechanisms of signal transmission to complex patterns of memory and decision making, is at the basis of the modern research in experimental and computational neurophysiology. While mechanistic knowledge of neurons and synapses structure increased, the study of functional and effective networks is more complex, involving emergent phenomena, nonlinear responses, collective waves, correlation and causal interactions. Refined data analysis may help in inferring functional/effective interactions and connectivity from neuronal activity. The Transfer Entropy (TE) technique is, among other things, well suited to predict structural interactions between neurons, and to infer both effective and structural connectivity in small- and large-scale networks. To efficiently disentangle the excitatory and inhibitory neural activities, in the article we present a revised version of TE, split in two contributions and characterized by a suited delay time. The method is tested on in silico small neuronal networks, built to simulate the calcium activity as measured via calcium imaging in two-dimensional neuronal cultures. The inhibitory connections are well characterized, still preserving a high accuracy for excitatory connections prediction. The method could be applied to study effective and structural interactions in systems of excitable cells, both in physiological and in pathological conditions.
Use of 3D Printing for the Development of Biodegradable Antiplatelet Materials for Cardiovascular Applications

Small-diameter synthetic vascular grafts are required for surgical bypass grafting when there is a lack of suitable autologous vessels due to different reasons, such as previous operations. Thrombosis is the main cause of failure of small-diameter synthetic vascular grafts when used for this revascularization technique. Therefore, the development of biodegradable vascular grafts capable of providing a localized and sustained antithrombotic drug release mark a major step forward in the fight against cardiovascular diseases, which are the leading cause of death globally. The present paper describes the use of an extrusion-based 3D printing technology for the production of biodegradable antiplatelet tubular grafts for cardiovascular applications. For this purpose, acetylsalicylic acid (ASA) was chosen as a model molecule due to its antiplatelet activity. Poly(caprolactone) and ASA were combined for the fabrication and characterization of ASA-loaded tubular grafts. Moreover, rifampicin (RIF) was added to the formulation containing the higher ASA loading, as a model molecule that can be used to prevent vascular prosthesis infections. The produced tubular grafts were fully characterized through multiple techniques and the last step was to evaluate their drug release, antiplatelet and antimicrobial activity and cytocompatibility. The results suggested that these materials were capable of providing a sustained ASA release for periods of up to 2 weeks. Tubular grafts containing 10% (w/w) of ASA showed lower platelet adhesion onto the surface than the blank and grafts containing 5% (w/w) of ASA. Moreover, tubular grafts scaffolds containing 1% (w/w) of RIF were capable of inhibiting the growth of Staphylococcus aureus. Finally, the evaluation of the cytocompatibility of the scaffold samples revealed that the incorporation of ASA or RIF into the composition did not compromise cell viability and proliferation at short incubation periods (24 h).
Mechanisms of Exercise Capacity Improvement after Cardiac Rehabilitation Following Myocardial Infarction Assessed with Combined Stress Echocardiography and Cardiopulmonary Exercise Testing

Cardiac rehabilitation (CR) is indicated in all patients after acute myocardial infarction (AMI) to improve prognosis and exercise capacity (EC). Previous studies reported that up to a third of patients did not improve their EC after CR (non-responders). Our aim was to assess the cardiac and peripheral mechanisms of EC improvement after CR using combined exercise echocardiography and cardiopulmonary exercise testing (CPET-SE). The responders included patients with an improved EC assessed as a rise in peak oxygen uptake (VO2) ≥ 1 mL/kg/min. Peripheral oxygen extraction was calculated as arteriovenous oxygen difference (A-VO2Diff). Out of 41 patients (67% male, mean age 57.5 ± 10 years) after AMI with left ventricular ejection fraction (LVEF) ≥ 40%, 73% improved their EC. In responders, peak VO2 improved by 27% from 17.9 ± 5.2 mL/kg/min to 22.7 ± 5.1 mL/kg/min, p < 0.001, while non-responders had a non-significant 5% decrease in peak VO2. In the responder group, the peak exercise heart rate, early diastolic myocardial velocity at peak exercise, LVEF at rest and at peak exercise, and A-VO2Diff at peak exercise increased, the minute ventilation to carbon dioxide production slope decreased, but the stroke volume and cardiac index were unchanged after CR. Non-responders had no changes in assessed parameters. EC improvement after CR of patients with preserved LVEF after AMI is associated with an increased heart rate response and better peripheral oxygen extraction during exercise.
Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions

High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria and host interactions. However, data interpretation using this technique is mainly based on relative abundance and ignores total bacteria load. In certain cases, absolute abundance is more important than compositional relative data, and interpretation of microbiota data based solely on relative abundance can be misleading. The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features. In this review, we first illustrate the importance of integrating absolute abundance into microbiome data interpretation. Second, we briefly discuss the most widely used cell-based and molecular-based bacterial load quantification methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, 16S qRT-PCR, ddPCR, and reference spike-in. Last, we present a specific decision-making scheme for absolute quantification methods based on different biological questions and some of the latest quantitative methods and procedure modifications.