Integrating Omics Data and AI for Cancer Diagnosis and Prognosis.

Cancer is one of the leading causes of death, making timely diagnosis and prognosis very important. Utilization of AI (artificial intelligence) enables providers to organize and process patient data in a way that can lead to better overall outcomes. This review paper aims to look at the varying uses of AI for diagnosis and prognosis and clinical utility. PubMed and EBSCO databases were utilized for finding publications from 1 January 2020 to 22 December 2023. Articles were collected using key search terms such as "artificial intelligence" and "machine learning." Included in the collection were studies of the application of AI in determining cancer diagnosis and prognosis using multi-omics data, radiomics, pathomics, and clinical and laboratory data. The resulting 89 studies were categorized into eight sections based on the type of data utilized and then further subdivided into two subsections focusing on cancer diagnosis and prognosis, respectively. Eight studies integrated more than one form of omics, namely genomics, transcriptomics, epigenomics, and proteomics. Incorporating AI into cancer diagnosis and prognosis alongside omics and clinical data represents a significant advancement. Given the considerable potential of AI in this domain, ongoing prospective studies are essential to enhance algorithm interpretability and to ensure safe clinical integration.

Polydopamine contained hydrogel nanocomposites with combined antimicrobial and antioxidant properties for accelerated wound healing.

Overproduction of reactive oxygen species (ROS) in infected wounds induces a tremendous inflammatory reaction to delay wound healing. To address this problem, we designed a multifunctional polyacrylamide/PVA-based hydrogel containing synthesized poly(1-glycidyl-3-butylimidazolium salicylate) (polyGBImSal) and fabricated polydopamine-coated polyphenolic nanosheet (PDA@PNS) for wound dressing. The PDA@PNS particles were designed to induce I) antioxidant and anti-inflammatory features through ROS-scavenging and II) cell adhesive properties by the existing polydopamine into the hydrogels. The poly(ionic liquid)-based polyGBImSal was designed to allocate effective hydrogel antimicrobial activity. The fabricated hydrogel nanocomposites showed excellent properties in the swelling ratio, cell adhesiveness, protein adsorption, and anti-inflammatory, proving their general performance for application in wound healing. Furthermore, these hydrogels showed high antimicrobial activity (over 95 %) against three common wound-infecting pathogenic microbes: Escherichia coli, Staphylococcus aureus, and Candida albicans. The healing process of full-thickness dermal wounds in rats was accelerated by applying hydrogel nanocomposites with 0.5 wt% of PDA@PNS and 28 wt% of polyGBImSal. The wound closure contraction attained full closure, reaching 100 %, after 14 days, contrasted with the control group employing commercial wound dressing (Tegaderm), which achieved a closure rate of 68 % within the equivalent timeframe. These results make these hydrogel nanocomposites promising candidates for multifunctional wound dressing applications.

The relationship between cumulative dose of immunosuppressive agents and COVID-19-associated mucormycosis: A multicenter cross-sectional study.

Background and Aims: Immunosuppressive therapy has a key role in developing coronavirus disease-2019 (COVID-19)-associated mucormycosis. In this study, we investigated the effect of the type and cumulative dose of immunosuppressive agents on COVID-19-associated mucormycosis. Methods: We designed a descriptive cross-sectional study involving three COVID-19 hospitals in Iran. Clinical and demographic data were gathered from the medical records and checked by two independent researchers to minimize errors in data collection. Results: Seventy-three patients were included in the study. The mean age of cases was 57.41 (SD = 12.64) and 43.8% were female. Among patients, 20.5% were admitted to the intensive care unit (ICU) during COVID-19. Furthermore, 17 patients (23.29%) had a history of diabetes mellitus. Sixty-nine patients (94.52%) had a history of receiving corticosteroids (dexamethasone) during treatment of COVID-19, and of those, five patients (6.85%) received Tocilizumab beside. The mean cumulative dose of corticosteroids prescribed was 185.22 mg (SD = 114.738). The average cumulative dosage of tocilizumab was 720 mg (SD = 178.89). All of the included patients received amphotericin B for mucormycosis treatment, and 42 survived (57.53%). Also, there was a significant relationship between hospitalization in ICU for COVID-19 and the mucormycosis outcome (p = 0.007). However, there weren't any significant associations between cumulative doses of immunosuppressive drugs and mucormycosis outcome (p = 0.52). Conclusion: The prevalence of COVID-19-associated mucormycosis is increasing and should be considered in the treatment protocols of COVID-19. Controlling risk factors such as diabetes, malignancy and the administration of immunosuppressive agents based on recommended dosage in validated guidelines are ways to prevent mucormycosis.

Risk Factors of COVID-19 Associated Mucormycosis (CAM) in Iranian Patients: A Single-Center Retrospective Study.

BACKGROUND: COVID-19 associated mucormycosis (CAM) has been known as one of the most severe post-COVID morbidities. OBJECTIVES: To describe CAM cases, identify possible risk factors, and report outcomes of patients. METHODS: This retrospective study was performed in Amir-Alam Hospital, Tehran, Iran between February 2020 and September 2021. Patients with mucormycosis who had an active or previous diagnosis of COVID-19 have been included. RESULTS: Of 94 patients with mucormycosis, 52 (33 men and 19 women; mean age: 57.0 ± 11.82 years) were identified with an active or history of COVID-19. Rhino-orbital, rhino maxillary, rhino-orbito cerebral subtypes of mucormycosis were detected in 6 (11.5%), 18(34.6%), and 28(53.8%) patients. As a control group, 130 (69 men and 61 women; mean age: 53.10 ± 14.49 years) random RT-PCR-confirmed COVID-19 patients without mucormycosis have been included. The mean interval between COVID-19 diagnosis and initial mucormycosis symptoms was 16.63 ± 8.4 days (range 0-51). Those in the CAM group had a significantly more severe course of COVID-19 (OR = 3.60, P-value < 0.01). Known history of previous diabetes mellitus (OR = 7.37, P-value < 0.01), smoking (OR = 4.55, P-value < 0.01), and history of receiving high-dose corticosteroid pulse therapy because of more severe COVID-19 (P-value = 0.022) were found as risk factors. New-onset post-COVID hyperglycemia was lower in the CAM group (46.2% vs. 63.8%; OR = 0.485, P-value = 0.028). After treatment of the CAM group, 41(78.8%) of patients recovered from mucormycosis. The mean ages of the expired patients in the CAM group were significantly higher than those who recovered from mucormycosis (66.18 ± 9.56 vs. 54.56 ± 11.22 years; P < 0.01); and COVID-19 disease was more severe (P = 0.046). CONCLUSION: Either active or history of COVID-19 can cause an increase in the risk of mucormycosis development. Some of the most important risk factors are the medical history of diabetes mellitus, smoking, and high-dose corticosteroid therapy. CAM is important possible comorbidity related to COVID-19, which could make the post-COVID conditions more complicated. More research and studies with greater sample sizes among different ethnicities are needed to explore the association between COVID-19 and mucormycosis.

Coronavirus: proteomics analysis of chicken kidney tissue infected with variant 2 (IS-1494)-like avian infectious bronchitis virus.

Avian infectious bronchitis virus is one of the most important gammacoronaviruses, which causes a highly contagious disease. In this study, we investigated changes in the proteome of kidney tissue of specific-pathogen-free (SPF) chickens that were infected with an isolate of the nephrotropic variant 2 genotype (IS/1494/06) of avian coronavirus. Twenty 1-day-old SPF White Leghorn chickens were randomly divided into two groups, each comprising 10 chickens, which were kept in separate positive-pressure isolators. Chickens in group A served as a virus-free control group up to the end of the experiment, whereas chickens in group B were inoculated with 0.1 ml of 104.5 EID50 of the IBV/chicken/Iran/UTIVO-C/2014 isolate of IBV, and kidney tissue samples were collected at 2 and 7 days post-inoculation (dpi) from both groups. Sequencing of five protein spots at 2 dpi and 22 spots at 7 dpi that showed differential expression by two-dimensional electrophoresis (2DE) along with fold change greater than 2 was done by MS-MALDI/TOF/TOF. Furthermore, the corresponding protein-protein interaction (PPI) networks at 2 and 7 dpi were identified to develop a detailed understanding of the mechanism of molecular pathogenesis. Topological graph analysis of this undirected PPI network revealed the effect of 10 genes in the 2 dpi PPI network and nine genes in the 7 dpi PPI network during virus pathogenesis. Proteins that were found by 2DE analysis and MS/TOF-TOF mass spectrometry to be down- or upregulated were subjected to PPI network analysis to identify interactions with other cellular components. The results show that cellular metabolism was altered due to viral infection. Additionally, multifunctional heat shock proteins with a significant role in host cell survival may be employed circuitously by the virus to reach its target. The data from this study suggest that the process of pathogenesis that occurs during avian coronavirus infection involves the regulation of vital cellular processes and the gradual disruption of critical cellular functions.

The Neuromodulatory Effects of ω-3 Fatty Acids and Nano-Curcumin on the COX-2/ iNOS Network in Migraines: A Clinical Trial Study from Gene Expression to Clinical Symptoms.

BACKGROUND: Migraine is a common neuroinflammatory disorder characterized by recurrent attacks of pain. Human and experimental models of migraine studies have demonstrated the role played by COX-2/ iNOS in migraine's neuroinflammatory pathogenesis. COX-2 and iNOS are closely linked and both contribute to inflammation and neurogenic pain in the central nervous system. Omega- 3 fatty acids and curcumin, an active polyphenol of turmeric, have anti-inflammatory and neuroprotective effects through several mechanisms, including the suppression of COX-2 and iNOS gene expression, as well as their serum levels. The aim of the present study is to evaluate the nutrigenomic effects of ω-3 fatty acids, nano-curcumin, and a combination of the two, on neuroinflammation and clinical symptoms in migraine patients. METHODS: This study reports the results of a clinical trial over a 2-month period, involving 74 episodic migraine patients who received ω-3 fatty acids, nano-curcumin, a combination of them, or a placebo. At the start and end of the study, the expression of COX-2/iNOS (in peripheral mononuclear blood cells isolated from patients) and COX-2/iNOS serum levels were measured, using real-time PCR and ELISA respectively. The frequency, severity and duration of pain attacks were also recorded. RESULTS: The results of the present trial showed that ω-3 fatty acids and nano-curcumin can reinforce each other's effects in the downregulation of COX-2/iNOS mRNA, as well as reduce their serum levels. In addition, the combination of ω-3 and nano-curcumin significantly reduced the frequency, severity and duration of headaches (P<0.05). CONCLUSION: These findings indicate that combination therapy of ω-3 fatty acids and nano-curcumin can be considered as a promising new approach in migraine prevention.

Protein interaction mapping interpretation of none alcoholic fatty liver disease model of rats after fat diet feeding.

AIM: This study investigates the effect of fat diet on gene expression profile in rat liver via protein-protein interaction mapping analysis. BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a prevalent condition of liver in the world. This progressive metabolic disease is representative with fat accumulation in the patients' liver that can led to advance stages, namely, cirrhosis and eventually cancer. METHODS: Differentially expressed genes of NAFLD rat liver after 2, 4 and 6 weeks fat diet feeding were analyzed via GEO2R and protein-protein interaction network by Cytoscape v3.6.0. and the related plug-ins. The important genes were assigned based on degree and betweenness centrality analysis and enriched using ClueGO+CluePedia Plug-in. RESULTS: GAPDH, PRDM10, TP53, AKT1, INS, ALB, SRC, MAPK1, ACLY, ACACA, DECR1, ACACB, MBOAT4, TNF, EHHADH and JUN genes were introduced as key genes related to the fat diet fed NAFLD rats. Fatty acid biosynthesis and four other terms were introduced as the main related ones to the essential genes. CONCLUSION: The introduced critical genes and the related terms may describe NAFLD molecular condition and its progression to the other severe metabolic diseases. Moreover, these potential biomarkers may be monitored for diagnosis and treatment approaches after validation investigations.