Machine learning algorithms and biomarkers identification for pancreatic cancer diagnosis using multi-omics data integration.

PURPOSE: Pancreatic cancer is a lethal type of cancer with most of the cases being diagnosed in an advanced stage and poor prognosis. Developing new diagnostic and prognostic markers for pancreatic cancer can significantly improve early detection and patient outcomes. These biomarkers can potentially revolutionize medical practice by enabling personalized, more effective, targeted treatments, ultimately improving patient outcomes. METHODS: The search strategy was developed following PRISMA guidelines. A comprehensive search was performed across four electronic databases: PubMed, Scopus, EMBASE, and Web of Science, covering all English publications up to September 2022. The Newcastle-Ottawa Scale (NOS) was utilized to assess bias, categorizing studies as "good," "fair," or "poor" quality based on their NOS scores. Descriptive statistics for all included studies were compiled and reviewed, along with the NOS scores for each study to indicate their quality assessment. RESULTS: Our results showed that SVM and RF are the most widely used algorithms in machine learning and data analysis, particularly for biomarker identification. SVM, a supervised learning algorithm, is employed for both classification and regression by mapping data points in high-dimensional space to identify the optimal separating hyperplane between classes. CONCLUSIONS: The application of machine-learning algorithms in the search for novel biomarkers in pancreatic cancer represents a significant advancement in the field. By harnessing the power of artificial intelligence, researchers are poised to make strides towards earlier detection and more effective treatment, ultimately improving patient outcomes in this challenging disease.

Diagnostic, prognostic, and predictive biomarkers in gastric cancer: from conventional to novel biomarkers.

Gastric cancer is a major health concern worldwide. The survival rate of Gastric cancer greatly depends on the stage at which it is diagnosed. Early diagnosis is critical for improving survival outcomes. To improve the chances of early diagnosis, regular screening tests, such as an upper endoscopy or barium swallow, are recommended for individuals at a higher risk due to factors like family history or a previous diagnosis of gastric conditions. Biomarkers can be detected and measured using non-invasive methods such as blood tests, urine tests, breath analysis, or imaging techniques. These non-invasive approaches offer many advantages, including convenience, safety, and cost-effectiveness, making them valuable tools for disease diagnosis, monitoring, and research. Biomarker-based tests have emerged as a useful tool for identifying gastric cancer early, monitoring treatment response, assessing the recurrence risk, and personalizing treatment plans. In this current review, we have explored both classical and novel biomarkers for gastric cancer. We have centralized their potential clinical application and discussed the challenges in Gastric cancer research.

Heterologous Expression of Human IFNγ and Anti-IL17 Antibody in Leishmania tarentolae Promastigote.

BACKGROUND: Leishmania is an intracellular flagellate protozoan parasite that causes a wide range of clinical diseases in humans. The basis of immunological resistance against leishmaniasis depends on Thl reactions and is within the time period of cytokine function. METHODS: In this study, human anti-IL17 antibody and IFNγ-producing promastigote were produced to be used in leishmanization. A sequence of light and heavy chains' gene of anti-IL17 antibody and human IFNγ (hIFNγ) was obtained from the NCBI database and synthesized in the ECORV reaction site in the plasmid pGH, which it's called pGH-hIFNγ-antiIL17. The synthesized part using the restriction enzyme ECORV was extracted from the plasmid and after purification by electroporation was transferred to Iranian lizard Leishmania (I.L.L). Evaluation of structural presence in the I.L.L genome at the level of DNA and mRNA was assessed. The expressions of hIFNγ and anti-IL17 were evaluated and confirmed using ELISA and western blot analysis. The hIFNγ secreted from the culture medium was collected at high concentrations of 124.36 ± 6.47 pg/mL. RESULTS: Targeted gene replacement into the I.L.L genome was successfully performed for the first time using the pGH-hIFNγ-antiIL17 plasmid in an identical replacement process. Stabilized recombinant DNA contains a target gene that has no toxicity to the parasite. CONCLUSIONS: The effective achievement of producing a recombinant gene was done for the first time by replacing the I.L.L-CPC gene with plasmid pGH-hIFNγ-antiIL17 by targeted gene replacement. This cab can regulate the production of hIFNγ and anti-IL17. This makes it a viable choice for eliminating leishmania.

Investigating the Effect of Satureja khuzestanica Essential oil on MDR1 Gene Expression in Leishmania major.

BACKGROUND: Cutaneous leishmaniasis is among the neglected diseases in the world. Pentavalent antimonial compounds are considered the first-line treatment for this disease. However, using alternative natural products has received great attention due to the side effects of chemical drugs and drug resistance of the Leishmania parasite. The present study aims to investigate the effect of Satureja khuzestanica essential oil (SKEO) on MDR1 gene expression. METHODS: In this study, standard strains of Leishmania major promastigotes were exposed to 5, 10, 15, and 20 µg/ml of SKEO. MDR1 gene expression of parasites exposed to essential oil was evaluated using real-time PCR. GAPDH was employed as the housekeeping gene for internal control. RESULTS: Despite the increase, no statistically significant difference was observed in the relative expression of the MDR1 gene between the control group and the groups containing 5, 10, and 20 µg/ml of SKEO (P > 0.05). The relative expression of the MDR1 gene significantly increased in the group containing 15 µg/ml of essential oil compared to the control one (P < 0.05). CONCLUSION: This study showed that the use of essential oil of Satureja khuzestanica plant can have an increasing effect on the expression of MDR1 gene of Leishmania promastigotes, which is the best case if Satureja khuzestanica essential oil reduces the expression of MDR1 gene. So it seems that the use of essential oil of Satoria plant is effective in controlling Leishmania parasite, but its concentrations induce drug resistance. As a result, concentrations of essential oil should be used that have a controlling effect on the growth and proliferation of Leishmania parasite and also have the least effect on the induction of MDR1 gene expression.

Fractional Exhalation Nitric Oxide (FeNO) changes in cystic fibrosis patients induced by compound honey syrup: a pretest-posttest clinical trial.

OBJECTIVE: To evaluate the effect of Persian medicine Syrup 'compound honey syrup (CHS)' on fractional exhalation nitric oxide (FENO) changes in patients with cystic fibrosis (CF). STUDY DESIGN: We conducted a before-after clinical trial on 70 CF patients. All patients received classical treatments for CF along with CHS (including honey, Ginger, cinnamon, saffron, cardamom and galangal), 5-10 cc (depending on the age and weight of patients) in 100 cc of warm boiled water twice a day, 30 min after meals. In this clinical trial, before and 12 weeks after the start of the CHS, FeNO test was evaluated. RESULTS: From 70 patients were enrolled, 44 patients completed this 12-week course of treatment. At the end of the study, changes in FeNO was significantly different before and after treatment (P-value < 0.05). At the end of the study, no dangerous side effects of CHS was reported. CONCLUSIONS: This study revealed that CHS can be effective as a complementary and safe drug in the medication of CF patients.

Neopterin as a Potential Biomarker for the Early Diagnosis of Heart Failure: A Systematic Review and Meta-analysis.

BACKGROUND: Neopterin (NEO) is an inflammatory biomarker with proposed diagnostic value in cardiovascular diseases. Some correlations have been discovered between NEO levels and the incidence, severity, and adverse outcomes of heart failure (HF). However, there are discrepancies in the results reported in the literature. METHODS: We conducted a systematic review and meta-analysis of studies comparing urinary and blood NEO concentrations between individuals with HF, cardiac insufficiency, or dilated cardiomyopathy (DCM) with control groups or those monitoring the role of NEO concentrations as a predictive marker of adverse outcomes in HF patients. RESULTS: A total of 24 studies that met the inclusion criteria were reviewed. The studies demonstrated the alteration of NEO in blood or urine samples in subjects with HF, cardiac insufficiency, or DCM compared with control groups. Also, reviewing the studies suggested a link between reduced ejection fraction, higher NYHA classes, and a higher risk of adverse cardiac outcomes with increased NEO levels. The meta-analysis of three studies revealed a significant increase in serum NEO levels in HF cases compared to that in healthy controls with an effect size of 3.72 (95 % CI 0.16 to 7.28; p = 0.04). CONCLUSION: Meta-analysis demonstrated a significant difference between serum NEO levels of HF cases and healthy subjects. This evidence implies the potential of serum NEO as a valuable diagnostic biomarker in HF patients. Also, the review of the studies revealed the prognostic potential of NEO. Further research is required to assess the usefulness of NEO as a diagnostic/prognostic biomarker for HF.

Design of a multi-epitope-based peptide vaccine against the S and N proteins of SARS-COV-2 using immunoinformatics approach.

Background: As the new pandemic created by COVID-19 virus created the need of rapid acquisition of a suitable vaccine against SARS-CoV-2 to develop Immunity and to reduce the mortality, the aim of this study was to identify SARS-CoV-2 S protein and N antigenic epitopes by using immunoinformatic methods to design a vaccine against SARS-CoV-2, for which S and N protein-dependent epitopes are predicted. B cell, CTL and HTL were determined based on antigenicity, allergenicity and toxicity that were non-allergenic, non-toxic, and antigenic and were selected for the design of a multi-epitope vaccine structure. Then, in order to increase the safety of Hbd-3 and Hbd-2 as adjuvants, they were connected to the N and C terminals of the vaccine construct, respectively, with a linker. The three-dimensional structure of the structure was predicted and optimized, and its quality was evaluated. The vaccine construct was ligated to MHCI. Finally, after optimizing the codon to increase expression in E. coli K12, the vaccine construct was cloned into pET28a (+) vector. Results: Epitopes which were used in our survey were based on non-allergenic, non-toxic and antigenic. Therefore, 543-amino-acid-long multi-epitope vaccine formation was invented through linking 9 cytotoxic CTL, 5 HTL and 14 B cell epitopes with appropriate adjuvants and connectors that can control the SARS coronavirus 2 infection and could be more assessed in medical scientific researches. Conclusion: We believe that the proposed multi-epitope vaccine can effectively evoke an immune response toward SARS-CoV-2. Supplementary Information: The online version contains supplementary material available at 10.1186/s43042-022-00224-w.

Anti-Candida Activity of Curcumin: A Systematic Review.

Curcumin is one of the important natural compounds that is extracted from turmeric. This compound and its derivatives have numerous biological properties, including antioxidant, anticancer, anti-inflammatory, antimicrobial, and healing effects. Extensive research in various fields has been conducted on turmeric as it is widely used as a food additive. The significant antifungal activity is one of the major effects of curcumin. In this paper, recent studies on the effects of different forms of curcumin drug on the candidiasis were systematically examined and discussed. The data in this study were extracted from the articles and reports published in the Web of Science, Google Scholar, PubMed, and Scopus databases. After the preliminary investigation, relevant reports were selected and classified based on the incorporated formulation and purpose of the study. After a systematic discussion of the data, it was found that the use of medicinal forms based on nanoparticles can increase the absorption and target the controlled release of curcumin with a more effective role compared to other formulations. Consequently, it can be concluded that new methods of modern medicine can be employed to increase the efficacy of natural pharmaceutical compounds used in the past. In this regard, the present study analyzed the effect of curcumin against various Candida infections, using the recent data. It was found that applying a combination of drug formulation or the formulation of curcumin and its derivatives can be an effective strategy to overcome the medicine resistance in fungal infections, especially candidiasis.

A loop-mediated isothermal amplification (LAMP) assay for detection of Toxoplasma gondii infection in women with spontaneous abortion.

The present study aimed to use the loop-mediated isothermal amplification (LAMP) technique in comparison with serological tests to determine the rate of T. gondii infection in women suffering from spontaneous abortion (SA). A total of 140 women suffering from their first SA were included in this study. The collected aborted fetal remains and blood samples from each patient were examined in sterilized conditions using the LAMP technique and ELISA. Of the 140 women, 80 (57.1%) tested seropositive for anti-Toxoplasma antibodies by ELISA, 72 (51.4%) women tested seropositive for the IgG antibody, 8 (5.7%) tested seropositive for the IgM antibody. Among the eight women who'd had their first SA who tested seropositive for IgM antibody by ELISA, only five cases (62.5%) reported positively to the LAMP test. The difference in the frequency distribution of the LAMP results for measuring the Toxoplasma infection in pregnant women under study was statistically significant (P < 0.001) from the results of the serological test (ELISA). Although there was a significant difference between age and positivity in the LAMP test (P = 0.017), no significant difference was observed between positivity in the LAMP test and other variables. The findings of the present investigation suggest that LAMP is a preferred method for determining Toxoplasma infection in pregnant women suffering from SA compared with other routine serological tests. Even in a field with limited facilities and equipment, this technique can be effective and efficient in accurately and specifically diagnosing Toxoplasma infections in women at high risk of SA.

The first molecular detection of a Theileria-like species (Apicomplexa: Piroplasmida) in Meriones persicus from western Iran.

The archived blood of rodents species such as Meriones, Mus, and Microtus species was investigated in order to detect any piroplasms species. In this study 18S rRNA target gene of piroplasm parasite was amplified by PCR in a Meriones persicus; so, the Locus 1 and Locus 2 of 18S rRNA were sequenced, successfully. A Theileria-like taxa was suspected in accordance with the BLAST analysis of 18S rRNA L1 and L2 with 96% and 91% sequence homology, respectively. The present study was the first report of a Theileria-like species in M. persicus from Iran.