Novelty in Biomedicine

Background: Recent advances in transcriptomics have provided new insights to analyze a wide range of biological data. RNA sequencing (RNA-Seq) is a common method used to study the complete set of RNA molecules (the transcriptome) in different cell types, genetic backgrounds, and environments. While many computational tools exist for analyzing large RNA-Seq datasets, there is still a need to thoroughly compare methods used to separate mixed cell populations (deconvolution).

Materials and Methods: This review highlights recent software and database improvements for processing RNA-Seq data, including steps like matching sequences to the genome, reconstructing RNA molecules, and measuring RNA abundance.

Results: We examine how well different methods work under various experimental conditions and discuss important factors such as data quality, sequence alignment, data visualization, identifying gene expression differences, and data standardization. A novel approach is also introduced: an ensemble learning-based deconvolution method combining multiple techniques to improve accuracy, mitigate data contamination, and reduce errors. Our findings provide valuable guidance for using omics tools effectively and developing better analysis methods. This review offers detailed instructions for planning and evaluating Illumina sequencing experiments.

Conclusion: We cover basic concepts, RNA-Seq analysis steps, computational workflows, and potential difficulties.

Background: Multiple sclerosis (MS) is one of the most common and debilitating neurological diseases. Brain magnetic resonance imaging (MRI) is critical to determine the prognosis of MS. Using simple and accessible techniques is one of the researchers' concerns. So far, limited studies have been conducted on evaluating the relationship between the Bi-caudate ratio (BCR) and white matter atrophy in brain MRI of patients with MS. Therefore, in this study, we decided to evaluate this relationship.

Materials and Methods: In this cross-sectional study, which was conducted to determine the relationship between BCR and white matter atrophy in brain MRI patients with MS, patients with MS who were evaluated by MRI at Imam Hossein Hospital (Tehran-Iran) in 2022 were assessed. BCR is determined by dividing the shortest distance between two caudate nuclei by the length of the brain at the imaging. The symbol digit modalities test (SDMT) was used to check the cognitive function of patients, and the relationship between BCR and MS-related parameters was evaluated. Expanded disability status score (EDSS) was also evaluated. A significance level was considered less than 0.05.

Results: Eighty-five patients with a mean age of 40.73 ± 8.45 years and female gender was more prevalent (65.9%). The mean EDSS in all participants was 2.64 ± 2.49, and the mean BCR was 0.11 ± 0.03. EDSS score, age of the disease onset, SDMT score, and BCR were significantly different between different MS types (secondary progressive MS, primary progressive MS, and relapsing-remitting MS) (P-values<0.05). There was a statistically significant relationship between age, disease duration, EDSS score, onset age of the disease, and SDMT score with BCR (P<0.05). There was a statistically significant difference in the amount of BCR between sexes (P<0.045).

Conclusion: BCR is a valuable method for evaluating the condition of multiple sclerosis, and it can be used as a simple and accessible technique for evaluating MS conditions.

Background: The pandemic of the coronavirus disease 2019 (COVID-19) is a major cause of death worldwide; thus, disease prediction is important. This study aimed to evaluate dynamic changes of complete blood count parameters in adult patients to predict disease severity.

Materials and Methods: Data from 980 consecutive hospitalized patients diagnosed with COVID-19 were analyzed prospectively. Patients were categorized into moderate disease-cured (n = 682), severe disease-cured (n = 136), and deceased (n = 162) groups. Clinical conditions at the admission and blood samples every other day were collected for each patient from hospital admission to discharge or death. Mean values of serum parameters were compared among the three groups; the Hazard ratio of different indices for death was calculated, and repeated measured ANOVA was employed to assess the prognostic importance of dynamic changes in blood parameters during the disease.

Results: Univariable and multivariable regression analysis showed that the only important clinical risk factor associated with death was needing invasive ventilation at admission (HR of 18.97 and 23.82 in univariable and multivariable regression analysis, respectively). Considering dynamic changes in blood elements, repeated measured ANOVA showed patients who survived had a decrease in WBC and Neutrophil count as well as Neutrophil to lymphocyte ratio (NLR) compared to expired patients; in contrast, platelet and lymphocyte count increased in survivors while dropped in deceased ones.

Conclusion: Dynamic changes in blood indices are prognostic indicators of an unfavorable prognosis for COVID-19 infection.

Background: This study aimed to evaluate the relationship between mean platelet volume (MPV) and myocardial perfusion abnormalities in patients with and without Type 2 diabetes mellitus (DM) using myocardial perfusion scans.

Materials and Methods: This cross-sectional study compared 49 patients with Type 2 DM without overt cardiovascular symptoms with 49 healthy controls. Both groups underwent myocardial perfusion scans at rest and under stress conditions. Risk factors were assessed and recorded using a special research-made questionnaire. A complete blood count and MPV results were obtained using the Sysmex - KX-21 system. Data were analyzed using SPSS, with a p-value below 0.05 considered statistically significant.

Results: No significant differences were observed between the two groups in terms of Summed Stress Score (SSS), Summed Rest Score (SRS), Summed Difference Score (SDS), Ejection Fraction (EF), and End Systolic Volume (ESV). The only marked variance was a higher average platelet count in the control group. Regression analysis revealed that a one-unit increase in MPV correlated with a 0.46 average increase in SRS in the control group (CI: 0.08-0.83, β: 0.46).

Conclusion: MPV may serve as a predictive marker for myocardial perfusion abnormalities, especially in individuals without diabetes. This simple metric could act as an early indicator for coronary artery disease.

Background: Few trials have been conducted regarding using PET/CT metabolic parameters as a predictor for the long-term survival of patients with lymphoma. The present study aimed to determine the prognostic value of quantitative metabolic parameters based on FDG-PET/CT in predicting 2-year mortality and disease recurrence in patients with diffuse large B-cell lymphoma (DLBCL).

Materials and Methods: This cross-sectional study was performed on patients who suffered DLBCL and assessed by FDG-PET/CT. All patients have been scheduled for first-line therapy, including the R-CHOP regimen (Rituximab, Cyclophosphamide, Hydroxydaunomycin, Oncovin, and Prednisone). The records of patients eligible for the study were extracted from the hospital archive. All subjects were followed up for 2 years to assess progression-free survival (PFS) and overall survival (OS).

Results: Complete response to treatment was revealed in 80.0%, while the disease was progressive in 5.7% and stable in 2.9%. At the end of 2 years of follow-up, in all groups, five people (14.2%) experienced disease relapse, and one person (2.9%) died. Comparing metabolic parameters of PET/CT between survived and non-survived groups showed no difference between the two groups. Similarly, the median value of pointed metabolic parameters was insignificant between groups with and without disease relapse. The comparison of the treatment metabolic response state between non-survived and survived subgroups showed no difference. However, regarding the metabolic response status according to the presence or lack of recurrence, those with disease recurrence experienced a higher rate of progressive metabolic disease condition. Treatment metabolic non-response status and higher Deauville 5-point score (D5PS) score could effectively differentiate the groups with and without disease recurrence.

Conclusion: FDG-PET/CT complete metabolic response can predict longer PFS in patients with DLBCL, but its related metabolic parameters may not predict disease outcome.

Background: Brain magnetic resonance imaging (MRI) is crucial to determine the prognosis of multiple sclerosis (MS). The use of simple and accessible techniques that can be used for examining and managing the cognitive status and disability of patients with MS is one of the important concerns. This study aimed to investigate the relationship between corpus callosum index in brain MRI and clinical subgroups of MS, severity of cognitive disorders, and disability in multiple sclerosis.

Materials and Methods: This cross-sectional study was conducted to determine the relationship between CCI and clinical subgroups of MS, the severity of cognitive disorders, and disability in patients with MS referred to Imam Hossein Hospital in 2020. The maximum length of the corpus callosum (anterior, posterior diameter) was measured, and the height of the corpus callosum was measured on a line perpendicular to its long axis. Corpus callosum index (CCI), symbol digit modalities test (SDMT), and expanded disability status scale (EDSS) were assessed in patients. A significance level of less than 0.05 was considered.

Results: A total of 85 patients with a mean age of 40.73 ± 8.45 years were assessed, and 65.9% were women. The CCI value was significantly lower in women (P-value: 0.001). The mean value of EDSS in all participants was 2.64±2.49. There was a statistically significant difference between the different subgroups of MS with the EDSS score, age of disease onset, SDMT score, CCI index, and mean disease duration (all P-values<0.05). There was a significant negative correlation between the CCI index and age (P:0.02, r:-0.24), duration of the disease (P:0.001, r:-0.38), EDSS (P:0.001, r:-0.71), while the correlation between SDMT and CCI was positive (P:0.001, r:0.67).

Conclusion: CCI is a quick and cost-beneficial parameter to evaluate cognitive disorders and disability in patients with MS.

Background: Obesity is one of the most common diseases in the world, and type 2 diabetes (T2DM) is one of the common complications of obesity. Bariatric surgery is one of the main treatments for the obese. It is recommended that this procedure can improve the status of T2DM, but there is limited data about the short-term effects of bariatric surgery on T2DM status. In this study, we aimed to evaluate the short-term effect of bariatric surgery on the level of HbA1c as a parameter of the status of T2DM during 6 months.

Materials and Methods: In this cross-sectional study that was conducted on patients who underwent bariatric surgery in Mortaz and Mojibinia Hospitals (Yazd-Iran) from 2016 to 2020 to evaluate the short-term effect of bariatric surgery on HbA1C level, patients who were candidates for performing bariatric surgery were evaluated for 6 months. Age, sex, body mass index (BMI) before surgery, and surgery types (sleeve gastrectomy or gastric bypass) were recorded. The patients were followed up for six months, and HbA1C was assessed before the operation, at 3 months, and at 6 months after the surgery. All data was recorded and analyzed by SPSSv.25, and the significance level was considered less than 0.05.

Results: A total of 713 patients were assessed (27 in the sleeve gastrectomy group and 286 in gastric bypass surgery). The mean level of HbA1C was 8.59±1.85 % at the baseline, and it decreased to 8.41±1.85 % after 3 months (P-value: 0.06). After 6^th month, the HbA1C level decreased to 7.79±5.04 %, significantly decreasing from the baseline (P-values<0.05). There was no association between the type of bariatric surgery (sleeve gastrectomy or gastric bypass) and the amount of HbA1C reduction (P-values> 0.05).

Conclusion: Bariatric surgery reduces HbA1C level, and a significant reduction can be seen after 6 months. Sleeve gastrectomy and gastric bypass have similar effects in terms of HbA1C improvement.

Background: Nonalcoholic fatty liver disease (NAFLD) is common. Noninvasive methods to assess fibrosis stage are limited, and biopsy remains the gold standard. We aimed to compare the Doppler ultrasound indices (resistive index (RI), pulsatility index (PI), and arterial waveform) at the place of division of the hepatic artery in patients with and without nonalcoholic non-diabetic fatty liver.

Materials and Methods: This cross-sectional study involved patients with fatty and normal liver. For this purpose, 50 patients with fatty liver with a grade higher than II and confirmed and 50 patients without signs of fatty infiltration in sonography were examined by standard Doppler sonography from the location of the hepatic artery. The patients' waveform, RI, and PI were investigated based on this. The evaluated indicators were analyzed as the average of three consecutive measurements. Finally, the results obtained in the two groups were compared using SPSS statistical software.

Results: One hundred patients were equally divided into two groups with and without NAFLD. The two groups were similar in age, sex, and body mass index (BMI) (all P-values ​​> 0.05). In the case group, the average RI was 0.5 ± 0.08; in the control group, it was 0.63 ± 0.04 (P-value<0.001). PI was 0.5 ± 0.08 in the case group and 0.63 ± 0.04 in the control group (P-value<0.001). In the case group, 74% of the subjects showed a Tardus parvus wave pattern, while in the control group, 100% had a normal wave pattern (P-value<0.001).

Conclusion: RI, PI, and arterial waveform at the site of division of the hepatic artery can be used to diagnose these patients who need a biopsy. They reduce the liver.

Background: Mucorales and Aspergillus have invasive fungal infections with high mortality, mainly in immunocompromised and diabetic patients. The diagnosis is microbiological and pathological, with a strong clinical suspicion. The treatment is medical and surgical debridement. Invasive fungal coinfection by these two is reported as a case report. Here, we highlight the importance of considering the coinfection of Aspergillus and Mucor in the maxillary bone and paranasal sinuses in patients with systemic lupus erythematosus (SLE).

Cases Report: A 38-year-old woman had a fever and toothache 1.5 months before and had been treated for a dental abscess, which continued to fever, epistaxis, teeth out spontaneously, left Bell’s Palsy, and swelling in the left side of her face. She had a history of immunosuppressive therapy and steroid-induced hyperglycemia for SLE. The PNS CT Scan found increased mucosal thickness of the left maxilla and sphenoid sinuses. Extensive debridement was done. Pathologic study of debrided samples showed coinfection of invasive mucormycosis and aspergillosis. She was treated with liposomal amphotericin B and voriconazole with complete recovery without recurrence after a one-year follow-up.

Conclusion: In mucor and aspergillus coinfection, no one should be missed at first and treated by specific antifungal amphotericin B, with no time-wasting for a better prognosis.