A Comprehensive Methodological Review of Major Developments in Bioinformatics Pipelines for Transcriptomic Data Analysis

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

Plasma Glycosaminoglycans: A new Promising tool for Assessment of Non-Metastatic Renal Cell Carcinoma Patients Following Nephrectomy

Background: Non-invasive detection of renal cell carcinoma (RCC) recurrence is a major challenge that could radically affect patient survival. To date, there are no approved biomarkers for inclusion in the monitoring and follow-up of RCC; therefore, assessment of treatment response is lacking. Materials and Methods: A Cross-sectional study was carried out on biopsy-proven renal cell carcinoma patients scheduled for nephrectomy at Hayatabad Medical Complex (HMC) Hospital, Peshawar, Pakistan, between September 2022 and January 2024. Results: A total of 160 samples were included in the study. Eighty samples were obtained from biopsy-proven non-metastatic renal cell carcinoma patients, of which 40 were collected pre-nephrectomy, 40 were collected post-nephrectomy from the same patients, and 80 samples were collected from age and gender-matched healthy individuals. Total plasma glycosaminoglycans (GAGs) levels were analyzed through a manual enzyme-linked immunosorbent assay using a non-competitive sandwich technique. Quantitative variables were summarized as means and standard deviation, while qualitative variables were summarized as frequency and percentage. A paired t-test was performed to check whether the difference between the mean plasma GAG levels in pre-nephrectomy and post-nephrectomy groups was significant. Conclusion: The results revealed that post-nephrectomy GAG levels have significantly decreased compared to pre-nephrectomy levels (P<0.001). Plasma glycosaminoglycan levels could be promising markers for monitoring renal cell carcinoma patients post-nephrectomy

Management of congenital talipes equinovarus by Ponseti technique and percutaneous needle tenotomy

Background: This study evaluates the Ponseti technique combined with percutaneous needle tenotomy for treating congenital talipes equinovarus (CTEV), or clubfoot, assessing efficacy, complications, and outcomes. Conducted at a tertiary medical center in Hyderabad from 2021 to 2024, it included patients of all ages presenting with CTEV. Methods: This is a prospective and retrospective study. The Ponseti method, a conservative approach involving serial casting and gentle foot manipulation, was applied, with percutaneous needle tenotomy used for achilles tendon lengthening when necessary. Compared to traditional surgical methods, this minimally invasive approach is associated with fewer complications and improved correction rates. Patients were assessed using Pirani scores, with data on cast numbers, tenotomy needs, and relapses. Results: The study demonstrated significant efficacy, particularly when treatment began early, reducing the number of casts required. Needle tenotomy, preferable over blade tenotomy, was particularly effective in India and among patients from lower socioeconomic backgrounds, proved more effective than blade tenotomy. The approach was associated with fewer complications and better correction rates. Conclusions: The Ponseti technique is an effective, accessible, and economical option with minimal complications. Early diagnosis and intervention were found essential for optimal outcomes. Further research is suggested to refine treatment protocols for older children and severe deformities

Are ESG Stocks Safe-Haven during COVID-19?

This study contributes to the debate on safe-haven characteristics of environmental, social, and governance (ESG) stocks during COVID-19 pandemic. Using wavelet coherence framework on four major ESG stock indices from global and emerging stock markets, and two proxies of COVID-19 fear over the period from February 5th, 2020, to March 18th, 2021, we find a strong and positive co-movement between health fear index of COVID-19 and returns on ESG stocks suggesting the existence of safe-haven properties in ESG stocks. However, we also observe a negative co-movement between stock market base proxy of COVID-19 and returns on ESG indices, suggesting that safe-haven properties of ESG stocks are contingent upon the proxy of COVID-19 pandemic. Our findings are of particular interest for the investors and asset managers who may use ESG stocks to diversify their portfolios during health crisis due to COVID-19 pandemic

On the Simulation of Turbulent Fluid-Structure Interaction

The fluid-structure interaction (FSI) phenomena are relevant in a significant number of naturally occurring as well as industrial applications. Simulations of FSI have gained noteworthy attention with rapid advancements of computational technology in the last decade. Efficiency and accuracy of these simulations are still a concern, specially with a turbulent flow, the challenge is compounded by an additional computational cost for a turbulence modeling approach. Partitioned coupling approaches owing to software modularity and reusability are favored by engineers to solve FSI problems. The turbulence in flow is simulated through models with varying levels of complexity and computational requirements. In industrial applications, the use of Reynolds Averaged Navier Stokes (RANS) modeling of turbulence is dominant, whereas turbulence resolving approaches like Large-Eddy simulation (LES) are still not considered feasible due to computational requirements. To get as much accuracy by using as least as possible computer resources, a reasonable compromise are hybrid RANS-LES of turbulence, which are becoming more and more frequent. The goal of this work is to enable efficient and reliable simulations of FSI in turbulent flow. To this end, validation studies of three different turbulence modeling approaches available in the in-house flow solver FASTEST are performed. The structural subproblem in the coupling environment is solved with the Finite Element Method based code FEAP, while the data transfer and interpolation on non-matching grid interfaces can be handled with MpCCI or preCICE. For this work, the turbulence modeling approaches in FASTEST are extended with an implementation of the Wall Adapting Local Eddy (WALE) viscosity model for LES, and a validation study of the model is performed for a two dimensional periodic hill flow test case. An economical method based on a Poisson equation for the calculation of the nearest wall distance is also implemented, which is required by some turbulence models. The accuracy of the method is assessed with two computations on stationary grids. In turbulent flow simulations with moving grids, the height of cells on a wall changes and it can make a wall treatment approach unsuitable. This issue is addressed with an implementation of wall boundary conditions that work regardless of the first cell position in a boundary layer. The implementation is tested on stationary grids in a channel flow with a variation of the first cell height on the wall. A test of the method with an FSI test case showed satisfactory results. Validation studies of a RANS and a hybrid RANS-LES approach are performed with simulations of two FSI test cases. The two and three dimensional RANS and the hybrid RANS-LES produce a good agreement with the experimental results for oscillation characteristics of the structure. A hybrid RANS-LES and an LES is performed for another FSI test case with a very dense mesh. The LES and the hybrid RANS-LES on two different, but relatively dense meshes produced very similar results with a satisfactory prediction of the structural deflections

Screening of Diabetes and HIV Infection in Newly Diagnosed Pulmonary Tuberculosis Patients

Objective: Aim of the study was to investigate the prevalence of diabetes and HIV infection by screening in newly diagnosed pulmonary tuberculosis patients. Methods: This cross sectional study was conducted in Pulmonology department Bahawal Victoria Hospital Bahawalpur.  From  1 June 2018 to 1 June 2019 after taking approval from the institutional ethical committee. Total 159 newly diagnosed pulmonary tuberculosis patients were recruited by non-probability consecutive sampling. Mean and SD was calculated for numerical variables like age , BMI, FBG, Hemoglobin and monthly income. Ferquancy and percentages were calculated for categorical variables like gender, smooking status, educational status, alcohol consumption, prevelance of HIV and diabetes, Ch square test was use to check significant different in PTB and Non PTB patients. P value of < 0.05 was taken as significant. Results: Significant difference was found between age (p=0.000), BMI (p=0.000), FBG (p=0.000), hemoglobin (p=0.000), gender (p=0.002) and alcohol consumption (p=0.034), in groups, except education status (p=0.090) and monthly income (p=0.068). The main outcome variables of this study were HIV infection and diabetes. HIV infection was noted in 3.1% (n=5) and 1.9% (n=3) patients for PTB and non-PTB group respectively. While, 8.2% (n=13) and 4.4% (n=4) patients suffered from diabetes, for both the groups respectively. Conclusion: The results of our study revealed that on screening of newly diagnosed pulmonary tuberculosis patients with HIV infection and diabetes, their prevalence was high as compared to non-pulmonary tuberculosis group. But this difference was statistically non significant (P value 0.474 and 0.166). Key words:   Pulmonary tuberculosis, Diabetes, HIV infection DOI: 10.7176/JMPB/55-21 Publication date:May 31st 201

Are Cryptos Safe-Haven Assets during COVID-19? Evidence from Wavelet Coherence Analysis

We use wavelet coherence analysis on global COVID-19 fear index, cryptocurrency market specific implied volatility index (VCRIX) and cryptocurrency returns to investigate safe-haven properties of cryptocurrencies during COVID-19 pandemic. The findings of our paper show that a non-financial market-based proxy of market stress that represents fear of households and retail investors reveals cryptocurrencies as safe-haven assets; however, a financial market-based proxy of the market turbulence exposes that cryptocurrencies behave like traditional assets during the times of COVID-19 pandemic. Our findings support that long-term investors can invest in the cryptocurrency market to hedge the risks during the COVID-19 pandemic

Frequency of various risk factors for Meconium aspiration syndrome

Objective: To study the frequency of various factor leading to meconium aspiration syndrome. Material & Method: This present descriptive cross sectional study was carried out at Department of Pediatrics Medicine Bahawal Victoria  Hospital Multan. for 6 months i.e. from October 8, 2018 to April 8, 2019. The non-probability, consecutive sampling technique was used. Newborns having staining of vocal cords and respiratory distress were included in this study. ABG and X ray Chest was done in all neonates. Factors like, Post-term pregnancy, IUGR, thick meconium, low APGAR score at 1 and 5 minutes were noted. All the collected data was entered and analyzed on SPSS version 23. Chi square and T test were used to check significant relation of risk factors with meconium aspiration syndrome. P value of 0,05 was consider significant. Results: Among total enrolled 150 babies, the mean age of babies was 37.37±18.96 hours, the male to female ratio of the babies was 1.03:1. The mean maternal age was 28.85±6.602 years. The thick meconium was observed in 89(59.33%) patients, 79(52.7%) patients went through vaginal delivery, postdate pregnancy was noted in 68(45.3%) patients, IUGR was observed in 52(34.7%) patients and poor APGAR score at 1 min was noted in 79(52.7%) patients. Conclusion: The observations of our study revealed that Meconium aspiration syndrome has significant relation with maternal age(P value 0.000), postdated pregnancy(P Value 0.001), IUGR (P value 0.021), poor APGAR score at 5 minutes( P value 0.034), and thick meconium(P value 0.000). Keywords: Postdate, Meconium  Aspiration , Syndrome, APGAR, Pregnancy DOI: 10.7176/JMPB/55-19 Publication date:May 31st 201