Saad Jawaid Khan

Membrane proteins constitute essential biomolecules attached to or integrated into cellular and organelle membranes, playing diverse roles in cellular processes. Their precise localization is crucial for understanding their functions. Existing protein subcellular localization predictors are predominantly trained on globular proteins; their performance diminishes for membrane proteins, explicitly via deep learning models. To address this challenge, the proposed study segregates membrane proteins into three distinct locations, including the plasma membrane, internal membrane, and membrane of the organelle, using deep learning algorithms including recurrent neural networks (RNN) and Long Short-Term Memory (LSTM). A redundancy-curtailed dataset of 3000 proteins from the MemLoci approach is selected for the investigation, along with incorporating pseudo amino acid composition (PseAAC). PseAAC is an exemplary technique for extracting protein information hidden in the amino acid sequences. After extensive testing, the results show that the accuracy for LSTM and RNN is 83.4% and 80.5%, respectively. The results show that the LSTM model outperforms the RNN and is most commonly employed in proteomics.

HLA is vital for effective immune responses against viruses. The virus responsible for COVID-19, SARS-CoV-2, highlights the significance of this immune response. The unpredictable nature of COVID-19 prompts investigation into how HLA, a component of host genetics, impacts disease susceptibility and outcomes. Understanding HLA variants' influence on COVID-19 susceptibility and severity can aid in identifying at-risk individuals. Significant HLAs that had been previously investigated for their association with COVID-19 were sought. Articles from January 2001 to February 2022 were reviewed in 2 databases: Science Direct and PubMed, employing the search terms "COVID-19" AND "HLA." Studies of genetic association measuring the severity or susceptibility to COVID-19 were analyzed in accordance with PRISMA guidelines. A total of 1326 studies related to the novel coronavirus and HLA conducted between the first month of 2001 and the second month of 2022 were identified in our search. Following the screening process, 15 relevant publications were selected. With the exception of one publication that did not demonstrate any connection, significant correlations between the incidence and mortality due to COVID-19 were found in all investigations. In severe cases, HLA class II, DRB113, was notably more prevalent. Among Black hospitalized patients positive for HLA-B53, there was an observed 7.4-fold higher risk of mortality, while HLA-B51:01 and HLA-A*26:01 were indicative of protective effects. HLAs play an essential role in immunological responses, potentially contributing to varying COVID-19 infection rates and outcomes across populations. These findings underscore the need for national networks to collect patient samples for HLA typing, identifying HLA genotypes associated with disease vulnerability.

Introduction: The coronavirus disease 2019 (COVID-19) pandemic caused global health, economic, and population loss. Variants of the coronavirus contributed to the severity of the disease and persistent rise in infections. This study aimed to identify potential drug candidates from fifteen approved antiviral drugs against SARS-CoV-2 (6LU7), SARS-CoV (5B6O), and SARS-CoV-2 spike protein (6M0J) using virtual screening and pharmacokinetics to gain insights into COVID-19 therapeutics. Methodology: We employed drug repurposing approach to analyze binding performance of fifteen clinically approved antiviral drugs against the main protease of SARS-CoV-2 (6LU7), SARS-CoV (5B6O), and SARS-CoV-2 spike proteins bound to ACE-2 receptor (6M0J), to provide an insight into the therapeutics of COVID-19. AutoDock Vina was used for docking studies. The binding affinities were calculated, and 2-3D structures of protein-ligand interactions were drawn. Results: Rutin, hesperidin, and nelfinavir are clinically approved antiviral drugs with high binding affinity to proteins 6LU7, 5B6O, and 6M0J. These ligands have excellent pharmacokinetics, ensuring efficient absorption, metabolism, excretion, and digestibility. Hesperidin showed the most potent interaction with spike protein 6M0J, forming four H-bonds. Nelfinavir had a high human intestinal absorption (HIA) score of 0.93, indicating maximum absorption in the body and promising interactions with 6LU7. Conclusions: Our results indicated that rutin, hesperidin, and nelfinavir had the highest binding results against the proposed drug targets. The computational approach effectively identified SARS-CoV-2 inhibitors. COVID-19 is still a recurrent threat globally and predictive analysis using natural compounds might serve as a starting point for new drug development against SARS-CoV-2 and related viruses.

Osteoporosis constitutes a significant public health concern necessitating proactive prevention, treatment, and monitoring efforts. Timely identification holds paramount importance in averting fractures and alleviating the overall disease burden. The realm of osteoporosis diagnosis has witnessed a surge in interest in machine learning applications. This burgeoning technology excels at recognizing patterns and forecasting the onset of osteoporosis, paving the way for more efficacious preventive and therapeutic interventions. Smart walkers emerge as valuable tools in this context, serving as data acquisition platforms for datasets tailored to machine learning techniques. These datasets, trained to discern patterns indicative of osteoporosis, play a pivotal role in enhancing diagnostic accuracy. In this study, encompassing 40 participants—20 exhibiting robust health and 20 diagnosed with osteoporosis—data from force sensors embedded in the handlebars of conventional walkers were gathered. A windowing action was used to increase the size of the dataset. The data were normalized, and k-fold cross-validation was applied to assess how well our model performs on untrained data. We used multiple machine learning algorithms to create an accurate model for automatic monitoring of users’ gait, with the Random Forest classifier performing the best with 95.40% accuracy. To achieve the best classification accuracy on the validation dataset, the hyperparameters of the Random Forest classifier were further adjusted on the training data. The results suggest that machine learning-based automatic monitoring of gait parameters could lead to accurate, non-laborious, cost-effective, and efficient diagnostic tools for osteoporosis and other musculoskeletal disorders. Further research is needed to validate these findings.

Fragility fractures, caused by low-energy trauma, are a significant global health concern, with 158 million people aged 50 and over at risk. Hip fractures, a common issue in elderly patients, are often linked to underlying conditions such as osteoporosis. This study proposed a cost-effective solution using a non-wheeled smart walker with load sensors to measure gait parameters, addressing the high cost of traditional gait analysis equipment, the prototype used PASCO load cells PS2200 for force measurement, eliminating the need for Arduino UNO or microcontroller-based hardware. A lightweight amplifier PS2198 amplified the signal, which was transmitted via USB to a personal computer. PASCO capstone software was used for data recording and visualization. The smart walker was tested on forty volunteers divided into two equal groups: those with osteoporosis and those without, by performing a 10 m walk test three times. ANOVA comparing spatiotemporal parameters (TSPs) of the two participant groups (α = 0.05) showed that significant differences lay in terms of time taken to complete the walk test (p < 0.01), left step length (p = 0.03), walking speed (p = 0.02), and stride length (p < 0.02). The results indicate that this smart walker is a reliable tool for assessing gait patterns in individuals with osteoporosis. The proposed system can be an alternative for time consuming and costly methods such as motion capture, and for socially stigmatizing devices such as exoskeletons. It can also be used further to identify risk factors of osteoporosis.

Protein subcellular localization is a promising research question in Proteomics and associated fields, including Biological Sciences, Biomedical Engineering, Computational Biology, Bioinformatics, Proteomics, Artificial Intelligence, and Biophysics. However, computational techniques are preferred to explore this attribute for a massive number of proteins. The byproduct of this conjunction yields diversified location identifiers of proteins. These protein subcellular localization identifiers are unique regarding the database used, organisms, Machine Learning Technique, and accuracy. Despite the availability of these identifiers, the majority of the work has been done on the subcellular localization of proteins and, less work has been done specifically on locations of transmembrane proteins. This systematic review accounts for computational techniques implemented on transmembrane protein localization. Moreover, a literature search on PubMed, Science Direct, and IEEE Databases disclosed no systematic review or meta-analysis on the cell's transmembrane protein locale. A Systematic review was formed under the guidelines of PRISMA by using Science Direct, PubMed, and IEEE Databases. Journal publications from 2000 to 2023 were taken into consideration and screened. This review has focused only on computational studies rather than experimental techniques. 1004 studies were reviewed and were categorized as relevant and non-relevant according to inclusion and exclusion criteria. All the screening was done through Endnote after importing citations. This systematic review characterizes the gap in targeting the locale of the transmembrane protein and will aid researchers in exploring its new horizons.

In order to perform their daily activities, a person is required to communicating with others. This can be a major obstacle for the deaf population of the world, who communicate using sign languages (SL). Pakistani Sign Language (PSL) is used by more than 250,000 deaf Pakistanis. Developing a SL recognition system would greatly facilitate these people. This study aimed to collect data of static and dynamic PSL alphabets and to develop a vision-based system for their recognition using Bag-of-Words (BoW) and Support Vector Machine (SVM) techniques. A total of 5120 images for 36 static PSL alphabet signs and 353 videos with 45,224 frames for 3 dynamic PSL alphabet signs were collected from 10 native signers of PSL. The developed system used the collected data as input, resized the data to various scales and converted the RGB images into grayscale. The resized grayscale images were segmented using Thresholding technique and features were extracted using Speeded Up Robust Feature (SURF). The obtained SURF descriptors were clustered using K-means clustering. A BoW was obtained by computing the Euclidean distance between the SURF descriptors and the clustered data. The codebooks were divided into training and testing using fivefold cross validation. The highest overall classification accuracy for static PSL signs was 97.80% at 750 × 750 image dimensions and 500 Bags. For dynamic PSL signs a 96.53% accuracy was obtained at 480 × 270 video resolution and 200 Bags.

Prostheses control using electromyography signals have shown promising aspects in various fields including rehabilitation sciences and assistive technology controlled devices. Pattern recognition and machine learning methods have been observed to play a significant role in evaluating features and classifying different limb motions for enhanced prosthetic executions. This paper proposes feature extraction and evaluation method using intramuscular electromyography (iEMG) signals at different arm positions and hand postures based on the RES Index value statistical criterion method. Sixteen-time domain features were selected for the study at two main circumstances; fixed arm position (FAP) and fixed hand posture (FHP). Eight healthy male participants (30.62 ± 3.87 years) were asked to execute five motion classes including hand grip, hand open, rest, hand extension, and hand flexion at four different arm positions that comprise of 0°, 45°, 90°, and 135°. The classification process is accomplished via the application of the k-nearest neighbor (KNN) classifier. Then RES index was calculated to investigate the optimal features based on the proposed statistical criterion method. From the RES Index, we concluded that Variance (VAR) is the best feature while WAMP, Zero Crossing (ZC), and Slope Sign Change (SSC) are the worst ones in FAP conditions. On the contrary, we concluded that Average Amplitude Change (AAC) is the best feature while WAMP and Simple Square Integral (SSI) resulted in least RES Index values for FHP conditions. The proposed study has possible iEMG based applications such as assistive control devices, robotics. Also, working with the frequency domain features encapsulates the future scope of the study.