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U-Net for genomic sequencing: A novel approach to DNA sequence classification
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The precise classification of DNA sequences is pivotal in genomics, holding significant implications for personalized medicine. The stakes are particularly high when classifying key genetic markers such as BRAC, related to breast cancer susceptibility; BRAF, associated with various malignancies; and KRAS, a recognized oncogene. Conventional machine learning techniques often necessitate intricate feature engineering and may not capture the full spectrum of sequence dependencies. To ameliorate these limitations, this study employs an adapted UNet architecture, originally designed for biomedical image segmentation, to classify DNA sequences.The attention mechanism was also tested LONG WITH u-Net architecture to precisely classify DNA sequences into BRAC, BRAF, and KRAS categories. Our comprehensive methodology includes rigorous data preprocessing, model training, and a multi-faceted evaluation approach. The adapted U-Net model exhibited exceptional performance, achieving an overall accuracy of 0.96. The model also achieved high precision and recall rates across the classes, with precision ranging from 0.93 to 1.00 and recall between 0.95 and 0.97 for the key markers BRAC, BRAF, and KRAS. The F1-score for these critical markers ranged from 0.95 to 0.98. These empirical results substantiate the architecture’s capability to capture local and global features in DNA sequences, affirming its applicability for critical, sequence-based bioinformatics challenges

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Publication Date
Fri Sep 29 2023
Journal Name
International Journal Of Nanoscience
Preparation of N-A Cysteine-capped CdTe/CdS/ZnS core/shell/shell QDs as a Selective Probe for Detecting Damaged DNA
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In this study, NAC-capped CdTe/CdS/ZnS core/double shell QDs were synthesized in an aqueous medium to investigate their utility in distinguishing normal DNA from mutated DNA extracted from biological samples. Following the interaction between the synthesized QDs with DNA extracted from leukemia cases (represents damaged DNA) and that of healthy donors (represents undamaged DNA), differential fluorescent emission maxima and intensities were observed. It was found that damaged DNA from leukemic cells DNA-QDs conjugates at 585 nm while intact DNA (from healthy subjects) DNA–QDs conjugates at 574 nm. The obtained results from the optical analyses indicate that the prepared QDs could be utilized as probe for detecting disrupted DNA th

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Publication Date
Sun Oct 10 2021
Journal Name
Journal Of Physics
A novel kite cross hexagonal search algorithm for fast block motion estimation
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The performance quality and searching speed of Block Matching (BM) algorithm are affected by shapes and sizes of the search patterns used in the algorithm. In this paper, Kite Cross Hexagonal Search (KCHS) is proposed. This algorithm uses different search patterns (kite, cross, and hexagonal) to search for the best Motion Vector (MV). In first step, KCHS uses cross search pattern. In second step, it uses one of kite search patterns (up, down, left, or right depending on the first step). In subsequent steps, it uses large/small Hexagonal Search (HS) patterns. This new algorithm is compared with several known fast block matching algorithms. Comparisons are based on search points and Peak Signal to Noise Ratio (PSNR). According to resul

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Publication Date
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
Small Nuclear RNA 64 (snoRNA64): A novel Tumor Biomarker for Pancreatic Cancer
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The pancreatic ductal adenocarcinoma (PDAC), which represents over 90% of pancreatic cancer cases,
has the highest proliferative and metastatic rate in comparison to other pancreatic cancer compartments. This
study is designed to determine whether small nucleolar RNA, H/ACA box 64 (snoRNA64) is associated with
pancreatic cancer initiation and progression. Gene expression data from the Gene Expression Omnibus (GEO)
repository have shown that snoRNA64 expression is reduced in primary and metastatic pancreatic cancer as
compared to normal tissues based on statistical analysis of the in Silico analysis. Using qPCR techniques,
pancreatic cancer cell lines include PK-1, PK-8, PK-4, and Mia PaCa-2 with differ

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Publication Date
Fri May 18 2018
Journal Name
Thesis
The Arabian killifish (Aphanius dispar) as a novel model for mycophysiological studies.
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Abstract Candida albicans is a commensal fungal pathogen that grows in yeast and hyphal forms in the human gut. C. albicans causes mucosal and cutaneous diseases that can result in significant mortality following systematic infections and it also exhibits drug resistance. Zebrafish have been an excellent model to investigate C. albicans infections because of their transparency and the availability of many transgenic lines. However, there is a limitation in using zebrafish as a model because the fish embryos cannot survive at 37°C therefore it is not suitable for studying Candida infections at physiological relevant human body temperature. In this thesis, the normal embryonic development of Arabian killifish (A. dispar) is investigated, rev

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Publication Date
Sat Sep 01 2018
Journal Name
King's College London
A novel sol-gel silica formulation for management of methadone hydrochloride abuse
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Introduction: Methadone hydrochloride (MDN) is an effective pharmacological substitution treatment for opioids dependence, adopted in different countries as methadone maintenance treatment (MMT) programmes. However, MDN can exacerbate the addiction problem if it is abused and injected intravenously, and the frequent visits to the MMT centres can reduce patient compliance. The overall aim of this study is to develop a novel extended-release capsule of MDN using the sol-gel silica (SGS) technique that has the potential to counteract medication-tampering techniques and associated health risks and reduce the frequent visits to MMT centres. Methods: For MDN recrystallisation, a closed container method (CCM) and hot-stage method (HSM) were conduc

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Publication Date
Mon Jun 09 2025
Journal Name
Journal Of Discrete Mathematical Sciences And Cryptography
A novel improvement of skew tent map for generating Pseudo random numbers
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An encryption system needs unpredictability and randomness property to maintain information security during transmission and storage. Although chaotic maps have this property, they have limitations such as low Lyapunov exponents, low sensitivity and limited chaotic regions. The paper presents a new improved skewed tent map to address these problems. The improved skew tent map (ISTM) increases the sensitivity to initial conditions and control parameters. It has uniform distribution of output sequences. The programs for ISTM chaotic behavior were implemented in MATLAB R2023b. The novel ISTM produces a binary sequence, with high degree of complexity and good randomness properties. The performance of the ISTM generator shows effective s

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Publication Date
Sat Jan 01 2022
Journal Name
Ieee Access
Wrapper and Hybrid Feature Selection Methods Using Metaheuristic Algorithms for English Text Classification: A Systematic Review
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Feature selection (FS) constitutes a series of processes used to decide which relevant features/attributes to include and which irrelevant features to exclude for predictive modeling. It is a crucial task that aids machine learning classifiers in reducing error rates, computation time, overfitting, and improving classification accuracy. It has demonstrated its efficacy in myriads of domains, ranging from its use for text classification (TC), text mining, and image recognition. While there are many traditional FS methods, recent research efforts have been devoted to applying metaheuristic algorithms as FS techniques for the TC task. However, there are few literature reviews concerning TC. Therefore, a comprehensive overview was systematicall

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Publication Date
Thu Jan 25 2024
Journal Name
Biomedical Materials
Enhancing the therapeutic potential of curcumin: a novel nanoformulation for targeted anticancer therapy to colorectal cancer with reduced miR20a and miR21 expression
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Abstract<p>Curcumin (Cur) possesses remarkable pharmacological properties, including cardioprotective, neuroprotective, antimicrobial, and anticancer activities. However, the utilization of Cur in pharmaceuticals faces constraints owing to its inadequate water solubility and limited bioavailability. To overcome these hurdles, there has been notable focus on exploring innovative formulations, with nanobiotechnology emerging as a promising avenue to enhance the therapeutic effectiveness of these complex compounds. We report a novel safe, effective method for improving the incorporation of anticancer curcumin to induce apoptosis by reducing the expression levels of miR20a and miR21. The established</p> ... Show More
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Publication Date
Wed Apr 26 2023
Journal Name
Journal Of Contemporary Medical Sciences
A potential role of extracellular DNA in biofilm and ciprofloxacin resistance
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Objectives: This study aims to broaden our knowledge of the role of eDNA in bacterial biofilms and antibiotic-resistance gene transfer among isolates. Methods: Staphylococcus aureus, E. coli, and Pseudomonas aeruginosa were isolated from different non-repeated 170 specimens. The bacterial isolates were identified using morphological and molecular methods. Different concentrations of genomic DNA were tested for their potential role in biofilms formed by study isolates employing microtiter plate assay. Ciprofloxacin resistance was identified by detecting a mutation in gyrA and parC. Results: The biofilm intensity significantly decreased (P < 0.05) concerning S. aureus isolates and insignificantly (P > 0.05) concernin

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Publication Date
Sun Jun 01 2025
Journal Name
Journal Of Physics: Conference Series
Classification of East Shatt al-Arab Using the Novel Scene Optimum Index Factor (SOIF) and Spectral Angle Mapper classifier
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Abstract<p>Accurate land use and land cover (LU/LC) classification is essential for various geospatial applications. This research applied a Spectral Angle Mapper (SAM) classifier on the Landsat 7 (ETM+ 2010) & 8 (OLI 2020) satellite scenes to identify the land cover materials of the Shatt al-Arab region which is located in the east of Basra province during ten years with an estimate of the spectral signature using ENVI 5.6 software of each cover with the proportion of its area to the area of the study region and produce maps of the classified region. The bands of these datasets were analyzed using the Optimum Index Factor (OIF) statistic. The highest OIF represents the best and most appropr</p> ... Show More
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