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Fulltext Selection and classification of gene expression in autism disorder: Use of a combination of statistical filters and a GBPSO-SVM algorithm

Hameed SS, Hassan R, Muhammad FF

PLoS One, 2017;12(11):e0187371.
PMID: 29095904 DOI: 10.1371/journal.pone.0187371

In this work, gene expression in autism spectrum disorder (ASD) is analyzed with the goal of selecting the most attributed genes and performing classification. The objective was achieved by utilizing a combination of various statistical filters and a wrapper-based geometric binary particle swarm optimization-support vector machine (GBPSO-SVM) algorithm. The utilization of different filters was accentuated by incorporating a mean and median ratio criterion to remove very similar genes. The results showed that the most discriminative genes that were identified in the first and last selection steps included the presence of a repetitive gene (CAPS2), which was assigned as the gene most highly related to ASD risk. The merged gene subset that was selected by the GBPSO-SVM algorithm was able to enhance the classification accuracy.
A Study On the Optoelectronic Parameters of Natural Dyes Extracted from Beetroot, Cabbage, Walnut, and Henna for Potential Applications in Organic Electronics

Amin PO, Muhammadsharif FF, Saeed SR, Sulaiman K

J Fluoresc, 2022 Jan;32(1):203-213.
PMID: 34694548 DOI: 10.1007/s10895-021-02837-7

In this work, the optoelectronic parameters of natural dyes extracted from beetroot, red cabbage, walnut leaves, and henna were comprehensively investigated, namely the optical energy gap (Eg), extinction coefficient (k), refractive index (n), dielectric constant ([Formula: see text], and optical conductivity ([Formula: see text]. Results showed a high refractive index, dielectric constant and optical conductivity ([Formula: see text] and [Formula: see text]) for the dye extracted from red cabbage, while minimum values of [Formula: see text] and [Formula: see text] were obtained for the henna dye. The transition type of the optical absorption of the dyes was found to be a direct allowed transition, which is taken place between the bonding and antibonding molecular energy levels. The reported results herein are essential in revealing the viability of these natural dyes for potential applications in organic electronics, including organic photovoltaics, photodiodes, and sensors.
A study on the spectroscopic, energy band, and optoelectronic properties of α,ω-dihexylsexithiophene/tris(8-hydroxyquinolinate) gallium blends; DH6T/Gaq3 composite system

Muhammad FF, Yahya MY, Ketuly KA, Muhammad AJ, Sulaiman K

Spectrochim Acta A Mol Biomol Spectrosc, 2016 Dec 05;169:144-51.
PMID: 27372510 DOI: 10.1016/j.saa.2016.06.031

In this work the optical response, spectroscopic behaviour, and optoelectronic properties of solution and solid state composite systems based on α,ω-dihexylsexithiophene/tris(8-hydroxyquinolinate) gallium (DH6T/Gaq3) are studied upon the incorporation of different molar percentages of Gaq3. UV-vis, PL, FTIR spectrophotometers and SEM technique were utilized to perform the investigations. The results showed a reduced energy band (Eg) (from 2.33eV to 1.83eV) and a broadened absorption spectrum for the blend system when 29.8% molar of Gaq3 was incorporated. These were attributed to the enhanced intermolecular interactions that are brought about by the increased strength of π-π overlap between the molecular moieties. A mathematical formula was developed to interpret the non-monotonic change occurred in Eg, while numerical calculations have been made to assign the type and nature of the electronic transitions governing the spectroscopic behaviour of the system. The results were elaborated and comprehensively discussed in terms of the exciton generation, energy band theory, molecular interactions, and spatial geometry.
Fulltext Employment of single-diode model to elucidate the variations in photovoltaic parameters under different electrical and thermal conditions

Muhammad FF, Yahya MY, Hameed SS, Aziz F, Sulaiman K, Rasheed MA, et al.

PLoS One, 2017;12(8):e0182925.
PMID: 28793325 DOI: 10.1371/journal.pone.0182925

In this research work, numerical simulations are performed to correlate the photovoltaic parameters with various internal and external factors influencing the performance of solar cells. Single-diode modeling approach is utilized for this purpose and theoretical investigations are compared with the reported experimental evidences for organic and inorganic solar cells at various electrical and thermal conditions. Electrical parameters include parasitic resistances (Rs and Rp) and ideality factor (n), while thermal parameters can be defined by the cells temperature (T). A comprehensive analysis concerning broad spectral variations in the short circuit current (Isc), open circuit voltage (Voc), fill factor (FF) and efficiency (η) is presented and discussed. It was generally concluded that there exists a good agreement between the simulated results and experimental findings. Nevertheless, the controversial consequence of temperature impact on the performance of organic solar cells necessitates the development of a complementary model which is capable of well simulating the temperature impact on these devices performance.
Fulltext Synthesis, spectroscopic, electrochemical and photophysical properties of high band gap polymers for potential applications in semi-transparent solar cells

Amin PO, Ketuly KA, Saeed SR, Muhammadsharif FF, Symes MD, Paul A, et al.

BMC Chem, 2021 Apr 21;15(1):25.
PMID: 33883016 DOI: 10.1186/s13065-021-00751-4

BACKGROUND: The design of new polymers able to filter the electromagnetic spectrum and absorb distinctly in the UV and high-energy part of visible spectrum is crucial for the development of semi-transparent solar cells. Herein, we report on the synthesis and spectroscopic, electrochemical, and photophysical characteristics of three new polymers, namely (i) Poly(triamterene-co-terephthalate), (ii) Poly[triamterene-co- 3-(2-pyridyl)-5,6-diphenyl-1,2,4-triazine-p,p'-disulfonamide], and (iii) Poly(5-hydroxyindole-2-carboxylate) that might show promise as materials for semi-transparent solar cells.
RESULTS: The energy band gap, refractive index, dielectric constant, and optical conductivity of the electron donor polymer, poly(triamterene-co-terephthalate), were determined to be 2.92 eV, 1.56, 2.44 and 2.43 × 104 S cm-1, respectively. The synthesized electron acceptor polymers showed a relatively high refractive index, dielectric constant, and optical conductivity. The presence of a direct allowed transition was confirmed between intermolecular energy bands of the polymers.
CONCLUSIONS: The polymers showed relatively high energy gap and deep HOMO levels, making them strong absorbers of photons in the UV region and high energy part of the visible region. The synthesized donor and acceptors performed well relative to P3HT and fullerenes due to the close match of the HOMO and LUMO levels. With further development, the polymers could be viable for use as the active layers of semi-transparent solar cells.
Fulltext Simple and efficient estimation of photovoltaic cells and modules parameters using approximation and correction technique

Muhammad FF, Karim Sangawi AW, Hashim S, Ghoshal SK, Abdullah IK, Hameed SS

PLoS One, 2019;14(5):e0216201.
PMID: 31048867 DOI: 10.1371/journal.pone.0216201

The behavior of solar cells and modules under various operational conditions can be determined effectively when their intrinsic parameters are accurately estimated and used to simulate the current-voltage (I-V) characteristics. This work proposed a new computational approach based on approximation and correction technique (ACT) for simple and efficient extraction of solar cells and modules parameters from the single-diode model. In this technique, an approximated value of series resistance (Rs) was first derived and used to determine the initial value of parallel resistance (Rp). Later, the final corrected values of Rs and Rp were obtained by resubstituting their approximated values in a five-loop iteration using the manipulated equations. For rapid evaluation and validation of the proposed technique, a software application was also created using MATLAB program. The correctness and robustness of the proposed technique was validated on five types of solar cells and modules operated at varied temperatures and irradiances. The lowest RMSE value was achieved for RTC France (7.78937E-4) and PVM 752 GaAs (2.10497E-4) solar cell. The legitimacy of ACT extracted parameters was established using a simple yet competitive implementation approach wherein the performance of the developed technique was compared with several state-of-the-art methods recently reported in the literature.
Fulltext HDG-select: A novel GUI based application for gene selection and classification in high dimensional datasets

Hameed SS, Hassan R, Hassan WH, Muhammadsharif FF, Latiff LA

PLoS One, 2021;16(1):e0246039.
PMID: 33507983 DOI: 10.1371/journal.pone.0246039

The selection and classification of genes is essential for the identification of related genes to a specific disease. Developing a user-friendly application with combined statistical rigor and machine learning functionality to help the biomedical researchers and end users is of great importance. In this work, a novel stand-alone application, which is based on graphical user interface (GUI), is developed to perform the full functionality of gene selection and classification in high dimensional datasets. The so-called HDG-select application is validated on eleven high dimensional datasets of the format CSV and GEO soft. The proposed tool uses the efficient algorithm of combined filter-GBPSO-SVM and it was made freely available to users. It was found that the proposed HDG-select outperformed other tools reported in literature and presented a competitive performance, accessibility, and functionality.
Fulltext Analysis of DICOM Image Compression Alternative Using Huffman Coding

Rahmat RF, Andreas TSM, Fahmi F, Pasha MF, Alzahrani MY, Budiarto R

J Healthc Eng, 2019;2019:5810540.
PMID: 31316743 DOI: 10.1155/2019/5810540

Compression, in general, aims to reduce file size, with or without decreasing data quality of the original file. Digital Imaging and Communication in Medicine (DICOM) is a medical imaging file standard used to store multiple information such as patient data, imaging procedures, and the image itself. With the rising usage of medical imaging in clinical diagnosis, there is a need for a fast and secure method to share large number of medical images between healthcare practitioners, and compression has always been an option. This work analyses the Huffman coding compression method, one of the lossless compression techniques, as an alternative method to compress a DICOM file in open PACS settings. The idea of the Huffman coding compression method is to provide codeword with less number of bits for the symbol that has a higher value of byte frequency distribution. Experiments using different type of DICOM images are conducted, and the analysis on the performances in terms of compression ratio and compression/decompression time, as well as security, is provided. The experimental results showed that the Huffman coding technique has the capability to compress the DICOM file up to 1 : 3.7010 ratio and up to 72.98% space savings.