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Fulltext In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms

Filho JAF, de Brito LS, Leão AP, Alves AA, Formighieri EF, Júnior MTS

Bioinform Biol Insights, 2017;11:1177932217702388.
PMID: 28469420 DOI: 10.1177/1177932217702388

Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v.1, Embrapa, unpublished; v.8, Malaysian Palm Oil Board [MPOB], public), Elaeis guineensis (African oil palm, v.5, MPOB, public), and Phoenix dactylifera (date palm). The estimated total coverage of TEs was 50.96% (523 572 kb) and 42.31% (593 463 kb), 39.41% (605 015 kb), and 33.67% (187 361 kb), respectively. A total of 155 726 microsatellite loci were identified in the genomes of oil and date palms. This is the first detailed description of repeats in the genomes of oil and date palms. A relatively high diversity and abundance of TEs were found in the genomes, opening a range of further opportunities for applied research in these genera. The development of molecular markers (mainly simple sequence repeat), which may be immediately applied in breeding programs of those species to support the selection of superior genotypes and to enhance knowledge of the genetic structure of the breeding and natural populations, is the most notable opportunity.

Matched MeSH terms: Software
Fulltext Selection of various coagulants for sugar industry waste water treatment

Nur Shazweena Samsudin, Jami, Mohammed Saedi, Kabbashi, Nassereldeen Ahmed

Biological and Natural Resources Engineering Journal, 2019;2(1):1-9.
MyJurnal

sugar industry is one of the industries that produce a high amount of
pollutant since its wastewater contains high amount of organic material, biochemical
oxygen demand (bod) and chemical oxygen demand (cod). if this waste is
discharged without a proper treatment into the watercourse, it can cause problem to aquatic
life and environment. for the primary treatment process, sugar wastewater can be treated
by using chemical precipitation method which involves coagulation process. currently,
ferric chloride has been used as the coagulant but it consumes more alkalinity and
corrosive. in this study, the suitable coagulant to be used to treat the wastewater from sugar
industry and the optimum conditions to achieve high percentage removal of cod was
determined. the characteristic of the wastewater was firstly determined. then, the most
suitable coagulant to be used for the treatment was studied by determining their efficiency
to reduce cod and tss in the wastewater at different dosages. aluminium sulphate
(alum), ferric chloride and polyaluminium chloride (pac) were chosen to be studied for
suitable coagulant. The optimum condition of the coagulant (ph, coagulant dosage, fast
mixing speed) was determined by using design expert software. results showed that alum
can be used to effectively remove 42.9% of cod and 100% of tss at high dosage (50
mg/l). the optimum condition of alum was at ph 5.2, 10 mg/l of alum and 250 rpm of
mixing speed. this shows that at optimum condition, alum can be used to treat wastewater
from sugar industry.

Matched MeSH terms: Software
Fulltext Effect of curcumin dose, treatment duration and intervention type on tumor inhibition in animal models: a systematic literature review using meta-analysis techniques

Arina Nasruddin, Azura Amid

Biological and Natural Resources Engineering Journal, 2019;2(2):1-12.
MyJurnal

Curcuma longa L. uses widely as a traditional medicine especially in India and China for the treatment of diabetic wounds, inflammatory, hepatic, and digestive disorders. These effects lead to the research of this plant for the treatment of chronic diseases. To assess the tumour inhibition effect of curcumin in animal models by integrating various studies into a systematic literature review (SLR) and meta-analysis. Studies of curcumin treatment in tumor-induced animal models were searched in electronic databases. The assessment of the quality of the studies included and the tumor inhibition effect used SYRCLE’s Risk of Bias tool and Review Manager (The Cochrane Collaboration) software. From the 732 articles identified, only 11 studies met the selection criteria and included in the analysis. Curcumin significantly inhibited the tumor volume in the animal models in overall, and the subgroup analyses revealed that high dose, long-duration curcumin treatment, and intervention by injection have a more significant effect compared to the opposite group. Curcumin was effective in inhibiting tumor volume in animal models. The study quality and heterogeneity of the meta-analysis can probably be improved if a larger-scale bases of animal models and a well-designed study were available

Matched MeSH terms: Software
Fulltext Effects of daidzin and analogue of ganoderma sinense on bacterially-expressed human hexokinase isoform 2 for anti-dengue drug design

Nur Atikah Asman, Suriyea Tanbin, Fazia Adyani Ahmad Fuad

Biological and Natural Resources Engineering Journal, 2020;3(2):27-34.
MyJurnal

Dengue disease, which is caused by dengue virus (DENV) has been a major worldwide concern, with increased number of cases each year. Currently, there are no specific medications to treat the disease. Hence, there is a dire need to develop novel drugs for disease treatment. Glycolysis is a metabolic pathway that serves as the main source of energy for DENV replication and targeting the pathway is one of the ideal approach to discover new anti-DENV drugs. This paper focuses on the inhibition of human hexokinase isoform 2 (HK2) enzyme, which is one of the important enzymes in glycolysis, in the quest to disrupt DENV replication. In order to search for potential inhibitors, two methods were conducted, which are ligand-based screening and structure-based screening approaches. Docking of Daidzin , which was derived from Kudzu, a Japanese plant, into the active site of HK2 has shown the nearest binding affinity score (-7.94 kcal/mol) to glucose‘s (GLC), which is -8.15 kcal/mol. Meanwhile, Ethyl (2R)-2-[[3-[2-[(4-methylbenzoyl) amino]ethyl]-[1,2,4]triazolo[4,3-b]pyridazin-6-yl]sulfanyl]butanoate (Ethyl 2(R)), a compound which is the analogue of ((22E, 24R)-6β-methoxyergosta-7, 9(11), 22-triene-3β,5α-diol) or compound 2 from Ganoderma sinense obtained from ligand-based screening was also docked into the binding site of HK2, showing a binding affinity score of -8.43 kcal/mol. Both docking was conducted by using AutoDock4 software at virtual screening phase. These compounds were further analysed in an inhibition assay to determine the effects of these potential naturally-derived inhibitors on the activity of HK2. The outcome from the inhibition studies showed that both compounds exhibited substantial inhibition on the activity of HK2 enzyme, where Daidzin, at 0.5 mM, resulted in HK2 remaining activity of 87.28%, while Ethyl (2R) resulted in 70.09% of HK2 remaining activity at 0.5 mM concentration. The results also indicate that as the concentration of these compounds increased, the percentage of remaining enzyme activity decreased. In conclusion, this study has served as a platform for the development of anti-dengue drugs based on naturally-derived compounds, which is anticipated to be a safer option for dengue treatment.

Matched MeSH terms: Software
Fulltext Evidence-based gene models for structural and functional annotations of the oil palm genome

Chan KL, Tatarinova TV, Rosli R, Amiruddin N, Azizi N, Halim MAA, et al.

Biol. Direct, 2017 Sep 08;12(1):21.
PMID: 28886750 DOI: 10.1186/s13062-017-0191-4

BACKGROUND: Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools.
RESULTS: Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures.
CONCLUSIONS: We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database ( http://palmxplore.mpob.gov.my ), will provide important resources for studies on the genomes of oil palm and related crops.
REVIEWERS: This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov.

Matched MeSH terms: Software
Mechanical behaviour of in-situ chondrocytes subjected to different loading rates: a finite element study

Moo EK, Herzog W, Han SK, Abu Osman NA, Pingguan-Murphy B, Federico S

Biomech Model Mechanobiol, 2012 Sep;11(7):983-93.
PMID: 22234779 DOI: 10.1007/s10237-011-0367-2

Experimental findings indicate that in-situ chondrocytes die readily following impact loading, but remain essentially unaffected at low (non-impact) strain rates. This study was aimed at identifying possible causes for cell death in impact loading by quantifying chondrocyte mechanics when cartilage was subjected to a 5% nominal tissue strain at different strain rates. Multi-scale modelling techniques were used to simulate cartilage tissue and the corresponding chondrocytes residing in the tissue. Chondrocytes were modelled by accounting for the cell membrane, pericellular matrix and pericellular capsule. The results suggest that cell deformations, cell fluid pressures and fluid flow velocity through cells are highest at the highest (impact) strain rate, but they do not reach damaging levels. Tangential strain rates of the cell membrane were highest at the highest strain rate and were observed primarily in superficial tissue cells. Since cell death following impact loading occurs primarily in superficial zone cells, we speculate that cell death in impact loading is caused by the high tangential strain rates in the membrane of superficial zone cells causing membrane rupture and loss of cell content and integrity.

Matched MeSH terms: Software
Fulltext Telepointer technology in telemedicine: a review

Abdul Karim R, Zakaria NF, Zulkifley MA, Mustafa MM, Sagap I, Md Latar NH

Biomed Eng Online, 2013;12:21.
PMID: 23496940 DOI: 10.1186/1475-925X-12-21

Telepointer is a powerful tool in the telemedicine system that enhances the effectiveness of long-distance communication. Telepointer has been tested in telemedicine, and has potential to a big influence in improving quality of health care, especially in the rural area. A telepointer system works by sending additional information in the form of gesture that can convey more accurate instruction or information. It leads to more effective communication, precise diagnosis, and better decision by means of discussion and consultation between the expert and the junior clinicians. However, there is no review paper yet on the state of the art of the telepointer in telemedicine. This paper is intended to give the readers an overview of recent advancement of telepointer technology as a support tool in telemedicine. There are four most popular modes of telepointer system, namely cursor, hand, laser and sketching pointer. The result shows that telepointer technology has a huge potential for wider acceptance in real life applications, there are needs for more improvement in the real time positioning accuracy. More results from actual test (real patient) need to be reported. We believe that by addressing these two issues, telepointer technology will be embraced widely by researchers and practitioners.

Matched MeSH terms: Software
Synthesis, SAR elucidations and molecular docking study of newly designed isatin based oxadiazole analogs as potent inhibitors of thymidine phosphorylase

Javid MT, Rahim F, Taha M, Nawaz M, Wadood A, Ali M, et al.

Bioorg Chem, 2018 09;79:323-333.
PMID: 29803079 DOI: 10.1016/j.bioorg.2018.05.011

Thymidine phosphorylase is an enzyme involved in pyrimidine salvage pathway that is identical to platelet-derived endothelial cell growth factor (PD-ECGF) and gliostatin. It is enormously up regulated in a variety of solid tumors. Furthermore, surpassing of TP level protects tumor cells from apoptosis and helps cell survival. Thus TP is identified as a prime target for developing novel anticancer therapies. A new class of exceptionally potent isatin based oxadiazole (1-30) has been synthesized and evaluated for thymidine phosphorylase inhibitory potential. All analogs showed potent thymidine phosphorylase inhibition when compared with standard 7-Deazaxanthine, 7DX (IC50 = 38.68 ± 1.12 µM). Molecular docking study was performed in order to determine the binding interaction of these newly synthesized compounds, which revealed that these synthesized compounds established stronger hydrogen bonding network with active site of residues as compare to the standard compound 7DX.

Matched MeSH terms: Software
13C NMR-based dereplication using MixONat software to decipher potent anti-cholinesterase compounds in Mesua lepidota bark

Leong ST, Liew SY, Khaw KY, Ahmad Hassali H, Richomme P, Derbré S, et al.

Bioorg Chem, 2023 Dec;141:106859.
PMID: 37742494 DOI: 10.1016/j.bioorg.2023.106859

A bio-assay guided fractionation strategy based on cholinesterase assay combined with 13C NMR-based dereplication was used to identify active metabolites from the bark of Mesua lepidota. Eight compounds were identified with the aid of the 13C NMR-based dereplication software, MixONat, i.e., sitosterol (1), stigmasterol (2), α-amyrin (3), friedelin (6), 3β-friedelinol (7), betulinic acid (9), lepidotol A (10) and lepidotol B (11). Further bio-assay guided isolation of active compounds afforded one xanthone, pyranojacareubin (12) and six coumarins; lepidotol A (10), lepidotol B (11), lepidotol E (13), lepidotin A (14), and lepidotin B (15), including a new Mammea coumarin, lepidotin C (16). All the metabolites showed strong to moderate butyrylcholinesterase (BChE) inhibition. Lepidotin B (15) exhibited the most potent inhibition towards BChE with a mix-mode inhibition profile and a Ki value of 1.03 µM. Molecular docking and molecular dynamics simulations have revealed that lepidotin B (15) forms stable interactions with key residues within five critical regions of BChE. These regions encompass residues Asp70 and Tyr332, the acyl hydrophobic pocket marked by Leu286, the catalytic triad represented by Ser198 and His438, the oxyanion hole (OH) constituted by Gly116 and Gly117, and the choline binding site featuring Trp82. To gauge the binding strength of lepidotin B (15) and to pinpoint pivotal residues at the binding interface, free energy calculations were conducted using the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) approach. This analysis not only predicted a favourable binding affinity for lepidotin B (15) but also facilitated the identification of significant residues crucial for the binding interaction.

Matched MeSH terms: Software
Fulltext Preliminary prediction of lipase 3D protein structure and function in Rhodococcus sp. NAM81 using bioinformatics approach

Hasdianty Abdullah, Mohd Fadzli Ahmad, Farah Aula Mohd Fauzi, Nor Suhaila Yaacob, Abdul Latif Ibrahim

Bioremediation Science and Technology Research, 2015;3(1):11-15.
MyJurnal

Protein function depends greatly on its structure. Based on this principle, it is vital to study the
protein structure in order to understand its function. This study attempts to build the predicted
model of lipase gene in Rhodococcus sp. NAM81 using homology modelling method. The
predicted structure was then used to investigate the function of protein through several
bioinformatic tools. The DNA sequence of lipase gene was obtained from the Rhodococcus sp.
NAM81 genome scaffold. Blastx analysis showed 100% identity to the target enzyme andthe
appropriate template for homology modelling was determined using Blastp analysis. The 3D
protein structure was built using two homology modelling software, EsyPred3D and Swiss
Model Server. Both structures built obtained LGScore of greater than 4, which means they are
extremely good models according to ProQ validation criteria. Both structures also satisfied the
Ramachandran plot structure validation analysis. The predicted structures were 100% matched
with each other when superimposed with DaliLite pairwise. This shows that both structure
validation servers agreed on the same model. Structure analysis using ProFunc had found seven
motifs and active sites that indicate similar function of this protein with other known proteins.
Thus, this study has successfully produced a good 3D protein structure for the target enzyme.

Matched MeSH terms: Software
Optimization of bioresource material from oil palm trunk core drying using microwave radiation; a response surface methodology application

Amouzgar P, Khalil HP, Salamatinia B, Abdullah AZ, Issam AM

Bioresour Technol, 2010 Nov;101(21):8396-401.
PMID: 20639118 DOI: 10.1016/j.biortech.2010.05.061

In this study optimization of drying oil palm trunk core lumber (OPTCL) biomass using microwave radiation was reported. Optimizing of the drying conditions using microwave, avoid burning, shrinkage and increasing the permeability of OPT was aimed to develop a new value added material. A set of experiments was designed by central composite design using response surface methodology (RSM) to statistically evaluate the findings. Three independent process variables including time (2-10 min), sample weight (300-1000 g) and input power (660-3300 W) were studied under the given conditions designed by Design Expert software. The results showed the effectiveness of microwave drying in reducing the time and better removal of moisture as compared to that of oven drying with no significant changes. Employing optimum conditions at 6.89 min of time with a microwave power set at 4 for a sample of 1000 g, predicting 14.62% of moisture content.

Matched MeSH terms: Software
A statistical experiment design approach for optimizing biodegradation of weathered crude oil in coastal sediments

Mohajeri L, Aziz HA, Isa MH, Zahed MA

Bioresour Technol, 2010 Feb;101(3):893-900.
PMID: 19773160 DOI: 10.1016/j.biortech.2009.09.013

This work studied the bioremediation of weathered crude oil (WCO) in coastal sediment samples using central composite face centered design (CCFD) under response surface methodology (RSM). Initial oil concentration, biomass, nitrogen and phosphorus concentrations were used as independent variables (factors) and oil removal as dependent variable (response) in a 60 days trial. A statistically significant model for WCO removal was obtained. The coefficient of determination (R(2)=0.9732) and probability value (P<0.0001) demonstrated significance for the regression model. Numerical optimization based on desirability function were carried out for initial oil concentration of 2, 16 and 30 g per kg sediment and 83.13, 78.06 and 69.92 per cent removal were observed respectively, compare to 77.13, 74.17 and 69.87 per cent removal for un-optimized results.

Matched MeSH terms: Software
Trends in digital image processing of isolated microalgae by incorporating classification algorithm

Chong JWR, Khoo KS, Chew KW, Ting HY, Show PL

Biotechnol Adv, 2023;63:108095.
PMID: 36608745 DOI: 10.1016/j.biotechadv.2023.108095

Identification of microalgae species is of importance due to the uprising of harmful algae blooms affecting both the aquatic habitat and human health. Despite this occurence, microalgae have been identified as a green biomass and alternative source due to its promising bioactive compounds accumulation that play a significant role in many industrial applications. Recently, microalgae species identification has been conducted through DNA analysis and various microscopy techniques such as light, scanning electron, transmission electron, and atomic force -microscopy. The aforementioned procedures have encouraged researchers to consider alternate ways due to limitations such as costly validation, requiring skilled taxonomists, prolonged analysis, and low accuracy. This review highlights the potential innovations in digital microscopy with the incorporation of both hardware and software that can produce a reliable recognition, detection, enumeration, and real-time acquisition of microalgae species. Several steps such as image acquisition, processing, feature extraction, and selection are discussed, for the purpose of generating high image quality by removing unwanted artifacts and noise from the background. These steps of identification of microalgae species is performed by reliable image classification through machine learning as well as deep learning algorithms such as artificial neural networks, support vector machines, and convolutional neural networks. Overall, this review provides comprehensive insights into numerous possibilities of microalgae image identification, image pre-processing, and machine learning techniques to address the challenges in developing a robust digital classification tool for the future.

Matched MeSH terms: Software
Fulltext Sleep belief factors among Diploma students in UiTM Sabah

Nowyannie Willie D. Tamsin, Norah Tuah, Mazalan Sarahintu, Herniza Roxanne Marcus

Borneo Akademika, 2019;3(1):20-29.
MyJurnal

University students are known to have different sleeping schedules. Students’ sleep difficulties will affect their health and their performances in studies. Sleep hygiene is a collection of healthy sleep habits that can improve one’s ability to fall asleep and stay asleep. It is considered to be imperative to treat sleep disturbance especially among university students. The aim of this study is to examine the sleep beliefs among the students of UiTM Sabah based on gender and academic performance. This study was conducted on Diploma students between March and July 2018. The respondents were randomly selected from Diploma students of all faculties in UiTM Sabah: Accounting, Business Management, Public Administration, Science, Planting Industry Management, Hotel Management, and Tourism Management. This paper is based on the Sleep Belief Scale questionnaire to assess the sleep hygiene awareness. Questionnaires were distributed using online survey. Findings of this study were analyzed using SPSS statistical software. The result of findings showed that the Sleep Incompatible Behaviours (drinking coffee, taking sleep medication, smoking before sleep) is the highest contributor of the students’ sleep hygiene and therefore it affects the sleep quality. While the Sleep Wake Cycle Behaviours (going to bed & waking up always at the same hour, going to bed two hours earlier than the habitual hour) and Thoughts and Attitude to Sleep (over thinking before sleep, trying to fall asleep without having a sleep sensation)also contributed to the sleep hygiene of the students but not as high as the Sleep Incompatible Behaviours. Based on the results of the findings, the counseling department of UiTM Sabah may organise an education program to create awareness among students about the intervention and prevention strategies as well as the incorrect beliefs about sleep.

Matched MeSH terms: Software
Fulltext Smartphone-based laser glucometer for non-invasive measurement of glucose level of diabetic patients

Tamrin, K.F., Adilah, A.N., Hamdi, M.M., Jong, R.P.

Borneo International Journal, 2018;1(1):27-32.
MyJurnal

A glucose meter (or glucometer) is a medical device for determining the approximate concentration of glucose in the
blood by pricking a finger to draw blood sample using a sharp needle. However, diabetic patient has quite slow level in
wound healing process which causes their fingers constantly in a state of wounded and exposed to bacteria. More
importantly, two main factors for the weakness of invasive technique is a painful process and cost often because constant
monitoring of glucose level is very expensive. The main objective of this research is to design and develop a non-invasive
optical measuring technique to measure body glucose level automatically and painlessly using a laser pointer and a
smartphone. Images captured by the smartphone is analysed using a Matlab software to determine the refractive index of
the urine sample. Calibration of the system is performed by correlating the results with that of the glucometer. Both
results compare well with R-squared value of 92.9%. The system can be potentially used for remote health and patient
monitoring.

Matched MeSH terms: Software
Fulltext Effect of artificial structures on shoreline profile of Selingan Island, Sandakan, Sabah, Malaysia

Chen, Nuo-Geng, Ejria Saleh, Yap, Tzuen-Kiat, Irwan Isnain

Borneo Journal of Marine Science and Aquaculture, 2018;2(1):9-15.
MyJurnal

Selingan Island off Sandakan, Sabah is a famous turtle nesting ground and a part of the Turtle Islands Park (TIP) within the Coral Triangle region of Malaysia. This small island faces the serious problem of beach erosion that is reducing the turtle nesting area. Sabah Parks deployed stone revetments in 2005, followed by placement of reef balls at the southern part of the Selingan Island in 2007 for protecting the shoreline. The objective of this study was to determine the effectiveness of these measures for shoreline protection. Shoreline changes were determined from satellite images, beach profiling and field observations. Satellite images from 2010 to 2016 were obtained from Google Earth Pro analyzed to examine the changes in the shape and size of the island with QGIS software. Beach profiling was performed in December 2017 at three sites and compared with the condition in 2011. The findings indicated that the shape of the island was squeezed towards the east where the reef balls were located. The size of the island has not changed much in 9 years after the deployment of the reef balls, but a high volume of sediments accumulated at the south due to the presence of shoreline protection. Generally, the man-made structures in Selingan Island are effective in trapping the sediment and providing more nesting area for turtles. It is recommended that the shoreline dynamics of the island should be regularly monitored for better understanding of the changes and taking appropriate actions.

Matched MeSH terms: Software
Fulltext Study of Ebola virus outbreak dynamics, impact of vaccination and other preventive measures on transmission control

Che Ismail Che Noh, Fox, Anthony William

Borneo Journal of Medical Sciences, 2018;12(2):9-18.
MyJurnal

Ebola virus disease (EVD) is an emerging and remerging zoonosis associated with high fatality rate, mainly caused by the Zaire Ebola virus (ZEBOV) and Sudan Ebola virus (SEBOV) strains. Approximately 20 epidemics of EVD have been documented mainly in Central African countries since 1976. Currently, there are no therapeutics agents and vaccines yet approved for EVD. However, several promising therapeutics and vaccines candidates are actively undergoing various phase of clinical development. This study aims to study the EVD dynamics and evaluate the potential impacts of vaccines and other preventive measures on EVD transmission control and significance of medical intervention on outcome of the disease. An initial branch chain model of EVD dynamics was built based on data obtained from previous study. Different epidemiological scenarios for EVD with impacts of intervention were simulated using Berkeley-Madonna Version 8.3.18 software. Every reduction in the exposure rate of EBV infection by 10% produces two- to five-fold improvement in protection against EVD. Transmission control is optimum when the rate of exposure to EBV infection is reduced below 1%. Optimal control of EVD transmission can be achieved through strategic implementation of successful vaccination programme, and other preventive measures as well as rapid delivery of supportive medical care.

Matched MeSH terms: Software
scGGAN: single-cell RNA-seq imputation by graph-based generative adversarial network

Huang Z, Wang J, Lu X, Mohd Zain A, Yu G

Brief Bioinform, 2023 Mar 19;24(2).
PMID: 36733262 DOI: 10.1093/bib/bbad040

Single-cell RNA sequencing (scRNA-seq) data are typically with a large number of missing values, which often results in the loss of critical gene signaling information and seriously limit the downstream analysis. Deep learning-based imputation methods often can better handle scRNA-seq data than shallow ones, but most of them do not consider the inherent relations between genes, and the expression of a gene is often regulated by other genes. Therefore, it is essential to impute scRNA-seq data by considering the regional gene-to-gene relations. We propose a novel model (named scGGAN) to impute scRNA-seq data that learns the gene-to-gene relations by Graph Convolutional Networks (GCN) and global scRNA-seq data distribution by Generative Adversarial Networks (GAN). scGGAN first leverages single-cell and bulk genomics data to explore inherent relations between genes and builds a more compact gene relation network to jointly capture the homogeneous and heterogeneous information. Then, it constructs a GCN-based GAN model to integrate the scRNA-seq, gene sequencing data and gene relation network for generating scRNA-seq data, and trains the model through adversarial learning. Finally, it utilizes data generated by the trained GCN-based GAN model to impute scRNA-seq data. Experiments on simulated and real scRNA-seq datasets show that scGGAN can effectively identify dropout events, recover the biologically meaningful expressions, determine subcellular states and types, improve the differential expression analysis and temporal dynamics analysis. Ablation experiments confirm that both the gene relation network and gene sequence data help the imputation of scRNA-seq data.

Matched MeSH terms: Software*
Identification of metabolic pathways using pathfinding approaches: a systematic review

Abd Algfoor Z, Shahrizal Sunar M, Abdullah A, Kolivand H

Brief Funct Genomics, 2017 03 01;16(2):87-98.
PMID: 26969656 DOI: 10.1093/bfgp/elw002

Metabolic pathways have become increasingly available for various microorganisms. Such pathways have spurred the development of a wide array of computational tools, in particular, mathematical pathfinding approaches. This article can facilitate the understanding of computational analysis of metabolic pathways in genomics. Moreover, stoichiometric and pathfinding approaches in metabolic pathway analysis are discussed. Three major types of studies are elaborated: stoichiometric identification models, pathway-based graph analysis and pathfinding approaches in cellular metabolism. Furthermore, evaluation of the outcomes of the pathways with mathematical benchmarking metrics is provided. This review would lead to better comprehension of metabolism behaviors in living cells, in terms of computed pathfinding approaches.

Matched MeSH terms: Software
Comparison between field experiment and PERSIST model simulation: dissipation of fenvalerate in a Malaysian agricultural soil

Ismail BS, Maznah Z

Bull Environ Contam Toxicol, 2005 Jun;74(6):1143-50.
PMID: 16158853
Matched MeSH terms: Software

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