| 1. |
- Ali, Raja Hashim, 1985-, et al.
(författare)
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VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Motivation: MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. There are, however, sometimes practical diculties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Currently, multiple software are required to perform, e.g., convergence, mixing and interactive exploration of both continuous and tree parameters.Results: We have written a software called VMCMC to simplify post-processing of MCMC traces with, for example, automatic burn-in estimation. VMCMC can also be used both as a GUI-based application, supporting interactive exploration, and as a command-line tool suitable for automated pipelines. Availability: VMCMC is available for Java SE 6+ under the New BSD License. Executable jar les, tutorial manual and source code can be downloaded from https://bitbucket.org/rhali/visualmcmc/.
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| 2. |
- Fakhar-e-Alam, Muhammad, et al.
(författare)
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Sensitivity of A-549 human lung cancer cells to nanoporous zinc oxide conjugated with Photofrin
- 2012
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Ingår i: Lasers in Medical Science. - : Springer Verlag (Germany). - 0268-8921 .- 1435-604X. ; 27:3, s. 607-614
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Tidskriftsartikel (refereegranskat)abstract
- In the present study, we demonstrated the use of nanoporous zinc oxide (ZnO NPs) in photodynamic therapy. The ZnO NPs structure possesses a high surface to volume ratio due to its porosity and ZnO NPs can be used as an efficient photosensitizer carrier system. We were able to grow ZnO NPs on the tip of borosilicate glass capillaries (0.5 mu m diameter) and conjugated this with Photofrin for efficient intracellular drug delivery. The ZnO NPs on the capillary tip could be excited intracellularly with 240 nm UV light, and the resultant 625 nm red light emitted in the presence of Photofrin activated a chemical reaction that produced reactive oxygen species (ROS). The procedure was tested in A-549 cells and led to cell death within a few minutes. The morphological changes in necrosed cells were examined by microscopy. The viability of control and treated A-549 cells with the optimum dose of UV/visible light was assessed using the MTT assay, and ROS were detected using a fluorescence microscopy procedure.
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| 3. |
- Hashim, Ahmed, et al.
(författare)
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Pattern of novel psychoactive substance use among patients presented to the poison control centre of Ain Shams University Hospitals, Egypt : A cross-sectional study
- 2022
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Ingår i: Heliyon. - : Elsevier BV. - 2405-8440. ; 8:8
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Tidskriftsartikel (refereegranskat)abstract
- Background: Novel psychoactive substances (NPSs) are relatively new substances in the illicit drug market, notpreviously listed in the United Nations Office on Drugs and Crime (UNDOC). Strox and Voodoo are consideredsome of the most popular blends of NPS in the Egyptian drug market.Objectives: The current study was conducted to assess NPS's use pattern: Voodoo and Strox among acutelyintoxicated patients presented to the poison control center of Ain Shams University Hospitals (PCC- ASUH).Methods: A single center based cross-sectional study was carried out in the PCC-ASUH among acutely intoxicatedpatients presenting to the emergency department (ED) over four months (from January–April 2019. using apreviously adopted and validated Fahmy and El-Sherbini socioeconomic scale (SES). Data were presented asmean, median and range as appropriate. Both smoking and crowding indexes were calculated and presented aspreviously reported.Results: Fifty-one patients were presented to the ED of PCC-ASUH during the study period. A total of 96.1% (n ¼49) were males. The mean age was 25 7.5 years. The most common NPS used was Strox: 54.9% (n ¼ 28),followed by Voodoo: 27.4% (n ¼ 14). Neurological and gastrointestinal (GI) symptoms were the most frequentpresentations. The most common motive behind NPS use was the desire to give a trial of new psychoactivesubstances. The mean SES score was 35.1 13.17. Most patients have the preparatory as the highest education36.0% (n ¼ 18).Conclusions: NPS use is common among young males in preparatory education from different social classes,starting it most commonly as a means to experiencing a new high. Neurological and GI manifestations are themost common presenting symptoms of NPS intoxication.
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| 4. |
- Abdul Manan, Muhammad Marizwan, et al.
(författare)
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Road characteristics and environment factors associated with motorcycle fatal crashes in Malaysia
- 2018
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Ingår i: IATSS Research. - : Elsevier BV. - 0386-1112. ; 42:4, s. 207-220
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Tidskriftsartikel (refereegranskat)abstract
- This study aims to determine risk factors contributing to traffic crashes in 9,176 fatal cases involving motorcycle in Malaysia between 2010 and 2012. For this purpose, both multinomial and mixed models of motorcycle fatal crash outcome based on the number of vehicle involved are estimated. The corresponding model predicts the probability of three fatal crash outcomes: motorcycle single-vehicle fatal crash, motorcycle fatal crash involving another vehicle and motorcycle fatal crash involving two or more vehicles. Several road characteristic and environmental factors are considered including type of road in the hierarchy, location, road geometry, posted speed limit, road marking type, lighting, time of day and weather conditions during the fatal crash. The estimation results suggest that curve road sections, no road marking, smooth, rut and corrugation of road surface and wee hours, i.e. between 00.00. am to 6. am, increase the probability of motorcycle single-vehicle fatal crashes. As for the motorcycle fatal crashes involving multiple vehicles, factors such as expressway, primary and secondary roads, speed limit more than 70. km/h, roads with non-permissible marking, i.e. double lane line and daylight condition are found to cause an increase the probability of their occurrence. The estimation results also suggest that time of day (between 7. pm to 12. pm) has an increasing impact on the probability of motorcycle single-vehicle fatal crashes and motorcycle fatal crashes involving two or more vehicles. Whilst the multinomial logit model was found as more parsimonious, the mixed logit model is likely to capture the unobserved heterogeneity in fatal motorcycle crashes based on the number of vehicles involved due to the underreporting data with two random effect parameters including 70. km/h speed limit and double lane line road marking.
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| 5. |
- Ali, Raja Hashim, 1985-, et al.
(författare)
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GenFamClust : an accurate, synteny-aware and reliable homology inference algorithm
- 2016
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- Background: Homology inference is pivotal to evolutionary biology and is primarily based on significant sequence similarity, which, in general, is a good indicator of homology. Algorithms have also been designed to utilize conservation in gene order as an indication of homologous regions. We have developed GenFamClust, a method based on quantification of both gene order conservation and sequence similarity. Results: In this study, we validate GenFamClust by comparing it to well known homology inference algorithms on a synthetic dataset. We applied several popular clustering algorithms on homologs inferred by GenFamClust and other algorithms on a metazoan dataset and studied the outcomes. Accuracy, similarity, dependence, and other characteristics were investigated for gene families yielded by the clustering algorithms. GenFamClust was also applied to genes from a set of complete fungal genomes and gene families were inferred using clustering. The resulting gene families were compared with a manually curated gold standard of pillars from the Yeast Gene Order Browser. We found that the gene-order component of GenFamClust is simple, yet biologically realistic, and captures local synteny information for homologs. Conclusions: The study shows that GenFamClust is a more accurate, informed, and comprehensive pipeline to infer homologs and gene families than other commonly used homology and gene-family inference methods.
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| 6. |
- Ali, Raja Hashim, et al.
(författare)
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Quantitative synteny scoring improves homology inference and partitioning of gene families
- 2013
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Ingår i: BMC Bioinformatics. - : BioMed Central. - 1471-2105. ; 14, s. S12-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Clustering sequences into families has long been an important step in characterization of genes and proteins. There are many algorithms developed for this purpose, most of which are based on either direct similarity between gene pairs or some sort of network structure, where weights on edges of constructed graphs are based on similarity. However, conserved synteny is an important signal that can help distinguish homology and it has not been utilized to its fullest potential. Results: Here, we present GenFamClust, a pipeline that combines the network properties of sequence similarity and synteny to assess homology relationship and merge known homologs into groups of gene families. GenFamClust identifies homologs in a more informed and accurate manner as compared to similarity based approaches. We tested our method against the Neighborhood Correlation method on two diverse datasets consisting of fully sequenced genomes of eukaryotes and synthetic data. Conclusions: The results obtained from both datasets confirm that synteny helps determine homology and GenFamClust improves on Neighborhood Correlation method. The accuracy as well as the definition of synteny scores is the most valuable contribution of GenFamClust.
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| 7. |
- Ali, Raja Hashim, et al.
(författare)
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VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces
- 2017
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Ingår i: Bmc Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- Background: MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. There are, however, sometimes practical difficulties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Currently, multiple software are required to perform, e.g., convergence, mixing and interactive exploration of both continuous and tree parameters. Results: We have written a software called VMCMC to simplify post-processing of MCMC traces with, for example, automatic burn-in estimation. VMCMC can also be used both as a GUI-based application, supporting interactive exploration, and as a command-line tool suitable for automated pipelines. Conclusions: VMCMC is a free software available under the New BSD License. Executable jar files, tutorial manual and source code can be downloaded from https://bitbucket. org/rhali/visualmcmc/.
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| 8. |
- Berron, David, et al.
(författare)
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A remote digital memory composite to detect cognitive impairment in memory clinic samples in unsupervised settings using mobile devices
- 2024
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Ingår i: npj Digital Medicine. - 2398-6352. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Remote monitoring of cognition holds the promise to facilitate case-finding in clinical care and the individual detection of cognitive impairment in clinical and research settings. In the context of Alzheimer’s disease, this is particularly relevant for patients who seek medical advice due to memory problems. Here, we develop a remote digital memory composite (RDMC) score from an unsupervised remote cognitive assessment battery focused on episodic memory and long-term recall and assess its construct validity, retest reliability, and diagnostic accuracy when predicting MCI-grade impairment in a memory clinic sample and healthy controls. A total of 199 participants were recruited from three cohorts and included as healthy controls (n = 97), individuals with subjective cognitive decline (n = 59), or patients with mild cognitive impairment (n = 43). Participants performed cognitive assessments in a fully remote and unsupervised setting via a smartphone app. The derived RDMC score is significantly correlated with the PACC5 score across participants and demonstrates good retest reliability. Diagnostic accuracy for discriminating memory impairment from no impairment is high (cross-validated AUC = 0.83, 95% CI [0.66, 0.99]) with a sensitivity of 0.82 and a specificity of 0.72. Thus, unsupervised remote cognitive assessments implemented in the neotiv digital platform show good discrimination between cognitively impaired and unimpaired individuals, further demonstrating that it is feasible to complement the neuropsychological assessment of episodic memory with unsupervised and remote assessments on mobile devices. This contributes to recent efforts to implement remote assessment of episodic memory for case-finding and monitoring in large research studies and clinical care.
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| 9. |
- Kashif, Muhammad, et al.
(författare)
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Structural and impedance spectroscopy study of Al-doped ZnO nanorods grown by sol-gel method
- 2012
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Ingår i: Microelectronics international. - : Emerald. - 1356-5362 .- 1758-812X. ; 29:3, s. 131-135
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Tidskriftsartikel (refereegranskat)abstract
- Purpose - The purpose of this paper is to investigate the electrical transport mechanism of the Al-doped ZnO nanorods at different temperatures by employing impedance spectroscopy. less thanbrgreater than less thanbrgreater thanDesign/methodology/approach - Al-doped ZnO nanorods were grown on silicon substrate using step sol-gel method. For the seed solution preparation Zinc acetate dihydrate, 2-methoxyethanol, monoethanolannine and aluminum nitrite nano-hydrate were used as a solute, solvent, stabilizer and dopant, respectively. Prior to the deposition, P-type Si (100) wafer was cut into pieces of 1 cm x 2 cm. The samples were then cleaned in an ultrasonic bath with acetone, ethanol, and de-ionized (DI) water for 5 min. The prepared seed solution was coated on silicon substrate using spin coater at spinning speed of 3000 rpm for 30s and then dried at 250 degrees C for 10 min followed by annealing at 550 degrees C for 1 h. The hydrothermal growth was carried out in a solution of zinc nitrate hexahydrate (0.025M), Hexamethyltetramine (0.025M) in DI water. less thanbrgreater than less thanbrgreater thanFindings - Al-doped ZnO nanorods were characterized using scanning electron microscope (SEM), X-ray diffraction (XRD) and impedance spectroscopy. The impedance measurements were carried out at various temperatures (100 degrees C-325 degrees C). The impedance results showed that temperature has great influence on the impedance; the impedance value decreased as the temperature increased. This decrement is attributed to the increase of the mobility of the defects, especially the oxygen vacancies. The surface morphology of the samples was measured by SEM and X-ray diffraction. The SEM images show that the high density of Al-doped ZnO nanorods covers the silicon substrate, whereas the XRD pattern shows the (002) crystal orientation. less thanbrgreater than less thanbrgreater thanOriginality/value - This paper demonstrates the electron transport mechanism of Al-doped ZnO nanorods, at different temperatures, to understand the charge transport model.
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| 10. |
- Mostafa, Reham R., et al.
(författare)
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Enhanced COOT optimization algorithm for Dimensionality Reduction
- 2022
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Ingår i: 2022 FIFTH INTERNATIONAL CONFERENCE OF WOMEN IN DATA SCIENCE AT PRINCE SULTAN UNIVERSITY (WIDS-PSU 2022). - : IEEE. - 9781665408127 - 9781665408134 ; , s. 43-48
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Konferensbidrag (refereegranskat)abstract
- COOT algorithm is a recent metaheuristic algorithm that simulates American coot birds when moving in the sea. However, the COOT algorithm like other metaheuristic techniques may be stuck in local regions. In this study, a modified COOT algorithm called (mCOOT) is presented which is based on 2 techniques: Opposition-based Learning (OBL) & Orthogonal Learning to overcome these limitations. Moreover, to test the novel algorithm called mCOOT, we apply it to the dimensionality reduction problem using 9 UCI datasets and compare it with the original algorithm and 3 other ones. Results prove the effectivness and superiority of the proposed algorithm in solving feature selection in terms of classification accuracy and selected features numbers.
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