| 1. |
- Abidi, Syed Hani, et al.
(författare)
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Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan
- 2021
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: In April 2019, an HIV-1 outbreak among children occurred in Larkana, Pakistan, affecting more than a thousand children. It was assumed that the outbreak originated from a single source, namely a doctor at a private health facility. In this study, we performed subtype distribution, phylogenetic and drug-resistance analysis of HIV-1 sequences from 2019 outbreak in Larkana, Pakistan. Methods: A total of 401 blood samples were collected between April–June 2019, from children infected with HIV-1 aged 0–15 years recruited into a case-control study to investigate the risk factors for HIV-1 transmission. Partial HIV-1 pol sequences were generated from 344 blood plasma samples to determine HIV-1 subtype and drug resistance mutations (DRM). Maximum-likelihood phylogenetics based on outbreak and reference sequences was used to identify transmission clusters and assess the relationship between outbreak and key population sequences between and within the determined clusters. Bayesian analysis was employed to identify the time to the most recent common recent ancestor (tMRCA) of the main Pakistani clusters. Results: The HIV-1 circulating recombinant form (CRF) 02_AG and subtype A1 were most common among the outbreak sequences. Of the treatment-naïve participants, the two most common mutations were RT: E138A (8%) and RT: K219Q (8%). Four supported clusters within the outbreak were identified, and the median tMRCAs of the Larkana outbreak sequences were estimated to 2016 for both the CRF02_AG and the subtype A1 clusters. Furthermore, outbreak sequences exhibited no phylogenetic mixing with sequences from other high-risk groups of Pakistan. Conclusion: The presence of multiple clusters indicated a multi-source outbreak, rather than a single source outbreak from a single health practitioner as previously suggested. The multiple introductions were likely a consequence of ongoing transmission within the high-risk groups of Larkana, and it is possible that the so-called Larkana strain was introduced into the general population through poor infection prevention control practices in healthcare settings. The study highlights the need to scale up HIV-1 prevention programmes among key population groups and improving infection prevention control in Pakistan.
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| 2. |
- Ahsan, Hajra, et al.
(författare)
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Photocatalysis and adsorption kinetics of azo dyes by nanoparticles of nickel oxide and copper oxide and their nanocomposite in an aqueous medium
- 2022
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Azo dyes are recalcitrant organic pollutants present in textile industry effluents. Conventional treatment methods to remove them come with a range of disadvantages. Nanoparticles and their nanocomposites offer more efficient, less expensive and easy to handle wastewater treatment alternative. Methods. In this study, nanoparticles of nickel oxide (NiO-NPs), copper oxide (CuO-NPs) and their nanocomposite (NiO/CuO-NC) were synthesized using co- precipitation method. The functional groups present on the surface of synthesized nanomaterials were verified using Fourier-transform infrared spectroscopy (FTIR). Surface morphology was assessed using scanning electron microscopy (SEM) whereas purity, shape and size of the crystallite were determined using X-ray diffraction (XRD) technique. The potential of these nanomaterials to degrade three dyes i.e., Reactive Red-2 (RR-2), Reactive Black-5 (RB-5) and Orange II sodium salt (OII) azo dyes, was determined in an aqueous medium under visible light (photocatalysis). The photodegradation effectiveness of all nanomaterials was evaluated under different factors like nanomaterial dose (0.02-0.1 g 10 mL-1), concentration of dyes (20-100 mg L-1), and irradiation time (60-120 min). They were also assessed for their potential to adsorb RR-2 and OII dyes. Results. Results revealed that at optimum concentration (60 mgL-1) of RR-2, RB-5, and OII dyes, NiO-NPs degraded 90, 82 and 83%, CuO-NPs degraded 49, 34, and 44%, whereas the nanocomposite NiO/CuO-NC degraded 92, 93, and 96% of the said dyes respectively. The nanomaterials were categorized as the efficient degraders of the dyes in the order: NiO/CuO-NC > NiO-NPs > CuO-NPs. The highest degradation potential shown by the nanocomposite was attributed to its large surface area, small particles size, and quick reactions which were proved by advance analytical techniques. The equilibrium and kinetic adsorption of RR-2 and OII on NiO-NPs, CuO-NPs, and NiO/CuO-NC were well explained with Langmuir and Pseudo second order model, respectively (R2 ≥0.96). The maximum RR-2 adsorption (103 mg/g) was obtained with NiO/CuO-NC. It is concluded that nanocomposites are more efficient and promising for the dyes degradation from industrial wastewater as compared with dyes adsorption onto individual NPs. Thus, the nanocomposite NiO/CuO-NC can be an excellent candidate for photodegradation as well as the adsorption of the dyes in aqueous media.
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| 3. |
- Asadi, Shahla, et al.
(författare)
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Determinants of Intention to Use Simulation-Based Learning in Computers and Networking Courses : An ISM and MICMAC Analysis
- 2024
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Ingår i: IEEE transactions on engineering management. - : IEEE. - 0018-9391 .- 1558-0040. ; 71, s. 6015-6030
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Tidskriftsartikel (refereegranskat)abstract
- Simulation-based learning (SBL) presents a wide variety of opportunities to practice complex computer and networking skills in higher education, employing various platforms to enhance educational outcomes. The integration of SBL tools in teaching computer networking courses is useful for both instructors and learners. Furthermore, the increasing importance of SBL in higher education highlights the necessity to further explore the factors that affect the adoption of SBL technologies, particularly in the field of computer networking courses. Despite these advantages, minimal effort has been made to examine the factors that impact instructors' intentions to use SBL tools for computers and networking courses. The main objective of this study is to examine the factors that affect instructors' intentions to utilize SBL tools in computer networking courses offered by higher education institutions. By employing Interpretive structural modeling (ISM) and Matriced' Impacts Croise's Multiplication Appliquee a UN Classement (MICMAC) analysis, the research attempts to provide an in-depth understanding of the interdependencies and hierarchical associations among twelve identified factors. Results showed that system quality, self-efficacy, technological knowledge, and information quality have high driving power. This study offers valuable perspectives for higher education institutions and for upcoming empirical studies and aids in comprehending the advantages of using SBL tools in teaching and higher education.
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| 4. |
- Bernchou, Uffe, et al.
(författare)
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End-to-end validation of the geometric dose delivery performance of MR linac adaptive radiotherapy
- 2021
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Ingår i: Physics in Medicine and Biology. - : Institute of Physics Publishing (IOPP). - 0031-9155 .- 1361-6560. ; 66:4
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Tidskriftsartikel (refereegranskat)abstract
- The clinical introduction of hybrid magnetic resonance (MR) guided radiotherapy (RT) delivery systems has led to the need to validate the end-to-end dose delivery performance on such machines. In the current study, an MR visible phantom was developed and used to test the spatial deviation between planned and delivered dose at two 1.5 T MR linear accelerator (MR linac) systems, including pre-treatment imaging, dose planning, online imaging, image registration, plan adaptation, and dose delivery. The phantom consisted of 3D printed plastic and MR visible silicone rubber. It was designed to minimise air gaps close to the radiochromic film used as a dosimeter. Furthermore, the phantom was designed to allow submillimetre, reproducible positioning of the film in the phantom. At both MR linac systems, 54 complete adaptive, MR guided RT workflow sessions were performed. To test the dose delivery performance of the MR linac systems in various adaptive RT (ART) scenarios, the sessions comprised a range of systematic positional shifts of the phantom and imaging or plan adaptation conditions. In each workflow session, the positional translation between the film and the adaptive planned dose was determined. The results showed that the accuracy of the MR linac systems was between 0.1 and 0.9 mm depending on direction. The highest mean deviance observed was in the posterior-anterior direction, and the direction of the error was consistent between centres. The precision of the systems was related to whether the workflow utilized the internal image registration algorithm of the MR linac. Workflows using the internal registration algorithm led to a worse precision (0.2-0.7 mm) compared to workflows where the algorithm was decoupled (0.2 mm). In summary, the spatial deviation between planned and delivered dose of MR-guided ART at the two MR linac systems was well below 1 mm and thus acceptable for clinical use.
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| 5. |
- Kügele, Malin, et al.
(författare)
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Surface guided radiotherapy (SGRT) improves breast cancer patient setup accuracy
- 2019
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Ingår i: Journal of Applied Clinical Medical Physics. - : Wiley. - 1526-9914. ; , s. 61-68
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The purpose of the study was to investigate if surface guided radiotherapy (SGRT) can decrease setup deviations for tangential and locoregional breast cancer patients compared to conventional laser-based setup (LBS). Materials and Methods: Both tangential (63 patients) and locoregional (76 patients) breast cancer patients were enrolled in this study. For LBS, the patients were positioned by aligning skin markers to the room lasers. For the surface based setup (SBS), an optical surface scanning system was used for daily setup using both single and three camera systems. To compare the two setup methods, the patient position was evaluated using verification imaging (field images or orthogonal images). Results: For both tangential and locoregional treatments, SBS decreased the setup deviation significantly compared to LBS (P < 0.01). For patients receiving tangential treatment, 95% of the treatment sessions were within the clinical tolerance of ≤ 4 mm in any direction (lateral, longitudinal or vertical) using SBS, compared to 84% for LBS. Corresponding values for patients receiving locoregional treatment were 70% and 54% for SBS and LBS, respectively. No significant difference was observed comparing the setup result using a single camera system or a three camera system. Conclusions: Conventional laser-based setup can with advantage be replaced by surface based setup. Daily SGRT improves patient setup without additional imaging dose to breast cancer patients regardless if a single or three camera system was used.
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| 6. |
- Mahmood, Aimen, et al.
(författare)
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CNN-HMM Model for Real Time DGA Categorization
- 2023
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Ingår i: PROCEEDINGS OF THE 20TH INTERNATIONAL CONFERENCE ON SECURITY AND CRYPTOGRAPHY, SECRYPT 2023. - : INSTICC. ; , s. 822-829
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Konferensbidrag (refereegranskat)abstract
- To remotely control the target machine, hackers manage to establish a connection between victim and their Command and Control server(C2). In order to hide their C2 they generate domain names algorithmically. Such algorithms are called Domain Generation algorithms(DGA). These algorithmically generated domain names are either gibberish as the characters are generated and concatenated randomly, or pure dictionary words or the combination of the two. This paper presents an algorithm that classifies the DGA running on a compromised system either as gibberish, dictionary oriented or the mixed one, in real time. The proposed algorithm consists of two distinct modules i) Network forensics to detect the DGA ii) Classification of the DGA using the combination of Hidden Markov Model and Convolution Neural Network in real time. The algorithm is trained and tested against more than 0.21 million samples taken from more than 50 different DGAs. The algorithm gives as good as 99% accuracy for all types of DGAs. In addition it can detect zero day DGA as well as multiple DGAs running on a system.
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| 7. |
- Speight, Richard, et al.
(författare)
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IPEM Topical Report : an international IPEM survey of MRI use for external beam radiotherapy treatment planning
- 2021
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Ingår i: Physics in Medicine and Biology. - : Institute of Physics (IOP). - 0031-9155 .- 1361-6560. ; 66:7
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Tidskriftsartikel (refereegranskat)abstract
- Introduction/Background: Despite growing interest in magnetic resonance imaging (MRI), integration in external beam radiotherapy (EBRT) treatment planning uptake varies globally. In order to understand the current international landscape of MRI in EBRT a survey has been performed in 11 countries. This work reports on differences and common themes identified.Methods: A multi-disciplinary Institute of Physics and Engineering in Medicine working party modified a survey previously used in the UK to understand current practice using MRI for EBRT treatment planning, investigate how MRI is currently used and managed as well as identify knowledge gaps. It was distributed electronically within 11 countries: Australia, Belgium, Denmark, Finland, France, Italy, the Netherlands, New Zealand, Sweden, the UK and the USA.Results: The survey response rate within the USA was <1% and hence these results omitted from the analysis. In the other 10 countries the survey had a median response rate of 77% per country. Direct MRI access, defined as either having a dedicated MRI scanner for radiotherapy (RT) or access to a radiology MRI scanner, varied between countries. France, Italy and the UK reported the lowest direct MRI access rates and all other countries reported direct access in ≥82% of centres. Whilst ≥83% of centres in Denmark and Sweden reported having dedicated MRI scanners for EBRT, all other countries reported ≤29%. Anatomical sites receiving MRI for EBRT varied between countries with brain, prostate, head and neck being most common. Commissioning and QA of image registration and MRI scanners varied greatly, as did MRI sequences performed, staffing models and training given to different staff groups. The lack of financial reimbursement for MR was a consistent barrier for MRI implementation for RT for all countries and MR access was a reported important barrier for all countries except Sweden and Denmark.Conclusion: No country has a comprehensive approach for MR in EBRT adoption and financial barriers are present worldwide. Variations between countries in practice, equipment, staffing models, training, QA and MRI sequences have been identified, and are likely to be due to differences in funding as well as a lack of consensus or guidelines in the literature. Access to dedicated MR for EBRT is limited in all but Sweden and Denmark, but in all countries there are financial challenges with ongoing per patient costs. Despite these challenges, significant interest exists in increasing MR guided EBRT planning over the next 5 years.
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