| 1. |
- Qureshi, Tayyab, et al.
(författare)
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Structural and thermal investigation of lignocellulosic biomass conversion for enhancing sustainable imperative in progressive organic refinery paradigm for waste-to-energy applications
- 2024
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Ingår i: Environmental Research. - : Elsevier. - 0013-9351 .- 1096-0953. ; 246
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Tidskriftsartikel (refereegranskat)abstract
- The depletion of finite fossil fuel reserves and the severe environmental degradation resulting from human activities have compelled the expeditious development and application of sustainable waste to energy technologies. To encapsulate energy and environment in sustainability paradigm, bio waste based energy production is need to be forged in organic bio refinery setup. According to world bioenergy association, biomass can cover 50 % of the primary energy demand of the world. Therefore, the present study focuses on reforming the energy mix for a clean energy generation, where, sample composition of cotton stalk was acidified in dilute (5% wt.) hydrochloric acid (HCL) for analyzing material burnout patterns in biomass conversion systems utilized in organic bio refinery sector. Advanced thermochemical burning technique, which includes pyrolysis and combustion was applied at four different leaching times from 0 to 180 min under nitrogen environment from 0 degrees C to 500 degrees C and air from 500 degrees C to 900 degrees C, respectively. Different analyses including proximate, ultimate, gross calorific value (GCV), thermos-gravimetric, kinetic, XRD, FTIR, SEM-EDS were used for analyzing the degradation of demineralized cotton stalk at different treatment rates. Proximate study demonstrated that cotton stalk leaching for 180 min has efficiently infused HCL, leading in a significant increase in fixed carbon and higher heating value of 20.23 % and 12.48%, respectively, as well as a reduction in carbon footprint of around 54.80%. The findings of proximate was validated by GCV analysis and CHNS analysis as value of carbon and hydrogen has shown increasing behavior with the time delay in demineralization Thermo-gravimetric and derivative thermo-gravimetric data analyses shows an increasing trend of conversion efficiency, with the maximum increase of 98 % reported for sample 3H. TT.DEM. XRD characterization has reported 23 degrees to 25 degrees angle for all the observed peaks. Sample 3H.TT.DEM has shown maximum angle inclination along with matured crystalline peak. The latter observations has been validated by FTIR spectroscopy as sample 3H.TT.DEM has reported maximum O-H group formation. Sample 3H.TT. DEM has reported lowest activation energy of 139.51 kJ*mole-1 and lowest reactivity of 0.000293649%*min 0C, due to moderate and stable reactiveness. In SEM examination, increment in pore size and number of pores within the structural matrix of cotton stalk was observed with the enhancement in acidulation process. Furthermore, in EDS analysis, 3H.TT.DEM has shown most balanced distribution of the elements. In this research, sustainable transformation of biomass is envisioned to improve the waste bio refinery system, significantly contributing to the achievement of Sustainable Development Goals 7, 12 and 13.
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| 2. |
- Goraya, Mohsan Ullah, et al.
(författare)
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Isolation of buffalo poxvirus from clinical case and variations in the genetics of the B5R gene over fifty passages
- 2015
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Ingår i: Virus genes. - : Springer Science and Business Media LLC. - 0920-8569 .- 1572-994X. ; 51:1, s. 45-50
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Tidskriftsartikel (refereegranskat)abstract
- Outbreaks of buffalopox affect udder and teats, which may ultimately lead to mastitis in dairy buffalo and can significantly compromise the production. In this study, we report isolation of buffalo poxvirus and sequence analysis of the B5R gene collected from the buffalo clinically suspected to be poxvirus infected. The virus was isolated on BHK-21 cell line and was passaged for 50 times, B5R gene was amplified and sequenced using gene-specific primers, and analyzed at both nucleotide and amino acid levels. Phylogenetically, the isolate can be classified close to the previously reported Pakistani and Indian isolates with certain level of differential clustering patterns. Three significant putative mutations (I2K, N64D, and K111E) were observed in the B5R protein. The K111E was common with previous human isolate from Karachi, Pakistan in 2005. These mutations differed from pox-viruses reported from the neighboring countries. Some deletion mutations were observed which were recovered in upcoming passages. The K111E mutation suggests potential to cause zoonotic infection in human all over the country.
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| 3. |
- Munir, M. Adeel, et al.
(författare)
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Blockchain Adoption for Sustainable Supply Chain Management : Economic, Environmental, and Social Perspectives
- 2022
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Ingår i: Frontiers in Energy Research. - : Frontiers Media S.A.. - 2296-598X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Due to the rapid increase in environmental degradation and depletion of natural resources, the focus of researchers is shifted from economic to socio-environmental problems. Blockchain is a disruptive technology that has the potential to restructure the entire supply chain for sustainable practices. Blockchain is a distributed ledger that provides a digital database for recording all the transactions of the supply chain. The main purpose of this research is to explore the literature relevant to blockchain for sustainable supply chain management. The focus of this review is on the sustainability of the blockchain-based supply chain concerning environmental conservation, social equality, and governance effectiveness. Using a systematic literature review, a total of 136 articles were evaluated and categorized according to the triple bottom-line aspects of sustainability. Challenges and barriers during blockchain adoption in different industrial sectors such as aviation, shipping, agriculture and food, manufacturing, automotive, pharmaceutical, and textile industries were critically examined. This study has not only explored the economic, environmental, and social impacts of blockchain but also highlighted the emerging trends in a circular supply chain with current developments of advanced technologies along with their critical success factors. Furthermore, research areas and gaps in the existing research are discussed, and future research directions are suggested. The findings of this study show that blockchain has the potential to revolutionize the entire supply chain from a sustainability perspective. Blockchain will not only improve the economic sustainability of the supply chain through effective traceability, enhanced visibility through information sharing, transparency in processes, and decentralization of the entire structure but also will help in achieving environmental and social sustainability through resource efficiency, accountability, smart contracts, trust development, and fraud prevention. The study will be helpful for managers and practitioners to understand the procedure of blockchain adoption and to increase the probability of its successful implementation to develop a sustainable supply chain network.
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| 4. |
- Ahsan, Ali, et al.
(författare)
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Formulation and evaluation of miconazole lipogel for enhanced drug permeation
- 2024
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Ingår i: Pakistan Journal of Pharmaceutical Sciences. - : UNIV KARACHI. - 1011-601X. ; 37:1, s. 95-105
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Tidskriftsartikel (refereegranskat)abstract
- Hydrophilic drugs could be incorporated into the skin surface by manes of Lipogel. This study aimed to prepare miconazole lipogel with natural ingredients to enhance drug permeability using dimethyl Sulfoxide (DMSO). The miconazole lipogels, A1 (without DMSO) and A2 (with DMSO) were formulated and evaluated for organoleptic evaluation, pH, viscosity, stability studies, freeze -thawing, drug release profile and drug permeation enhancement. Results had stated that prepared lipogel's pH falls within the acceptable range required for topical delivery (4 to 6) while both formulations show good results in organoleptic evaluation. The A2 formulation containing DMSO shows better permeation of miconazole (84.76%) on the artificial skin membrane as compared to A1 lipogel formulation (50.64%). In in -vitro drug release studies, A2 for-mulation showed 87.48% drug release while A1 showed just 60.1% drug release from lipogel. Stability studies were performed on model formulations under environmental conditions and both showed good spreadibility, stable pH, free of grittiness and good consistency in formulation. The results concluded that A2 formulation containing DMSO shows better results as compared to DMSO-free drug lipogel.
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| 5. |
- Gul, Lubna, et al.
(författare)
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Integrated Traceability Approach for an Effective Impact Analysis
- 2021
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Ingår i: Mehran University Research Journal of Engineering and Technology. - : MEHRAN UNIV ENGINEERING & TECHNOLOGY. - 0254-7821 .- 2413-7219. ; 40:2, s. 346-357
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Tidskriftsartikel (refereegranskat)abstract
- Change is inevitable, software undergoes continuous change during its life cycle. A small change can trigger high evolution because of the ripple effect identified during the activity of impact analysis. However, it depends on the traceability information, which is the connection between software development artifacts. The current traceability techniques lack the breadth and depth to carryout informative impact analysis. We have performed a detailed literature survey of traceability techniques from the year 2008-2018. These techniques are evaluated on the criteria for effective impact analysis present in the literature. The results highlight that no single technique fulfills the criteria for effective impact analysis alone, they can be combined together to achieve promising results. We have presented a hybrid approach that combines four traceability techniques to achieve the entire criteria for an effective impact analysis after careful evaluation. The techniques combined are: Information Retrieval, Pre-Requirement Specification Traceability, Value based Requirements Traceability Technique and Goal Centric Traceability Technique. Our proposed hybrid approach is empirically validated via a field experiment. Results are analyzed for time and effort utilized in maintaining and retrieving the traceability information. The results are promising as the hybrid approach achieves effective impact analysis within minimal time and effort. We plan to extend the validation to real world impact analysis situation via case study.
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| 6. |
- Munir, Muhammad Akhtar, et al.
(författare)
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Bridging Precision and Confidence: A Train-Time Loss for Calibrating Object Detection
- 2023
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Ingår i: 2023 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR). - : IEEE COMPUTER SOC. - 9798350301298 - 9798350301304 ; , s. 11474-11483
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Konferensbidrag (refereegranskat)abstract
- Deep neural networks (DNNs) have enabled astounding progress in several vision-based problems. Despite showing high predictive accuracy, recently, several works have revealed that they tend to provide overconfident predictions and thus are poorly calibrated. The majority of the works addressing the miscalibration of DNNs fall under the scope of classification and consider only in-domain predictions. However, there is little to no progress in studying the calibration of DNN-based object detection models, which are central to many vision-based safety-critical applications. In this paper, inspired by the train-time calibration methods, we propose a novel auxiliary loss formulation that explicitly aims to align the class confidence of bounding boxes with the accurateness of predictions (i.e. precision). Since the original formulation of our loss depends on the counts of true positives and false positives in a mini-batch, we develop a differentiable proxy of our loss that can be used during training with other application-specific loss functions. We perform extensive experiments on challenging in-domain and out-domain scenarios with six benchmark datasets including MS-COCO, Cityscapes, Sim10k, and BDD100k. Our results reveal that our train-time loss surpasses strong calibration baselines in reducing calibration error for both in and out-domain scenarios. Our source code and pre-trained models are available at https://github.com/akhtarvision/bpc_calibration
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| 7. |
- Munir, Muhammad Akhtar, et al.
(författare)
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Cal-DETR: Calibrated Detection Transformer
- 2023
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Ingår i: ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 36 (NEURIPS 2023). - : NEURAL INFORMATION PROCESSING SYSTEMS (NIPS).
-
Konferensbidrag (refereegranskat)abstract
- Albeit revealing impressive predictive performance for several computer vision tasks, deep neural networks (DNNs) are prone to making overconfident predictions. This limits the adoption and wider utilization of DNNs in many safety-critical applications. There have been recent efforts toward calibrating DNNs, however, almost all of them focus on the classification task. Surprisingly, very little attention has been devoted to calibrating modern DNN-based object detectors, especially detection transformers, which have recently demonstrated promising detection performance and are influential in many decision-making systems. In this work, we address the problem by proposing a mechanism for calibrated detection transformers (Cal-DETR), particularly for Deformable-DETR, UP-DETR and DINO. We pursue the train-time calibration route and make the following contributions. First, we propose a simple yet effective approach for quantifying uncertainty in transformer-based object detectors. Second, we develop an uncertainty-guided logit modulation mechanism that leverages the uncertainty to modulate the class logits. Third, we develop a logit mixing approach that acts as a regularizer with detection-specific losses and is also complementary to the uncertainty-guided logit modulation technique to further improve the calibration performance. Lastly, we conduct extensive experiments across three in-domain and four out-domain scenarios. Results corroborate the effectiveness of Cal-DETR against the competing train-time methods in calibrating both in-domain and out-domain detections while maintaining or even improving the detection performance. Our codebase and pre-trained models can be accessed at https://github.com/akhtarvision/cal-detr.
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| 8. |
- Tanveer, M. K., et al.
(författare)
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Prevalence and chemo-therapeutical investigations of gastrointestinal nematodes in domestic pigeons in Lahore, Pakistan
- 2011
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Ingår i: Tropical Biomedicine. - 0127-5720. ; 28:1, s. 102-110
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Tidskriftsartikel (refereegranskat)abstract
- The prevalence of gastrointestinal nematodes was studied in 143 (80 male and 63 female) domestic pigeons. Faecal samples were collected to determine the gastrointestinal nematodes of domestic pigeons through qualitative and quantitative faecal examinations. A total of 48 (male 33 and 25 female) naturally infected domestic pigeons were divided into G(1) (albendzdole) and G(2) (fenbendazole) treatment-groups along with one control group (C). The overall prevalence of gastrointestinal nematodes was 40.5% (58/143) in domestic pigeons. Likewise, the prevalence of gastrointestinal nematodes in males and females was found 41.3% (33/58) and 39.7% (25/58) respectively. The overall prevalence of Capillaria obsignata and Ascaridia columbae was found to be 67.2% and 32.8%, respectively. The prevalence of C. obsignata and A. columbae in males was 72.7% (24/33) and 27.8% (9/33) and in females was 60% (15/25) and 40% (10/25), respectively. There was no significant sex related difference seen in the prevalence of C. obsignata (p>0.56) and A. columbae (p>0.40) in domestic pigeons, respectively. The overall efficacy of albendazole and fenbendazole was calculated to be 66% and 71%. A remarkable significant difference (p<0.05) was observed in eggs per gram before and after treatment in both G(1) and G(2) treated-groups. The efficacy of fenbendazole was found to be more significant (p<0.02) than albendazole.
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| 9. |
- Ali, Amjad, et al.
(författare)
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Effect of Manganese Catalysts on the Performance of Anodes in Direct Carbon Fuel Cells
- 2022
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Ingår i: ACS Applied Energy Materials. - : AMER CHEMICAL SOC. - 2574-0962. ; 5:6, s. 6878-6885
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Tidskriftsartikel (refereegranskat)abstract
- The efficiency of direct carbon fuel cells is higher than that of solid oxide fuel cells. The direct carbon fuel cell transforms chemical energy into electrical energy. In this work, the La0.4Sr0.6MnxTi1-xO3-delta (x = 0.02, 0.04, 0.06, 0.08) anode material has been synthesized by the combustion method to examine the device performance. X-ray analysis confirmed the single-perovskite cubic structure with an average crystalline size of 80 nm. An electrical conductivity of 2.1 S cm-1 and fuel cell performance of 100 mW cm-2 at 600 degrees C are measured with sub-bituminous fuel. Theoretical results describe the minor contribution of manganese (Mn) in the valence band and the major one in the conduction band, and with minimum energy, the Mn electrons may jump in the conduction band. Moreover, density functional theory confirmed that with an increase in the Mn concentration, Mn and Ti energy states appear at the Fermi level, which reveals that the conductivity of the compound has improved, agreeing with the experimental results that the Mn concentration led to the enhancement of the conductivity.
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| 10. |
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| 11. |
- Berg, Mikael, et al.
(författare)
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Sequencing and analysis of the complete genome of Newcastle disease virus isolated from a commercial poultry farm in 2010
- 2012
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Ingår i: Archives of Virology. - : Springer Science and Business Media LLC. - 0304-8608 .- 1432-8798. ; 157, s. 765-768
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Tidskriftsartikel (refereegranskat)abstract
- Newcastle disease virus (NDV) infects wild and domestic birds but causes contagious and lethal disease in domestic poultry. ND is currently endemic in Pakistan, but no complete genome sequence of a Pakistani NDV isolate has been reported. An NDV strain isolated from a commercial poultry farm was completely sequenced. Phylogenetic analysis revealed that the isolate is closely related to genotype VII and, more specifically, to subgenotype VIIb, yet with substantial enough differences to be regarded as new subgenotype (VIIf). These findings provide insight into the genetic nature of NDV circulating in Pakistan and are useful for both laboratory diagnosis and vaccine development for NDV.
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| 12. |
- Bidokhti, Mehdi, et al.
(författare)
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Evolutionary dynamics of bovine coronaviruses: natural selection pattern of the spike gene implies adaptive evolution of the strains
- 2013
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Ingår i: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 94, s. 2036-2049
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Tidskriftsartikel (refereegranskat)abstract
- Coronaviruses demonstrate great potential for interspecies transmission, including zoonotic outbreaks. Although bovine coronavirus (BCoV) strains are frequently circulating in cattle farms worldwide, causing both enteric and respiratory disease, little is known about their genomic evolution. We sequenced and analysed the full-length spike (S) protein gene of 33 BCoV strains from dairy and feedlot farms collected during outbreaks that occurred from 2002 to 2010 in Sweden and Denmark. Amino acid identities were >97% for the BCoV strains analysed in this work. These strains formed a clade together with Italian BCoV strains and were highly similar to human enteric coronavirus HECV-4408/US/94. A high similarity was observed between BCoV, canine respiratory coronavirus (CRCoV) and human coronavirus OC43 (HCoV-OC43). Molecular clock analysis of the S gene sequences estimated BCoV and CRCoV diverged from a common ancestor in 1951, while the time of divergence from a common ancestor of BCoV and HCoV-OC43 was estimated to be 1899. BCoV strains showed the lowest similarity to equine coronavirus, placing the date of divergence at the end of the eighteenth century. Two strongly positive selection sites were detected along the receptor-binding subunit of the S protein gene: spanning amino acid residues 109-131 and 495-527. By contrast, the fusion subunit was observed to be under negative selection. The selection pattern along the S glycoprotein implies adaptive evolution of BCoVs, suggesting a successful mechanism for BCoV to continuously circulate among cattle and other ruminants without disappearance.
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| 13. |
- Cholleti, Harindranath, et al.
(författare)
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Equine arteritis virus induced cell death is associated with activation of the intrinsic apoptotic signalling pathway
- 2013
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Ingår i: Virus Research. - : Elsevier BV. - 0168-1702 .- 1872-7492. ; 171:1, s. 222-226
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Tidskriftsartikel (refereegranskat)abstract
- Equine arteritis virus (EAV) causes a respiratory and reproductive disease in horses, equine viral arteritis. Though cell death in infection with EAV is considered to occur by apoptosis, the underlying molecular mechanism has not been extensively elucidated. We investigated the expression of mRNA of pro-apoptotic and caspase genes during EAV infection in BHK21 cells, a well-established cell type for EAV replication. Using a SYBR Green real-time PCR, mRNA of p53, Bax, caspase 3 and caspase 9 were found up-regulated in a time dependent manner in EAV infected cells. Western blot analysis for caspase 3 and caspase 9 showed expression of cleaved forms of these proteins during EAV infection. In addition, a luminescence-based cell assay for caspase 3/7 activation as a hallmark in apoptosis confirmed apoptotic cell death. The findings demonstrate that cell death in EAV infected BHK21 cells results from apoptosis mediated through the intrinsic signalling pathway.
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| 14. |
- Imran, Muhammad, et al.
(författare)
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Low complexity FPGA based background subtraction technique for thermal imagery
- 2015
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Ingår i: ACM International Conference Proceeding Series. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450336819 ; , s. 1-6
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Konferensbidrag (refereegranskat)abstract
- Embedded smart camera systems are gaining popularity for a number of real world surveillance applications. However, there are still challenges, i.e. variation in illumination, shadows, occlusion, and weather conditions while employing the vision algorithms in outdoor environments. For safety-critical surveillance applications, the visual sensors can be complemented with beyond-visual-range sensors. This in turn requires analysis, development and modification of existing imaging techniques. In this work, a low complexity background modelling and subtraction technique has been proposed for thermal imagery. The proposed technique has been implemented on Field Programmable Gate Arrays (FPGAs) after in-depth analysis of different sets of images, characterizing poor signal-to-noise ratio challenges, e.g. motion of high frequency background objects, temperature variation and camera jitter etc. The proposed technique dynamically updates the background on pixel level and requires a single frame storage as opposed to existing techniques. The comparison of this approach with two other approaches show that this approach performs better in different environmental conditions. The proposed technique has been modelled in Register Transfer Logic (RTL) and implementation on the latest FPGAs shows that the design requires less than 1 percent logics, 47 percent block RAMs, and consumes 91 mW power consumption on Artix-7 100T FPGA.
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| 15. |
- Imran, Muhammad, et al.
(författare)
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STC-CAM1, IR-visual based smart camera system
- 2015
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Ingår i: ACM International Conference Proceeding Series. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450336819 ; , s. 195-196
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Konferensbidrag (refereegranskat)abstract
- Safety-critical applications require robust and real-time surveillance. For such applications, a vision sensor alone can give false positive results because of poor lighting conditions, occlusion, or different weather conditions. In this work, a visual sensor is complemented by an infrared thermal sensor which makes the system more resilient in unfavorable situations. In the proposed camera architecture, initial data intensive tasks are performed locally on the sensor node and then compressed data is transmitted to a client device where remaining vision tasks are performed. The proposed camera architecture is demonstrated as a proof-ofconcept and it offers a generic architecture with better surveillance while only performing low complexity computations on the resource constrained devices.
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| 16. |
- Johansson Wensman, Jonas, et al.
(författare)
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Epidemiological features of an outbreak of peste des petits ruminants depicting an endemic situation
- 2016
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Ingår i: British Journal of Virology. - : ResearchersLinks Ltd. - 2055-6128. ; 3, s. 123 - 129
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Tidskriftsartikel (refereegranskat)abstract
- An outbreak of Peste des Petits ruminants (PPR), possibly caused by the introduction of new animals in the herd, was investigated in an unvaccinated mixed herd of sheep and goats. Goats in the herd showed characteristic signs of PPR including nasal and ocular discharges, high temperature, diarrhea and ulcerative lesions in the oral cavity. A total of eighteen goats from a herd of sixty, were affected and two goats succumbed within two weeks. Interestingly, the disease was exclusively observed in goats and all sheep kept in the same herd were serologically positive but did not show any clinical signs of PPR. The active PPR virus (PPRV) infection was confirmed by antigen capture ELISA and RT-PCR in both swab and body tissue samples. The molecular characterization revealed clustering of the PPRV within lineage IV with significant substitutions in the nucleoprotein (NP) gene. Genetic variations within NP gene, and possibly in other proteins which are essentially mediating protective immunity, may explain the extreme infectious nature of the virus and its host-specific pathogenesis. Moreover, understanding the nature of such circulating field viruses is essential to underpin the endemic potential of PPRV and its possible spread to the susceptible wild or domestic small ruminants.
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| 17. |
- Johansson Wensman, Jonas, et al.
(författare)
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Genetic analysis of peste des petits ruminants virus from Pakistan
- 2013
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Ingår i: BMC Veterinary Research. - : Springer Science and Business Media LLC. - 1746-6148. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Peste des petits ruminants (PPR) is an endemic and highly contagious disease in small ruminants of Pakistan. Despite the fact that an effective vaccine is available, outbreaks are regularly occurring in the country. Thus so far, the diagnosis has primarily been made based on clinical outcome or serology. This study was carried out to characterize PPRV from an emerging wave of outbreaks from Punjab, Pakistan. RESULTS: A total of 32 blood samples from five different flocks were tested with real-time PCR for the presence of PPRV genome. The samples detected positive in real-time PCR (n = 17) were subjected to conventional PCR for the amplification of the nucleoprotein (N) gene. Phylogenetic analysis of the sequenced N genes (n = 8) indicated the grouping of all the sequences in lineage IV along with PPRV strains from Asian and Middle East. However, interestingly sequences were divided into two groups. One group of viruses (n = 7) clustered with previously characterized Pakistani isolates whereas one strain of PPRV was distinct and clustered with Saudi Arabian and Iranian strains of PPRV. CONCLUSIONS: Results demonstrated in this study expanded the information on the genetic nature of different PPRV population circulating in small ruminants. Such information is essential to understand genetic nature of PPRV strains throughout the country. Proper understanding of these viruses will help to devise control strategies in PPRV endemic countries such as Pakistan.
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| 18. |
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| 19. |
- Johansson Wensman, Jonas, et al.
(författare)
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The X proteins of bornaviruses interfere with type I interferon signalling
- 2013
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Ingår i: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 94, s. 263-269
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Tidskriftsartikel (refereegranskat)abstract
- Borna disease virus (BDV) is a neurotropic, negative-stranded RNA virus causing persistent infection and progressive neurological disorders in a wide range of warm-blooded animals. The role of the small non-structural X protein in viral pathogenesis is not completely understood. Here we investigated whether the X protein of BDV and avian bornavirus (ABV) interferes with the type I interferon (IFN) system, similar to other non-structural proteins of negative-stranded RNA viruses. In luciferase reporter assays, we found that the X protein of various bornaviruses interfered with the type I IFN system at all checkpoints investigated, in contrast to previously reported findings, resulting in reduced type I IFN secretion.
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| 20. |
- Khan, Muhammad Abbas, et al.
(författare)
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mmWave Four-Element MIMO Antenna for Future 5G Systems
- 2022
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Ingår i: Applied Sciences. - : MDPI AG. - 2076-3417. ; 12:9, s. 4280-
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents an S-shape four-port Multiple Input Multiple Output (MIMO) wideband mmWave antenna with bandwidth of 25 GHz to 39 GHz. The antenna is designed on 0.254 mm ultra-thin RO5880 with permittivity of 2.3. The dimensions of proposed S-shape antenna are 10 x 12 mm for single element and 24 x 24 mm for four-port MIMO configuration. A decoupling network is introduced to further compress mutual coupling among MIMO elements. The peak gain achieved is 7.1 dBi and MIMO assembly delivers diversity scheme. The proposed MIMO antenna is fabricated, and simulated results are found to be in excellent agreement with simulations. Through the results obtained, the proposed MIMO antenna system can be considered as a potential candidate for future mmWave devices.
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| 21. |
- Khan, Rizwan, et al.
(författare)
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Dental image enhancement network for early diagnosis of oral dental disease
- 2023
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Intelligent robotics and expert system applications in dentistry suffer from identification and detection problems due to the non-uniform brightness and low contrast in the captured images. Moreover, during the diagnostic process, exposure of sensitive facial parts to ionizing radiations (e.g., X-Rays) has several disadvantages and provides a limited angle for the view of vision. Capturing high-quality medical images with advanced digital devices is challenging, and processing these images distorts the contrast and visual quality. It curtails the performance of potential intelligent and expert systems and disincentives the early diagnosis of oral and dental diseases. The traditional enhancement methods are designed for specific conditions, and network-based methods rely on large-scale datasets with limited adaptability towards varying conditions. This paper proposed a novel and adaptive dental image enhancement strategy based on a small dataset and proposed a paired branch Denticle-Edification network (Ded-Net). The input dental images are decomposed into reflection and illumination in a multilayer Denticle network (De-Net). The subsequent enhancement operations are performed to remove the hidden degradation of reflection and illumination. The adaptive illumination consistency is maintained through the Edification network (Ed-Net). The network is regularized following the decomposition congruity of the input data and provides user-specific freedom of adaptability towards desired contrast levels. The experimental results demonstrate that the proposed method improves visibility and contrast and preserves the edges and boundaries of the low-contrast input images. It proves that the proposed method is suitable for intelligent and expert system applications for future dental imaging.
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| 22. |
- Linde, Anna-Malin, et al.
(författare)
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Complete genome characterisation of a Newcastle disease virus isolated during an outbreak in Sweden in 1997
- 2010
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Ingår i: Virus Genes. - : Springer Science and Business Media LLC. - 0920-8569 .- 1572-994X. ; 41, s. 165-173
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Tidskriftsartikel (refereegranskat)abstract
- The complete genome sequence of a Newcastle disease virus (NDV) isolated from a chicken in Sweden was determined and compared with other NDV sequences. The isolate was shown to belong to genotype VIIb, which arose in the Far East and spread around the world during the 1990s. It had a length of 15,192 bases and consisted of six genes in the order 3'-NP-P-M-F-HN-L-5'. The F protein cleavage site was 112-RRQRRF-117, corresponding to that of a virulent pathotype.
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| 23. |
- Munir, Muhammad, et al.
(författare)
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Alleles A and B of non-structural protein 1 of avian influenza A viruses differentially inhibit beta interferon production in human and mink lung cells
- 2011
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Ingår i: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 92, s. 2111-2121
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Tidskriftsartikel (refereegranskat)abstract
- Non-structural protein 1 (NS1) counteracts the production of host type I interferons (IFN-alpha/beta) for the efficient replication and pathogenicity of influenza A viruses. Here, we reveal another dimension of the NS1 protein of avian influenza A viruses in suppressing IFN-beta production in cultured cell lines. We found that allele A NS1 proteins of H6N8 and H4N6 have a strong capacity to inhibit the activation of IFN-beta production, compared with allele B from corresponding subtypes, as measured by IFN stimulatory response element (ISRE) promoter activation, IFN-beta mRNA transcription and IFN-beta protein expression. Furthermore, the ability to suppress IFN-beta promoter activation was mapped to the C-terminal effector domain (ED), while the RNA-binding domain (RBD) alone was unable to suppress IFN-beta promoter activation. Chimeric studies indicated that when the RBD of allele A was fused to the ED of allele B, it was a strong inhibitor of IFN-beta promoter activity. This shows that well-matched ED and RBD are crucial for the function of the NS1 protein and that the RBD could be one possible cause for this differential IFN-beta inhibition. Notably, mutagenesis studies indicated that the F103Y and Y103F substitutions in alleles A and B, respectively, do not influence the ISRE promoter activation. Apart from dsRNA signalling, differences were observed in the expression pattern of NS1 in transfected human and mink lung cells. This study therefore expands the versatile nature of the NS1 protein in inhibiting IFN responses at multiple levels, by demonstrating for the first time that it occurs in a manner dependent on allele type.
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| 24. |
- Munir, Muhammad
(författare)
-
Bioinformatics analysis of large-scale viral sequences From construction of data sets to annotation of a phylogenetic tree
- 2013
-
Ingår i: Virulence. - : Informa UK Limited. - 2150-5594 .- 2150-5608. ; 4, s. 97-106
-
Tidskriftsartikel (refereegranskat)abstract
- Due to a significant decrease in the cost of DNA sequencing, the number of sequences submitted to the public databases has dramatically increased in recent years. Efficient analysis of these data sets may lead to a significant understanding of the nature of pathogens such as bacteria, viruses, parasites, etc. However, this has raised questions about the efficacy of currently available algorithms for the study of pathogen evolution and construction of phylogenetic trees. While the advanced algorithms and corresponding programs are being developed, it is crucial to optimize the available ones in order to cope with the current need. The protocol presented in this study is optimized using a number of strategies currently being proposed for handling large-scale DNA sequence data sets, and offers a highly efficacious and accurate method for computing phylogenetic trees with limited computer resources. The protocol may take up to 36 h for construction and annotation of a final tree of about 20,000 sequences.
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| 25. |
- Munir, Muhammad, et al.
(författare)
-
Biological characterization and phylogenetic analysis of a novel genetic group of Newcastle disease virus isolated from outbreaks in commercial poultry and from backyard poultry flocks in Pakistan
- 2012
-
Ingår i: Infection, Genetics and Evolution. - : Elsevier BV. - 1567-1348 .- 1567-7257. ; 12, s. 1010-1019
-
Tidskriftsartikel (refereegranskat)abstract
- Newcastle disease (ND) is a contagious viral disease of many avian species particularly domestic poultry, and is responsible for devastating outbreaks in the poultry industries around the globe. In spite of its importance and endemicity in Southern Asia, data on the genetic nature of the viruses and epizootiological information of the disease is scarce. In this study, six isolates from an emerging wave of ND outbreaks in the north of Pakistan and two isolates from healthy poultry flocks were biologically and genetically characterized. Based on pathogenicity indices such as intracerebral pathogenicity index (ICPI), mean death time (MDT) and cleavage motifs in the fusion protein, all these isolates were classified as virulent. Phylogenetic analysis of the fusion (F), hemagglutinin-neuraminidase (HN) and matrix (M) genes indicated the emergence of a novel genetic group within lineage 5, distinct from isolates previously reported in the region. Several mutations in the neutralizing epitopes and functionally important motifs of the F and HN genes pose a need for re-evaluation of the currently used vaccine and vaccination practices. The characteristics of Newcastle disease virus (NDV) as virulent (F protein cleavage site, ICPI and MDT) in apparently healthy backyard poultry (BYP) explain that BYP can play crucial role in the epizootiology and spread of the disease. The present investigation provides essential information on the genetic nature of NDV circulating in Pakistan and its implication on disease diagnosis and control. Furthermore, these investigations emphasize the importance of continuous surveillance of ND in developing countries. (C) 2012 Elsevier B.V. All rights reserved.
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| 26. |
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| 27. |
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| 28. |
- Munir, Muhammad, et al.
(författare)
-
Complete Genome Analysis of an Avian Paramyxovirus Type 1 Strain Isolated in 1994 from an Asymptomatic Black-Headed Gull (Larus ridibundus) in Southern Sweden
- 2010
-
Ingår i: Avian Diseases. - 0005-2086. ; 54, s. 923-930
-
Tidskriftsartikel (refereegranskat)abstract
- The complete genome sequence of an avian paramyxovirus serotype 1 (APMV-1) isolated from a black-headed gull (Larus ridibundus) in Sweden was determined and compared with other APMV-1 sequences. Sequence analyses showed that this isolate consists of six genes in the order 3'-NP-P-M-F-HN-L-5', is 15,186 nucleotides long, and contains a typical, avirulent fusion protein cleavage site. It was also shown to have a hemagglutinin-neuraminidase protein with a length of 585 amino acids (aa) instead of the expected 616 aa. Phylogenetic analyses showed that the isolate belongs to genotype I, and the relationship with some other, known APMV-1 virus sequences was revealed. Waterfowl have been considered to act as a reservoir for APMV-1 and, therefore, it is important to broaden the knowledge of viruses circulating within this population.
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| 29. |
- Munir, Muhammad, et al.
(författare)
-
Complete Genome Sequence of a Velogenic Neurotropic Avian Paramyxovirus 1 Isolated from Peacocks (Pavo cristatus) in a Wildlife Park in Pakistan
- 2012
-
Ingår i: Journal of Virology. - 0022-538X .- 1098-5514. ; 86, s. 13113-13114
-
Annan publikation (refereegranskat)abstract
- Avian paramyxovirus serotype 1 (APMV-1) was isolated from an acute and highly contagious outbreak in peacocks (Pavo cristatus) in a wildlife park in Pakistan. A velogenic neurotropic form of APMV-1 caused a 100% case fatality rate and killed 190 peacocks within a week. Biological and serological characterizations showed features of a velogenic strain of APMV-1, and these results were further confirmed by sequence analysis of the cleavage site in the fusion protein. The complete genome of one of the isolates was sequenced, and phylogenetic analysis was conducted. The analysis showed that this isolate belonged to genotype VII, specifically, to subgenotype VIIa, and clustered closely with isolates characterized from Indonesia in the 1990s. Interestingly, the isolate showed significant differences from previously characterized APMV-1 isolates from commercial and rural chickens in Pakistan. The work presented here is the first complete genome sequence of any APMV-1 isolate from wild birds in the region and therefore highlights the need for increased awareness and surveillance in such bird species.
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| 30. |
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| 31. |
- Munir, Muhammad
(författare)
-
Complete Genome Sequencing of a Velogenic Viscerotropic Avian Paramyxovirus 1 Isolated from Pheasants (Pucrasia macrolopha) in Lahore, Pakistan
- 2012
-
Ingår i: Journal of Virology. - 0022-538X .- 1098-5514. ; 86, s. 13828-13829
-
Tidskriftsartikel (refereegranskat)abstract
- We report the complete genome sequence of avian paramyxovirus 1 (APMV-1) isolated from an acute and highly contagious outbreak in pheasants (Pucrasia macrolopha) in Lahore, Pakistan. Biological and serological characterization showed a velogenic strain of APMV-1, which was further confirmed by the sequence analysis of the cleavage site in the fusion protein. Complete genome sequencing and phylogenetic analysis indicated that this isolate belonged to genotype VII, specifically to subgenotype VIIa, and clustered closely with isolates characterized from Indonesia. Notably, the isolate showed significant differences from previously characterized APMV-1 from Pakistani commercial and rural chicken.
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| 32. |
- Munir, Muhammad, et al.
(författare)
-
Detection and Phylogenetic Analysis of Peste des Petits Ruminants Virus Isolated from Outbreaks in Punjab, Pakistan
- 2012
-
Ingår i: Transboundary and Emerging Diseases. - : Hindawi Limited. - 1865-1674 .- 1865-1682. ; 59, s. 85-93
-
Tidskriftsartikel (refereegranskat)abstract
- Peste des Petits Ruminants (PPR) is an important viral disease of small ruminants and is endemic in Pakistan. In the following study, samples from two outbreaks of PPR in goats have been subjected to laboratory investigations. The Peste des Petits Ruminants virus (PPRV) genome was detected using both conventional and real-time PCR. Genetic characterization of the local PPRV field isolates was conducted by sequencing 322 bp of the fusion (F) gene and 255 bp of the nucleoprotein (N) gene. The phylogenetic tree based on the F gene clustered samples from both outbreaks into lineage 4 along with other Asian isolates, specifically into subcluster 1 along with isolates from Middle East. Analysis of N gene revealed a different pattern. In this case, the Pakistani samples clustered with Chinese, Tajikistani and Iranian isolates, which probably represents the true geographical pattern of virus circulation. This is the first report presenting the phylogenetic tree based on N gene as well as performing a parallel comparison of the trees of F and N gene together from Pakistani isolates. The results of this study shed light on the PPRV population in Pakistan and emphasize the importance of using molecular methods to understand the epidemiology. Such understanding is essential in any efforts to control the number and impact of outbreaks that are occurring in endemic countries such as Pakistan, especially in the current scenario where OIE and FAO are eager to control and subsequently eradicate PPR from the globe, as has been achieved for Rinderpest.
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| 33. |
- Munir, Muhammad, et al.
(författare)
-
Differences in the ability to suppress interferon beta production between allele A and allele B NS1 proteins from H10 influenza A viruses
- 2010
-
Ingår i: Virology Journal. - 1743-422X. ; 7, s. 1-8
-
Tidskriftsartikel (refereegranskat)abstract
- Conclusions: These studies reveal that different non-structural protein 1 (NS1) of influenza viruses, one from allele A and another from allele B, show different abilities to suppress the type I interferon beta expression. It has been hypothesised that some of the differences in the different abilities of the alleles to suppress ISRE were because of the interactions and inhibitions at later stages from the IFN receptor, such as the JAK/STAT pathway. This might reflect the additional effects of the immune evasion potential of different NS1s.
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| 34. |
- Munir, Muhammad, et al.
(författare)
-
Double-Stranded RNA-Induced Activation of Activating Protein-1 Promoter Is Differentially Regulated by the Non-structural Protein 1 of Avian Influenza A Viruses
- 2012
-
Ingår i: Viral Immunology. - : Mary Ann Liebert Inc. - 0882-8245 .- 1557-8976. ; 25, s. 79-85
-
Tidskriftsartikel (refereegranskat)abstract
- Non-structural protein 1 (NS1) of influenza A viruses is a multifunctional protein that antagonizes the host immune response by interfering with several host signaling pathways. Based on putative amino acid sequences, NS1 proteins are categorized into two gene pools, allele A and allele B. Here we identified that allele A NS1 proteins of H6N8 and H4N6 are able to inhibit double-stranded RNA (dsRNA)-induced activating protein-1 (AP-1) promoter in cultured cell lines (human A549 and mink lung cells). Allele B NS1 proteins from corresponding subtypes of influenza A viruses are weak in this inhibition, despite significant levels of expression of each NS1 protein in human A549 cells. Furthermore, the capability to inhibit AP-1 promoter was mapped in the effector domain, since RNA binding domain alone lost its ability to inhibit this promoter activation. Chimeric forms of NS1 protein, composed of either RNA binding domain of allele A or B and effector domain of allele A or B, showed comparable inhibition to that of their wild-type NS1 proteins, or to the effector domain of corresponding NS1 proteins. Both alleles A and B NS1 proteins of H6N8 and H4N6 were expressed to significant levels, and were localized predominantly in the nucleus of human A549 cells. These results underscore the importance of the effector domain in inhibiting AP-1 promoter activation, and the biological function of the effector domain in stabilizing the RNA binding domain. Further, we revealed the versatile nature of NS1 in inhibiting the AP-1 transcription factor, in a manner dependent on allele type. Comprehensive studies, focusing on the molecular mechanisms behind this differential inhibition, may facilitate exploration of the zoonotic and pathogenic potential of influenza A viruses.
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| 35. |
- Munir, Muhammad
(författare)
-
Establishment of Stably Transfected Cells Constitutively Expressing the Full-Length and Truncated Antigenic Proteins of Two Genetically Distinct Mink Astroviruses
- 2013
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- Astroviruses are becoming a growing concern in veterinary and public health. To date there are no registered vaccines against astrovirus-induced disease, mostly due to the difficulty to cultivate astroviruses to high titer for vaccine development using conventional techniques. As means to circumvent this drawback, we have developed stably transfected mink fetal cells and BHK21 cells constitutively expressing the full-length and truncated capsid proteins of two distinct genotypes of mink astrovirus. Protein expression in these stably transfected cells was demonstrated by strong signals as evaluated by in-situ PLA and IFA, and confirmed by Western blotting. The recombinant full-length and truncated proteins induced a high level of antibodies in mink, evaluated by ELISA, demonstrating their immunogenicity. In a challenge experiment in mink, a reduction in presentation clinical signs and virus shedding was observed in mink kits born from immunized females. The gene integration and protein expression were sustained through cell passage, showing that the used approach is robust and reliable for expression of functional capsid proteins for vaccine and diagnostic applications.
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| 36. |
- Munir, Muhammad, et al.
(författare)
-
Evaluation of Risk Factors for Peste des Petits Ruminants Virus in Sheep and Goats at the Wildlife-Livestock Interface in Punjab Province, Pakistan
- 2016
-
Ingår i: BioMed Research International. - : Hindawi Limited. - 2314-6133 .- 2314-6141. ; 2016
-
Tidskriftsartikel (refereegranskat)abstract
- Peste des petits ruminants virus (PPRV) is causing infectious disease with high morbidity and mortality rate in domestic and wild small ruminants of Pakistan with valuable economical losses. The present study was carried out to investigate risk factors of PPRV in domestic small ruminants which were present in the vicinity of wildlife parks. A total of 265 sera samples (27 wild ruminants and 238 domesticated small ruminants) from apparently healthy animals from two different wildlife parks were collected and analysed for PPRV antibodies. Also, 20 nasal swabs from domestic small ruminants showing respiratory signs were collected to check for presence of PPRV antigen. Competitive ELISA revealed highest proportions of anti-PPRV antibodies in domestic small ruminants around the Wildlife Park at Lahore (35%) as compared to Faisalabad (13%), with no existence of PPRV antibodies in tested serum of wild ruminants at these parks. Higher seropositivity was observed in females (25.6%) than in males (5.1%) and in goats (34.5%) compared to sheep (11.2%). The results of N-gene based RT-PCR highlight the absence of PPRV due to lack of current PPR outbreak in the region during study period. Even though grazing was not a significant risk factor, there is still a possibility of wildlife-livestock interactions for feed and water reservoirs, resulting in spillover of PPR to wildlife. Keeping in view the high seropositivity and risk of PPR, vaccination should be adopted to avoid circulation of PPRV among wild and domestic small ruminants (sheep and goats).
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| 37. |
- Munir, Muhammad
(författare)
-
Genetic analysis of Newcastle disease virus from Punjab, Pakistan
- 2013
-
Ingår i: Virus Genes. - : Springer Science and Business Media LLC. - 0920-8569 .- 1572-994X. ; 46, s. 309-315
-
Tidskriftsartikel (refereegranskat)abstract
- The strains of Newcastle disease virus (NDV) were isolated from five suspected outbreaks of ND in broiler (n = 3) and layers (n = 2) poultry farms. The egg-isolated viruses were subjected to biological and genetic characterization. Based on the biological characterization, isolates showed haemagglutination titer a parts per thousand yenlog 2(7), mean death time < 55 h, intracerebral pathogenecity index a parts per thousand currency sign1.8, and egg lethal dose 50 from 10(-7.15) to 10(-9.31)/1 ml. Genetic characterization of the fusion (F) gene revealed that the isolates clustered with NDV strains of genotype VII (VIIf) within class II, which remained predominant genotype in the domestic poultry of Asia. The deduced amino acid sequence of the isolates confirmed virulent motif (112)RRQKRF(117) at the F protein cleavage site. A bioinformatics and pairwise comparison approach was applied to estimate the synonymous and non-synonymous substitution rates (dN/dS) and selective evolutionary pressure for the F protein. The dN/dS calculated for genotype VII indicate purifying selection, which resulted in a low evolution rate in F gene. The F protein shows a strong negative pressure throughout the length of the protein and no recombination event was determined. Collectively, the results suggest that very similar virulent strains of NDV are involved during current wave of disease outbreak throughout the country. From these results, in conjunction with our recent reports of NDV from Pakistan, it is possible to conclude that emergence of novel group may require revisiting the diagnostics and vaccine control strategies.
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| 38. |
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| 39. |
- Munir, Muhammad
(författare)
-
Hemoglobin Subunit Beta Interacts with the Capsid Protein and Antagonizes the Growth of Classical Swine Fever Virus
- 2013
-
Ingår i: Journal of Virology. - 0022-538X .- 1098-5514. ; 87, s. 5707-5717
-
Tidskriftsartikel (refereegranskat)abstract
- The capsid (C) protein of the Flaviviridae family members is involved in nucleocapsid formation and virion assembly. However, the influence of C protein-interacting partners on the outcome of pestivirus infections is poorly defined. In this study, hemoglobin subunit beta (HB) was identified as a C protein-binding protein by glutathione S-transferase pulldown and subsequent mass spectrometry analysis of PK-15 cells, which are permissive cells for classical swine fever virus (CSFV). Coimmunoprecipitation and confocal microscopy confirmed that HB interacts and colocalizes with the C protein in the cytoplasm. Silencing of HB with small interfering RNAs promoted CSFV growth and replication, whereas overexpression of HB suppressed CSFV replication and growth. Interestingly, HB was found to interact with retinoic acid-inducible gene I and increase its expression, resulting in increased production of type I interferon (IFN). However, HB was unable to suppress CSFV growth when the RIG-I pathway was blocked. Overall, our results suggest that cellular HB antagonizes CSFV growth and replication by triggering IFN signaling, and might represent a novel antiviral restriction factor. This study reports for the first time the novel role of HB in innate immunity.
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| 40. |
- Munir, Muhammad
(författare)
-
Immuno-regulatory dynamics of non-structural protein 1 of avian influenza A viruses : IFN-β, NF-κB and AP-1 perspectives
- 2011
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The type I interferon (IFN-α/β) system represents the first line of defense against influenza A viruses, and is mainly mediated by the interferon regulatory factors 3/7 (IRF3/7), nuclear factor kappa B (NF-κB) and activator protein 1 (AP-1) transcription factors. Therefore, the non-structural protein 1 (NS1) of influenza A viruses has intrinsic abilities to disarm the host cell IFN system, and as a consequence is deeply connected to influenza virus pathogenicity and virulence. Based on differences in the amino acid sequence of the NS1 genes, the influenza A viruses are divided into two distinct gene pools, named allele A and B. This division is strictly based on genetic characterization, and their functional consequences are largely unknown. The results in this thesis provide novel structural and functional insights, indicating that allele A NS1 proteins of various avian influenza A viruses have a stronger capacity to inhibit the activation of IFN-β production than allele B proteins from corresponding subtypes. This claim was further confirmed by measurement of IFN stimulatory response element (ISRE) promoter activation, IFN-β mRNA transcription and IFN-β protein expression. Intriguingly, the allele-specific levels of inhibition correlated with the nature of the disease, where for example allele A influenza virus appeared to be more pathogenic than allele B viruses in minks (Mustela vison). Further investigations demonstrated that allele B NS1 protein resembles to its IFN antagonistic nature in exerting similar effect in preventing double stranded RNA (dsRNA) induced NF-κB and AP-1 promoter activation, which subsequently results in an overall inhibition of IFN-β production. In an effort to understand the structural basis of IFN inhibition, it was revealed that inhibitory activities for ISRE, NF-κB and AP-1 promoters and subsequent inhibition of IFN-β were mapped to the C-terminal effector domain of the NS1 protein. Genetic characterization of a reassortant H9N2 influenza virus revealed that the virus acquired the NS segment from a H5N1 of genotype Z, clade 2.2. Screening the IFN antagonist abilities of both NS1 proteins (H5N1 and H9N2) demonstrated a high degree of functional homology at IRF3, ISRE, NF-κB and AP-1 levels, which resulted in strong inhibition of IFN-β production in cell culture system. Taken together, these studies expand the information concerning the versatile nature of the NS1 protein and highlight its indispensible role in reassortant influenza A virus pathogenesis
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| 41. |
- Munir, Muhammad, et al.
(författare)
-
Molecular Characterization of Peste des Petits Ruminants Viruses From Outbreaks Caused by Unrestricted Movements of Small Ruminants in Pakistan
- 2015
-
Ingår i: Transboundary and Emerging Diseases. - : Hindawi Limited. - 1865-1674 .- 1865-1682. ; 62, s. 108-114
-
Tidskriftsartikel (refereegranskat)abstract
- Peste des petits ruminants (PPR) is an endemic disease of small ruminants, and vaccination has been the method of control but outbreaks are continuously occurring in Pakistan. The following study presents a detailed investigation of an outbreak, suspected to be PPR, probably introduced by PPRV-infected sheep and goats from Sindh Province (north-west) to Punjab Province (central) of Pakistan during the flood relief campaign in 2011. A total of 70 serum samples from 28 different flocks were tested with competitive ELISA (H antibodies), which detected 24 (34.2%) samples positive for PPRV antibodies. Nasal swabs and faeces were tested with immunocapture ELISA (N antigen), which detected 18 (25.7%) samples positive for PPRV antigen. The RNA detected positive (n = 28, 40%) using real-time PCR was subjected to conventional PCR for the amplification of the fusion and nucleoprotein genes. Sequencing of both genes and subsequent phylogenetic analysis indicated the grouping of all the sequences to be in lineage IV along with other Asian isolates of PPRV. However, sequences of both genes were divided into two groups within lineage IV. One group of viruses clustered with previously characterized Pakistani isolates, whereas the other group was distinctly clustered with isolates from the Middle East or India. The sequence identity indicated the introduction of at least one population of PPRV from a different source and circulation in the local flocks of small ruminants, which emphasized the need to obtain health clearance certificate before movement of animals. The results of this study provide baseline data for the genetic characterization of different PPRV populations in Pakistan.
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| 42. |
- Munir, Muhammad, et al.
(författare)
-
Newcastle Disease Virus in Pakistan: Genetic Characterization and Implication in Molecular Diagnosis
- 2012
-
Ingår i: Indian Journal of Virology. - : Springer Science and Business Media LLC. - 0970-2822 .- 0974-0120. ; 23, s. 368-373
-
Tidskriftsartikel (refereegranskat)abstract
- Newcastle disease (ND) is a fatal and contagious disease that poses a constant threat to the poultry industry around the globe. Due to the complex clinico-pathological picture and high genetic variability, the efficient diagnosis of NDV strains is a challenge. In an emerging wave of ND in the north of Pakistan, samples from six outbreaks in commercial poultry and two from healthy backyard poultry flocks were screened for NDV. A real-time PCR based on the fusion and polymerase genes of NDV detected all six isolates whereas a validated real-time PCR based on the matrix gene failed to detect any of these isolates, most likely due to substantial mismatches in the probe-binding site. All isolates have shown ICPI and MDT values similar to the velogenic form of NDV strains. The cleavage site in the F protein was found to be (112)RRQKRa dagger"F-117, typical of virulent NDV. Phylogenetic reconstruction, based on fusion and matrix genes, provided enough evidences to consider these isolates as a new subgenotype within genotype VII. This study raised concerns about the genetic variability of NDV circulating in Pakistan, and sensitivity of the assays for the detection of the NDV isolates in clinical samples.
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| 43. |
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| 44. |
- Munir, Muhammad
(författare)
-
Role of Wild Small Ruminants in the Epidemiology of Peste Des Petits Ruminants
- 2014
-
Ingår i: Transboundary and Emerging Diseases. - : Hindawi Limited. - 1865-1674 .- 1865-1682. ; 61, s. 411-424
-
Forskningsöversikt (refereegranskat)abstract
- Peste des petits ruminants virus (PPRV) causes one of the most contagious and highly infectious respiratory diseases in sheep and goats known as peste des petits ruminants (PPR). Reports of outbreaks of PPR in captive and wild small ruminants have extended the known spectrum of susceptible species to include antelopes. Phylogenetic analysis of nucleoprotein and fusion genes indicates that all PPRVs isolated from wild ungulate outbreaks belong to lineage IV. While it is clear that a number of wildlife species are susceptible to infection, the role of wildlife in the epidemiology of PPR remains uncertain. The available information about the occurrence of disease in free-ranging wildlife is mainly derived from surveys based on serological evidence. Data on the genetic nature of circulating PPRV strains are scarce. Given the scope of PPR in wild ungulates that are widespread in many countries, current disease surveillance efforts are inadequate and warrant additional investment. This is crucial because domestic and wild ruminants mingle together at several points, allowing inter-species transmission of PPRV. There is no reason to believe that PPRV circulates in wild animals and acts as a potential source of virus for domestic species. Irrespective of the possibility of wild small ruminants as the reservoir of PPRV, concerns about the role of susceptible species of antelopes need to be addressed, due to the fact that the disease can pose a serious threat to the survival of endangered species of wild ruminants on the one hand and could act as a constraint to the global eradication of PPR on the other hand. In this review, knowledge gained through research or surveillance on the sustainability of PPRV in wild ruminants is discussed.
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| 45. |
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| 46. |
- Munir, Muhammad, et al.
(författare)
-
The multiple faces of proteinkinase R in antiviral defense
- 2013
-
Ingår i: Virulence. - : Informa UK Limited. - 2150-5594 .- 2150-5608. ; 4, s. 85-89
-
Tidskriftsartikel (refereegranskat)abstract
- Various pattern recognition receptors (PRRs) have been implicated in the detection of viral RNA and subsequent interferon (IFN) gene expression, including the double-stranded RNA-dependent proteinkinase R (PKR). Now, a novel role of PKR has been unveiled, as it was shown that, upon the infection with certain viruses, PKR is crucial for the integrity of newly synthesized IFN mRNA, thereby generating an optimal host antiviral immune response. There is a need of future studies to investigate additional roles of PKR in innate immunity and the molecular understanding of this novel function of PKR.
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| 47. |
- Munir, Muhammad
(författare)
-
TRIM Proteins: Another Class of Viral Victims
- 2010
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Ingår i: Science Signaling. - : American Association for the Advancement of Science (AAAS). - 1945-0877 .- 1937-9145. ; 3, s. 1-4
-
Forskningsöversikt (refereegranskat)abstract
- TRIM (tripartite motif) proteins are a family of RING (really interesting new gene) domain-containing proteins comprising more than 70 human members, with new members still being described. In addition to their involvement in cell proliferation, differentiation, development, morphogenesis, and apoptosis, roles in immune signaling and antiviral functions are emerging. In response to viral infection, TRIM25 ubiquitinates the N terminus of the viral RNA receptor retinoic acid-inducible gene-I (RIG-I), and this modification is essential for RIG- I to interact with its downstream partner mitochondrial antiviral signaling (MAVS). TRIM25 activity thus leads to activation of the RIG- I signaling pathway, which results in type I interferon production to limit viral replication. Recently, it has been demonstrated that influenza A viruses target TRIM25 and disable its antiviral function, thereby suppressing the host interferon response. This Journal Club article highlights the emerging roles of TRIM proteins in antiviral defense mechanisms and an immune evasion strategy in which influenza viruses target a member of the TRIM family.
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| 48. |
- Munir, Muhammad, et al.
(författare)
-
Whole genome sequencing and characterization of a virulent Newcastle disease virus isolated from an outbreak in Sweden
- 2011
-
Ingår i: Virus Genes. - : Springer Science and Business Media LLC. - 0920-8569 .- 1572-994X. ; 43, s. 261-271
-
Tidskriftsartikel (refereegranskat)abstract
- In this study, the complete genome sequence of a Newcastle disease virus (NDV) isolate collected from an outbreak in 1995 in chickens was fully characterized and compared with other NDV sequences. The genome was found to be 15,192 nucleotides long and to consist of six genes in the order 3'-NP-P-M-F-HN-L-5', similar to other avian paramyxoviruses type-I. However, a six-nucleotide insertion was observed in the 5' non-coding regions of the nucleoprotein (NP) gene, a feature that is unique to some NDV isolates. The isolate shows the amino acid sequence (112)RRQKRF(117) at the cleavage site of the F protein, which is identical to a known motif for virulent pathotypes of NDV. The phylogenetic analysis of the coding region of the F gene indicated that this isolate belongs to genotype VI, more specifically to genotype VId, along with isolates from the other European countries (Denmark, Switzerland and Austria). The same genotype caused outbreaks in the Middle East and Greece in the late 1960s, and in Hungary, in the early 1980s, suggesting a common source for these outbreaks.
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| 49. |
- Munir, Sameer, et al.
(författare)
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An Instance Based Schema Matching Between Opaque Database Schemas
- 2014
-
Ingår i: 2014 4TH INTERNATIONAL CONFERENCE ON ENGINEERING TECHNOLOGY AND TECHNOPRENEURSHIP (ICE2T). - : IEEE Computer Society. - 9781479946211 ; , s. 177-182
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Konferensbidrag (refereegranskat)abstract
- Schema matching is always needed amoung schemas of relational datasets in database integration applications. Heterogeneous database integration involves a significant role of schema matching Most of the previous solution to schema matching problem based on the identification of similarity between the columns names or by recognizing common domains in the data stored in the schemas. These approaches are not applicable on those datasets with unaligned schemas where the name of the columns in the schemas and the data in the columns are opaque. In this paper we proposed an instance based approach to find the matching between the schemas of heterogeneous datasets that share a common primary keys but it is unknown which columns are primary keys. The proposed approach consists of two main phases Row Similarity and Attribute Similarity. In the row similarity phase proposed approach determines all the pairs of rows among datasets that are representing same real world entity based on the same primary keys values. In attribute similarity phase, by comparing the data values within those similar pairs of rows our approach able to find the corresponding attributes. Different experiments are performed to validate proposed approach by using real world datasets. The results demonstrated the viability of the proposed approach.
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