Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 23

Search results for: Faraz Nikpour Arani

23 Thematic Redesign of “Nah Al Balaghe” Riverside Park: Constructing the First Cultural Tourism Center in City of Tehran

Authors: Faraz Nikpour Arani, Shahin Haghi Navand


After Two years of operation, the “Nahj Al Balaghe” riverside park, redesigning research was ordered by second region of Tehran municipality, the goal was to construct the first cultural tourism center in city of Tehran. After Pathological and analytical studies of existing situation, that made by field work research’s and interviews, the main problems was identified as lack of thematic design and some physical problems that reduced the activity and livability ratio of the park. The main approach of this project was thematic physical redesign and redefinition of activities in order to the “Nahj Al Balaghe’s” ideas, cultural days in “shamsi calendar”, the “7 artistic dimensions” and “four classical elements”. This paper is the abstraction of a full research that was done by writers.

Keywords: thematic redesign, Nah Al Balaghe riverside park, cultural tourism center, Tehran

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22 Reliability Analysis: A Case Study in Designing Power Distribution System of Tehran Oil Refinery

Authors: A. B. Arani, R. Shojaee


Electrical power distribution system is one of the vital infrastructures of an oil refinery, which requires wide area of study and planning before construction. In this paper, power distribution reliability of Tehran Refinery’s KHDS/GHDS unit has been taken into consideration to investigate the importance of these kinds of studies and evaluate the designed system. In this regard, the authors chose and evaluated different configurations of electrical power distribution along with the existing configuration with the aim of finding the most suited configuration which satisfies the conditions of minimum cost of electrical system construction, minimum cost imposed by loss of load, and maximum power system reliability.

Keywords: power distribution system, oil refinery, reliability, investment cost, interruption cost

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21 Rethinking of Self-Monitoring and Self-Response Roles in Teaching Grammar Knowledge to Iranian EFL Learners

Authors: Gholam Reza Parvizi, Ali Reza Kargar, Amir Arani


In the present days, learning and teaching researchers have emphasized the role which teachers, tutors, and trainers’ constraint knowledge treat in resizing and trimming what they perform in educational atmosphere. Regarding English language as subject to teaching, although the prominence of instructor’s knowledge about grammar has also been stressed, but the lack of empirical insights into the relationship between teacher’ self-monitoring and self-response of grammar knowledge have been observed. With particular attention to the grammar this article indicates and discusses information obtained self- feedback and conversing teachers of a kind who backwash the issue. The result of the study indicates that enabling teachers to progress and maintain a logical and realistic awareness of their knowledge about grammar have to be prominent goal for teachers’ education and development programs.

Keywords: grammar knowledge, self-monitoring, self-response, teaching grammar, language teaching program

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20 Automated Localization of Palpebral Conjunctiva and Hemoglobin Determination Using Smart Phone Camera

Authors: Faraz Tahir, M. Usman Akram, Albab Ahmad Khan, Mujahid Abbass, Ahmad Tariq, Nuzhat Qaiser


The objective of this study was to evaluate the Degree of anemia by taking the picture of the palpebral conjunctiva using Smartphone Camera. We have first localized the region of interest from the image and then extracted certain features from that Region of interest and trained SVM classifier on those features and then, as a result, our system classifies the image in real-time on their level of hemoglobin. The proposed system has given an accuracy of 70%. We have trained our classifier on a locally gathered dataset of 30 patients.

Keywords: anemia, palpebral conjunctiva, SVM, smartphone

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19 The Effect of Different Configurations of Square Panels on the Acoustic of Airport

Authors: Maryam Nikpour, Soude Valipour, Omid Rahaei


Noise disturbance at airports negatively affects people's health. In this study, Ahwaz International Airport in Iran was selected as the case study due to the very long resonance measured in the middle frequencies of 5-10 seconds on this site. To overcome this acoustics problem, we examined eight different square sound-absorbing panels installed on the walls and the ceiling of the airport lounge and were simulated using EASE 4.4 software. In our research, four variables, including acoustic time index (RT, or main index), auditory error coefficient (〖AL〗_CONSE), speech transmission index (STI), and total sound pressure level (SPL) were evaluated according to the international standards of ISO3382 and ISO 3382-1. After the simulation, it was concluded that our Model A compared to other sound-absorbing panels, showed the lowest sound pressure at different frequencies using the above indices.

Keywords: acoustics, flight lounge, noise, sound absorbing panels

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18 Secure Content Centric Network

Authors: Syed Umair Aziz, Muhammad Faheem, Sameer Hussain, Faraz Idris


Content centric network is the network based on the mechanism of sending and receiving the data based on the interest and data request to the specified node (which has cached data). In this network, the security is bind with the content not with the host hence making it host independent and secure. In this network security is applied by taking content’s MAC (message authentication code) and encrypting it with the public key of the receiver. On the receiver end, the message is first verified and after verification message is saved and decrypted using the receiver's private key.

Keywords: content centric network, client-server, host security threats, message authentication code, named data network, network caching, peer-to-peer

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17 Identifying Key Factors for Accidents’ Severity at Rail-Road Level Crossings Using Ordered Probit Models

Authors: Arefeh Lotfi, Mahdi Babaei, Ayda Mashhadizadeh, Samira Nikpour, Morteza Bagheri


The main objective of this study is to investigate the key factors in accidents’ severity at rail-road level crossings. The data required for this study is obtained from both accident and inventory database of Iran Railways during 2009-2015. The Ordered Probit model is developed using SPSS software to identify the significant factors in the accident severity at rail-road level crossings. The results show that 'train speed', 'vehicle type' and 'weather' are the most important factors affecting the severity of the accident. The results of these studies assist to allocate resources in the right place. This paper suggests mandating the regulations to reduce train speed at rail-road level crossings in bad weather conditions to improve the safety of rail-road level crossings.

Keywords: rail-road level crossing, ordered probit model, accidents’ severity, significant factors

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16 Algorithmic Fault Location in Complex Gas Networks

Authors: Soban Najam, S. M. Jahanzeb, Ahmed Sohail, Faraz Idris Khan


With the recent increase in reliance on Gas as the primary source of energy across the world, there has been a lot of research conducted on gas distribution networks. As the complexity and size of these networks grow, so does the leakage of gas in the distribution network. One of the most crucial factors in the production and distribution of gas is UFG or Unaccounted for Gas. The presence of UFG signifies that there is a difference between the amount of gas distributed, and the amount of gas billed. Our approach is to use information that we acquire from several specified points in the network. This information will be used to calculate the loss occurring in the network using the developed algorithm. The Algorithm can also identify the leakages at any point of the pipeline so we can easily detect faults and rectify them within minimal time, minimal efforts and minimal resources.

Keywords: FLA, fault location analysis, GDN, gas distribution network, GIS, geographic information system, NMS, network Management system, OMS, outage management system, SSGC, Sui Southern gas company, UFG, unaccounted for gas

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15 Plasma-Induced Modification of Biomolecules: A Tool for Analysis of Protein Structures

Authors: Yuting Wu, Faraz Choudhury, Daniel Benjamin, James Whalin, Joshua Blatz, Leon Shohet, Michael Sussman, Mark Richards


Plasma-Induced Modification of Biomolecules (PLIMB) has been developed as a technology, which, together with mass spectrometry, measures three-dimensional structural characteristics of proteins. This technique uses hydroxyl radicals generated by atmospheric-pressure plasma discharge to react with the solvent-accessible side chains of protein in an aqueous solution. In this work, we investigate the three-dimensional structure of hemoglobin and myoglobin using PLIMB. Additional modifications to these proteins, such as oxidation, fragmentations, and conformational changes caused by PLIMB are also explored. These results show that PLIMB, coupled with mass spectrometry, is an effective way to determine solvent access to hemoproteins. Furthermore, we show that many factors, including pH and the electrical parameters used to generate the plasma, have a significant influence on solvent accessibility.

Keywords: plasma, hemoglobin, myoglobin, solvent access

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14 Using an Epidemiological Model to Study the Spread of Misinformation during the Black Lives Matter Movement

Authors: Maryam Maleki, Esther Mead, Mohammad Arani, Nitin Agarwal


The proliferation of social media platforms like Twitter has heightened the consequences of the spread of misinformation. To understand and model the spread of misinformation, in this paper, we leveraged the SEIZ (Susceptible, Exposed, Infected, Skeptics) epidemiological model to describe the underlying process that delineates the spread of misinformation on Twitter. Compared to the other epidemiological models, this model produces broader results because it includes the additional Skeptics (Z) compartment, wherein a user may be Exposed to an item of misinformation but not engage in any reaction to it, and the additional Exposed (E) compartment, wherein the user may need some time before deciding to spread a misinformation item. We analyzed misinformation regarding the unrest in Washington, D.C. in the month of March 2020, which was propagated by the use of the #DCblackout hashtag by different users across the U.S. on Twitter. Our analysis shows that misinformation can be modeled using the concept of epidemiology. To the best of our knowledge, this research is the first to attempt to apply the SEIZ epidemiological model to the spread of a specific item of misinformation, which is a category distinct from that of rumor and hoax on online social media platforms. Applying a mathematical model can help to understand the trends and dynamics of the spread of misinformation on Twitter and ultimately help to develop techniques to quickly identify and control it.

Keywords: Black Lives Matter, epidemiological model, mathematical modeling, misinformation, SEIZ model, Twitter

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13 Production, Quality Control, and Biodistribution Studies of 141ce-Edtmp as a Potential Bone Pain Palliation Agent

Authors: Fatemeh Soltani, Simindokht Shirvani Arani, Ali Bahrami Samani, Mahdi Sadeghi, Kamal Yavari


Cerium-141 [T1/2 = 32.501 days, Eβ (max) = 0.580 (29.8%) and 0.435(70.2%) MeV, Eγ=145.44 (48.2%) keV] possesses radionuclidic properties suitable for use in palliative therapy of bone metastases. 141Ce also has gamma energy of 145.44 keV, which resembles that of 99mTc. Therefore, the energy window is adjustable on the Tc-99m energy because of imaging studies. 141Ce can be produced through a relatively easy route that involves thermal neutron bombardment on natural CeO2 in medium flux research reactors (4–5×1013 neutrons/cm2•s). The requirement for an enriched target does not arise. Ethylenediamine tetramethylene phosphonic acid (EDTMP) was synthesized and radiolabeled with 141Ce. Complexation parameters were optimized to achieve maximum yields (>99%). The radiochemical purity of 141Ce-EDTMP was evaluated by radio-thin layer chromatography. The stability of the prepared formulation was monitored for one week at room temperature, and results showed that the preparation was stable during this period (>99%). Biodistribution studies of the complexes carried out in wild-type rats exhibited significant bone uptake with rapid clearance from blood. The properties of produced 141Ce-EDTMP suggest applying a new efficient bone pain palliative therapeutic agent to overcome metastatic bone pains.

Keywords: bone pain palliative, cerium-141, EDTMP, radiopharmaceutical

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12 Vibration Frequency Analysis of Sandwich Nano-Plate on Visco Pasternak Foundation by Using Modified Couple Stress Theory

Authors: Hamed Khani Arani, Mohammad Shariyat, Armaghan Mohammadian


In this research, the free vibration of a rectangular sandwich nano-plate (SNP) made of three smart layers in the visco Pasternak foundation is studied. The core of the sandwich is a piezo magnetic nano-plate integrated with two layers of piezoelectric materials. First-order shear deformation plate theory is utilized to derive the motion equations by using Hamilton’s principle, piezoelectricity, and modified couple stress theory. Elastic medium is modeled by visco Pasternak foundation, where the damping coefficient effect is investigated on the stability of sandwich nano-plate. These equations are solved by the differential quadrature method (DQM), considering different boundary conditions. Results indicate the effect of various parameters such as aspect ratio, thickness ratio, shear correction factor, damping coefficient, and boundary conditions on the dimensionless frequency of sandwich nano-plate. The results are also compared by those available in the literature, and these findings can be used for automotive industry, communications equipment, active noise, stability, and vibration cancellation systems and utilized for designing the magnetostrictive actuator, motor, transducer and sensors in nano and micro smart structures.

Keywords: free vibration, modified couple stress theory, sandwich nano-plate, visco Pasternak foundation

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11 Development and Analysis of Multigeneration System by Using Combined Solar and Geothermal Energy Resources

Authors: Muhammad Umar Khan, Mahesh Kumar, Faraz Neakakhtar


Although industrialization marks to the economy of a country yet it increases the pollution and temperature of the environment. The world is now shifting towards green energy because the utilization of fossil fuels is resulting in global warming. So we need to develop systems that can operate on renewable energy resources and have low heat losses. The combined solar and geothermal multigeneration system can solve this issue. Rather than making rankine cycle purely a solar-driven, heat from solar is used to drive vapour absorption cycle and reheated to generate power using geothermal reservoir. The results are displayed by using Engineering Equation Solver software, where inputs are varied to optimize the energy and exergy efficiencies of the system. The cooling effect is 348.2 KW, while the network output is 23.8 MW and reducing resultant emission of 105553 tons of CO₂ per year. This eco-friendly multigeneration system is capable of eliminating the use of fossil fuels and increasing the geothermal energy efficiency.

Keywords: cooling effect, eco-friendly, green energy, heat loses, multigeneration system, renewable energy, work output

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10 LGG Architecture for Brain Tumor Segmentation Using Convolutional Neural Network

Authors: Sajeeha Ansar, Asad Ali Safi, Sheikh Ziauddin, Ahmad R. Shahid, Faraz Ahsan


The most aggressive form of brain tumor is called glioma. Glioma is kind of tumor that arises from glial tissue of the brain and occurs quite often. A fully automatic 2D-CNN model for brain tumor segmentation is presented in this paper. We performed pre-processing steps to remove noise and intensity variances using N4ITK and standard intensity correction, respectively. We used Keras open-source library with Theano as backend for fast implementation of CNN model. In addition, we used BRATS 2015 MRI dataset to evaluate our proposed model. Furthermore, we have used SimpleITK open-source library in our proposed model to analyze images. Moreover, we have extracted random 2D patches for proposed 2D-CNN model for efficient brain segmentation. Extracting 2D patched instead of 3D due to less dimensional information present in 2D which helps us in reducing computational time. Dice Similarity Coefficient (DSC) is used as performance measure for the evaluation of the proposed method. Our method achieved DSC score of 0.77 for complete, 0.76 for core, 0.77 for enhanced tumor regions. However, these results are comparable with methods already implemented 2D CNN architecture.

Keywords: brain tumor segmentation, convolutional neural networks, deep learning, LGG

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9 An Accurate Brain Tumor Segmentation for High Graded Glioma Using Deep Learning

Authors: Sajeeha Ansar, Asad Ali Safi, Sheikh Ziauddin, Ahmad R. Shahid, Faraz Ahsan


Gliomas are most challenging and aggressive type of tumors which appear in different sizes, locations, and scattered boundaries. CNN is most efficient deep learning approach with outstanding capability of solving image analysis problems. A fully automatic deep learning based 2D-CNN model for brain tumor segmentation is presented in this paper. We used small convolution filters (3 x 3) to make architecture deeper. We increased convolutional layers for efficient learning of complex features from large dataset. We achieved better results by pushing convolutional layers up to 16 layers for HGG model. We achieved reliable and accurate results through fine-tuning among dataset and hyper-parameters. Pre-processing of this model includes generation of brain pipeline, intensity normalization, bias correction and data augmentation. We used the BRATS-2015, and Dice Similarity Coefficient (DSC) is used as performance measure for the evaluation of the proposed method. Our method achieved DSC score of 0.81 for complete, 0.79 for core, 0.80 for enhanced tumor regions. However, these results are comparable with methods already implemented 2D CNN architecture.

Keywords: brain tumor segmentation, convolutional neural networks, deep learning, HGG

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8 Vibration Analysis of Magnetostrictive Nano-Plate by Using Modified Couple Stress and Nonlocal Elasticity Theories

Authors: Hamed Khani Arani, Mohammad Shariyat, Armaghan Mohammadian


In the present study, the free vibration of magnetostrictive nano-plate (MsNP) resting on the Pasternak foundation is investigated. Firstly, the modified couple stress (MCS) and nonlocal elasticity theories are compared together and taken into account to consider the small scale effects; in this paper not only two theories are analyzed but also it improves the MCS theory is more accurate than nonlocal elasticity theory in such problems. A feedback control system is utilized to investigate the effects of a magnetic field. First-order shear deformation theory (FSDT), Hamilton’s principle and energy method are utilized in order to drive the equations of motion and these equations are solved by differential quadrature method (DQM) for simply supported boundary conditions. The MsNP undergoes in-plane forces in x and y directions. In this regard, the dimensionless frequency is plotted to study the effects of small scale parameter, magnetic field, aspect ratio, thickness ratio and compression and tension loads. Results indicate that these parameters play a key role on the natural frequency. According to the above results, MsNP can be used in the communications equipment, smart control vibration of nanostructure especially in sensor and actuators such as wireless linear micro motor and smart nano valves in injectors.

Keywords: feedback control system, magnetostrictive nano-plate, modified couple stress theory, nonlocal elasticity theory, vibration analysis

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7 To Assess Variables Related to Self-Efficacy for Increasing Physical Activity in Advanced-Stage Cancer Patients

Authors: S. Nikpour, S. Vahidi, H. Haghani


Introduction: Exercise has mental and physical health benefits for patients with advanced stage cancer who actively receive chemotherapy, yet little is known about patients’ levels of interest in becoming more active or their confidence in increasing their activity level. Methods and materials: A convenience sample of 200 patients with advanced-stage cancer who were receiving chemotherapy completed self-report measures assessing physical activity level, mood, and quality-of-life variables. Qualitative data on patient-perceived benefits of, and barriers to, physical activity also were collected, coded by independent raters, and organized by predominant themes. Results: Current physical activity level, physical activity outcome expectations, and positive mood were significantly associated with self-efficacy. Fatigue was the most frequently listed barrier to physical activity; improved physical strength and health were the most commonly listed benefits. Participants identified benefits related to both general health and cancer-symptom management that were related to exercise. 59.5% of participants reported that they were seriously planning to increase or maintain their physical activity level, and over 40% reported having interest in receiving an intervention to become more active. Conclusion: These results suggested that many advanced-stage cancer patients who receive chemotherapy are interested in maintaining or increasing their physical activity level and in receiving professional support for exercise. In addition, these individuals identified general health and cancer-specific benefits of, and barriers to, physical activity. Future research will investigate how these findings may be incorporated into physical activity interventions for advanced-stage oncology patients receiving medical treatment.

Keywords: physical activity, cancer, self-efficacy

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6 Preparation of Frozen Bivalent Babesial (Babesia Bovis and Babesia Bigemina) Vaccine from Field Isolates and Evaluation of Its Efficacy in Calves

Authors: Muhammad Fiaz Qamar, Ahmad Faraz, Muhammad Arfan Zaman, Kazim Ali, Waleed Akram


Babesiosis is reflected as the most important disease of cattle that are transmitted by arthropods. In Pakistan, its prevalence is up to 29% in the cattle and buffalo population in different regions. Cattle show a long lasting and durable immunity by giving an infection of B.bovis, B. bigemina, or Babesiadivergens. this is used in cattle to immunize them in a few countries as anti-babesiosis vaccine. Development of frozen vaccine allows for complete testing after production of each batch, However, once thawed, its reduced its shelf life, frozen vaccines are more difficult to transport as well as expensive to produce as compared to chilled vaccine. The contamination of blood derived vaccine has the potential risk that makes pre-production and post-production quality control necessary. For the trail master seed production of whole blood frozen bivalent Babesia(Babesiabovis and Babesiabigemina), 100 blood samples of Babesial positive suspected cattle was taken and processed for separation microscopic detection and rectification by PCR. Vaccine passages were done to reduce the parasitaemiasis in live calves. After 8 passages, parasitemia of Babesia reduced from 80% to 15%. Infected donor calf’s blood was taken by jugular cannulation by using preservative free lithium heparin as an anticoagulant (5 International Units IU heparin/ml blood). In lab, parasite containing blood was mixed in equal volumes with 3 M glycerol in PBS supplemented with 5 mM glucose (final concentration of glycerol 1.5 M) at 37°C. The mixture was then equilibrized at 37°C for 30 minutes and were dispensed in required containers (e.g., 5 ml cryovials).

Keywords: distribution, babesia, primer sequences, PCV

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5 Awareness among Medical Students and Faculty about Integration of Artifical Intelligence Literacy in Medical Curriculum

Authors: Fatima Faraz


BACKGROUND: While Artificial intelligence (AI) provides new opportunities across a wide variety of industries, healthcare is no exception. AI can lead to advancements in how the healthcare system functions and improves the quality of patient care. Developing countries like Pakistan are lagging in the implementation of AI-based solutions in healthcare. This demands increased knowledge and AI literacy among health care professionals. OBJECTIVES: To assess the level of awareness among medical students and faculty about AI in preparation for teaching AI basics and data science applications in clinical practice in an integrated medical curriculum. METHODS: An online 15-question semi-structured questionnaire, previously tested and validated, was delivered among participants through convenience sampling. The questionnaire composed of 3 parts: participant’s background knowledge, AI awareness, and attitudes toward AI applications in medicine. RESULTS: A total of 182 students and 39 faculty members from Rawalpindi Medical University, Pakistan, participated in the study. Only 26% of students and 46.2% of faculty members responded that they were aware of AI topics in clinical medicine. The major source of AI knowledge was social media (35.7%) for students and professional talks and colleagues (43.6%) for faculty members. 23.5% of participants answered that they personally had a basic understanding of AI. Students and faculty (60.1%) were interested in AI in patient care and teaching domain. These findings parallel similar published AI survey results. CONCLUSION: This survey concludes interest among students and faculty in AI developments and technology applications in healthcare. Further studies are required in order to correctly fit AI in the integrated modular curriculum of medical education.

Keywords: medical education, data science, artificial intelligence, curriculum

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4 Chrysin-Loaded PLGA-PEG Nanoparticles Designed for Enhanced Inhibitory Effect on the Breast Cancer Cell Line

Authors: Faraz Zarghami, Elham Anari, Nosratollah Zarghami, Yones Pilehvar-Soltanahmadi, Abolfazl Akbarzadeh, Sepideh Jalilzadeh-Tabrizi


The development of nanotherapy has presented a new method of drug delivery targeted directly to the neoplasmic tissues, to maximize the action with fewer dose requirements. In the past two decades, poly(lactic-co-glycolic acid) (PLGA) has frequently been investigated by many researchers and is a popular polymeric candidate, due to its biocompatibility and biodegradability, exhibition of a wide range of erosion times, tunable mechanical properties, and most notably, because it is a FDA-approved polymer. Chrysin is a natural flavonoid which has been reported to have some significant biological effects on the processes of chemical defense, nitrogen fixation, inflammation, and oxidation. However, the low solubility in water decreases its bioavailability and consequently disrupts the biomedical benefits. Being loaded with PLGA-PEG increases chrysin solubility and drug tolerance, and decreases the discordant effects of the drug. The well-structured chrysin efficiently accumulates in the breast cancer cell line (T47D). In the present study, the structure and chrysin loading were delineated using proton nuclear magnetic resonance (HNMR), Fourier-transform infrared spectroscopy (FT-IR), and scanning electron microscopy (SEM), and the in vitro cytotoxicity of pure and nanochrysin was studied by the MTT assay. Next, the RNA was exploited and the cytotoxic effects of chrysin were studied by real-time PCR. In conclusion, the nanochrysin therapy developed is a novel method that could increase cytotoxicity to cancer cells without damaging the normal cells, and would be promising in breast cancer therapy.

Keywords: MTT assay, chrysin, flavonoids, nanotherapy

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3 Epidemiology of Cutaneous Malignant Melanoma in Pakistan: Incidence, Clinical Subtypes, Tumor Stage and Localization

Authors: Warda Jabeen, Romaisa Shamim Khan, Osama Shakeel, Ahmed Faraz Bhatti, Raza Hussain


Background: The worldwide incidence of cutaneous melanoma (CM) has been on the rise over the past few decades. Primary prevention and early treatment remain the focus of management to reduce the burden of disease. This entails identification of risk factors to prompt early diagnosis. In Pakistan, there is a scarcity of clinico-pathological data relating to cutaneous malignant melanoma. Objective: The purpose of this study was to analyze the epidemiological and clinical characteristics of patients presenting with cutaneous malignant melanoma in Pakistan, and to compare the results with other studies. Method: Shaukat Khanum Memorial Cancer Hospital and Research Centre is currently the only dedicated cancer hospital in the country, accepting patients from all over Pakistan. Majority of the patients, however, belong to the northern half of the country. From the recorded data of the hospital, all cutaneous melanoma cases were identified and evaluated. Results: Between 1997 and 2017, a total of 169 cutaneous melanoma patients were registered at Shaukat Khanum. Mean age was 47.5 years. The highest incidence of melanoma was seen in the age group 40-59 years (n=69, 40.8%). Most commonly reported clinical subtype was unspecified melanoma (n=154, 91%). Amongst those in which T stage was reported, the most frequently observed T-stage at presentation was T4 (n=23, 13.6%). With regards to body distribution, in our study CM was seen most commonly in the lower limb including the hip. The yearly incidence of melanoma has increased/remained stable from 2007 to 2017. Conclusion: cutaneous malignant melanoma is a fairly common disease in Pakistan. Patients tend to present at a more advanced stage as compared to patients in developed countries. Identification of risk factors and tumor characteristics is therefore of paramount importance to deal with these patients.

Keywords: epidemiology of cutaneous malignant melanoma, cutaneous malignant melanoma, Pakistan, skin cancer

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2 Isolate-Specific Variations among Clinical Isolates of Brucella Identified by Whole-Genome Sequencing, Bioinformatics and Comparative Genomics

Authors: Abu S. Mustafa, Mohammad W. Khan, Faraz Shaheed Khan, Nazima Habibi


Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: brucella, bioinformatics, comparative genomics, whole genome sequencing

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1 Evaluation of the Photo Neutron Contamination inside and outside of Treatment Room for High Energy Elekta Synergy® Linear Accelerator

Authors: Sharib Ahmed, Mansoor Rafi, Kamran Ali Awan, Faraz Khaskhali, Amir Maqbool, Altaf Hashmi


Medical linear accelerators (LINAC’s) used in radiotherapy treatments produce undesired neutrons when they are operated at energies above 8 MeV, both in electron and photon configuration. Neutrons are produced by high-energy photons and electrons through electronuclear (e, n) a photonuclear giant dipole resonance (GDR) reactions. These reactions occurs when incoming photon or electron incident through the various materials of target, flattening filter, collimators, and other shielding components in LINAC’s structure. These neutrons may reach directly to the patient, or they may interact with the surrounding materials until they become thermalized. A work has been set up to study the effect of different parameter on the production of neutron around the room by photonuclear reactions induced by photons above ~8 MeV. One of the commercial available neutron detector (Ludlum Model 42-31H Neutron Detector) is used for the detection of thermal and fast neutrons (0.025 eV to approximately 12 MeV) inside and outside of the treatment room. Measurements were performed for different field sizes at 100 cm source to surface distance (SSD) of detector, at different distances from the isocenter and at the place of primary and secondary walls. Other measurements were performed at door and treatment console for the potential radiation safety concerns of the therapists who must walk in and out of the room for the treatments. Exposures have taken place from Elekta Synergy® linear accelerators for two different energies (10 MV and 18 MV) for a given 200 MU’s and dose rate of 600 MU per minute. Results indicates that neutron doses at 100 cm SSD depend on accelerator characteristics means jaw settings as jaws are made of high atomic number material so provides significant interaction of photons to produce neutrons, while doses at the place of larger distance from isocenter are strongly influenced by the treatment room geometry and backscattering from the walls cause a greater doses as compare to dose at 100 cm distance from isocenter. In the treatment room the ambient dose equivalent due to photons produced during decay of activation nuclei varies from 4.22 mSv.h−1 to 13.2 mSv.h−1 (at isocenter),6.21 mSv.h−1 to 29.2 mSv.h−1 (primary wall) and 8.73 mSv.h−1 to 37.2 mSv.h−1 (secondary wall) for 10 and 18 MV respectively. The ambient dose equivalent for neutrons at door is 5 μSv.h−1 to 2 μSv.h−1 while at treatment console room it is 2 μSv.h−1 to 0 μSv.h−1 for 10 and 18 MV respectively which shows that a 2 m thick and 5m longer concrete maze provides sufficient shielding for neutron at door as well as at treatment console for 10 and 18 MV photons.

Keywords: equivalent doses, neutron contamination, neutron detector, photon energy

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