75 results on '"Sadia Rahman"'
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2. CHINA’S HUMAN RIGHTS DIPLOMACY AND THE UYGHUR CRACKDOWN: THE APPEARANCE OF CONSISTENCY AND THE REALITY OF CONTRADICTION. CHINA’S DOUBLE STANDARDS IN HUMAN RIGHTS
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Sadia Rahman and Wei-En Tan
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discourse ,double-standard diplomacy ,regime ,international human rights ,human rights abuse ,china ,uyghur ,Social Sciences ,Philosophy. Psychology. Religion - Abstract
What is the impact of Chinaâs official human rights stance on international human rights discourses/norms? Will Chinaâs ambition to change the international human rights framework succeed, resulting in a new normative order in the world of human rights? The article attempts to address these questions. First, it identifies the stateâs practice pursuing different standards when dealing with human rights issues internationally and domestically. Second, it argues that China is no different from other states when it behaves in a double standard way. The paper maintains, however, that Chinaâs double-standard human rights approach is critical for the future development of the international human rights regime since the CCP leadership intends to redefine human rights in its own interests. While Chinaâs interests align with most states in the third world, its pursuit of normative design is a threat to the current notion of universal human rights.
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- 2022
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3. Sequencing and curation strategies for identifying candidate glioblastoma treatments
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Mayu O. Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Heather Geiger, Vanessa Felice, Esra Dikoglu, Sadia Rahman, Alice Fang, Vladimir Vacic, Ewa A. Bergmann, Julia L. Moore Vogel, Catherine Reeves, Depinder Khaira, Anthony Calabro, Duyang Kim, Michelle F. Lamendola-Essel, Cecilia Esteves, Phaedra Agius, Christian Stolte, John Boockvar, Alexis Demopoulos, Dimitris G. Placantonakis, John G. Golfinos, Cameron Brennan, Jeffrey Bruce, Andrew B. Lassman, Peter Canoll, Christian Grommes, Mariza Daras, Eli Diamond, Antonio Omuro, Elena Pentsova, Dana E. Orange, Stephen J. Harvey, Jerome B. Posner, Vanessa V. Michelini, Vaidehi Jobanputra, Michael C. Zody, John Kelly, Laxmi Parida, Kazimierz O. Wrzeszczynski, Ajay K. Royyuru, and Robert B. Darnell
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Internal medicine ,RC31-1245 ,Genetics ,QH426-470 - Abstract
Abstract Background Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare the ability of different sequencing assays and analysis methods to analyze glioblastoma tumors and generate real-time potential treatment options for physicians. Methods A consortium of seven institutions in New York City enrolled 30 patients with glioblastoma and performed tumor whole genome sequencing (WGS) and RNA sequencing (RNA-seq; collectively WGS/RNA-seq); 20 of these patients were also analyzed with independent targeted panel sequencing. We also compared results of expert manual annotations with those from an automated annotation system, Watson Genomic Analysis (WGA), to assess the reliability and time required to identify potentially relevant pharmacologic interventions. Results WGS/RNAseq identified more potentially actionable clinical results than targeted panels in 90% of cases, with an average of 16-fold more unique potentially actionable variants identified per individual; 84 clinically actionable calls were made using WGS/RNA-seq that were not identified by panels. Expert annotation and WGA had good agreement on identifying variants [mean sensitivity = 0.71, SD = 0.18 and positive predictive value (PPV) = 0.80, SD = 0.20] and drug targets when the same variants were called (mean sensitivity = 0.74, SD = 0.34 and PPV = 0.79, SD = 0.23) across patients. Clinicians used the information to modify their treatment plan 10% of the time. Conclusion These results present the first comprehensive comparison of technical and machine augmented analysis of targeted panel and WGS/RNA-seq to identify potential cancer treatments.
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- 2019
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4. A Randomised Control Trial Comparing the Efficacy of LMA-Supreme and I-Gel as Rescue Ventilatory Device in Patients with Simulated Difficult Airway Undergoing Anaesthesia with Controlled Ventilation
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SADIA RAHMAN, NIDHI AGARWAL, SUSHIL GURIA, SWATI JAIN, and MONA SWAIN
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extrication collar ,laryngeal mask airway supreme ,oropharyngeal leak pressure ,supraglottic airway devices ,Medicine - Abstract
Introduction: In an unanticipated difficult airway or in an emergency situation of cannot-intubate-cannot-ventilate scenario, Supraglottic Airway Devices (SGD) are recommended as rescue devices for establishing airway quickly to prevent hypoxia. Aim: To compare efficacy of i-gel airway and Laryngeal Mask Airway supreme (LMA supreme) as ventilatory devices and the time taken for their insertion in anaesthetised and paralysed patients with simulated difficult airway. Materials and Methods: One hundred and eighty adult patients with simulated difficult airway were randomly allocated to two groups of 90 patients each. In group I: i-gel and in group S: LMA supreme was inserted. Primary outcome studied was time taken for insertion of SGD. Secondary outcomes were the number of attempts taken for insertion of device, oropharyngeal leak pressure, ease of gastric catheter insertion, fibreoptic bronchoscopic view of anatomical alignment of device with glottic opening. Quantitative variables were compared using unpaired t-test/Mann-Whitney Test, between the two groups. Qualitative variable were compared using Chi-Square test/ Fisher’s-exact test. Results: Total time taken for successful insertion was significantly shorter with group i-gel as compared to group LMA supreme {median (IQR) {19 (18.25-21)} versus {24 (23-24)} with p-value ≤0.0001. Overall success rate of insertion (96.67% vs 97.78%, p=1.000) and oropharyngeal leak pressure (p-value=0.555) of i-gel and LMA-S were comparable. i-gel has better anatomic alignment with glottic opening as compared to LMA-S (p-value ≤0.0001). Gastric tube insertion was easy in all patients in both the groups. Conclusion: Shorter time for the insertion of i-gel was observed due to absence of inflatable cuff, although both LMA-S and i-gel are equally efficacious as ventilatory devices in patients with simulated difficult airway under general anaesthesia with controlled ventilation.
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- 2021
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5. Correction to: Sequencing and curation strategies for identifying candidate glioblastoma treatments
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Mayu O. Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Heather Geiger, Vanessa Felice, Esra Dikoglu, Sadia Rahman, Xiaolan Fang, Vladimir Vacic, Ewa A. Bergmann, Julia L. Moore Vogel, Catherine Reeves, Depinder Khaira, Anthony Calabro, Duyang Kim, Michelle F. Lamendola-Essel, Cecilia Esteves, Phaedra Agius, Christian Stolte, John Boockvar, Alexis Demopoulos, Dimitris G. Placantonakis, John G. Golfinos, Cameron Brennan, Jeffrey Bruce, Andrew B. Lassman, Peter Canoll, Christian Grommes, Mariza Daras, Eli Diamond, Antonio Omuro, Elena Pentsova, Dana E. Orange, Stephen J. Harvey, Jerome B. Posner, Vanessa V. Michelini, Vaidehi Jobanputra, Michael C. Zody, John Kelly, Laxmi Parida, Kazimierz O. Wrzeszczynski, Ajay K. Royyuru, and Robert B. Darnell
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Internal medicine ,RC31-1245 ,Genetics ,QH426-470 - Abstract
Following publication of the original article [1], it was reported that the given name of the fourteenth author was incorrectly published. The incorrect and the correct names are given below.
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- 2019
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6. Sustainability of Rainwater Harvesting System in terms of Water Quality
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Sadia Rahman, M. T. R. Khan, Shatirah Akib, Nazli Bin Che Din, S. K. Biswas, and S. M. Shirazi
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Technology ,Medicine ,Science - Abstract
Water is considered an everlasting free source that can be acquired naturally. Demand for processed supply water is growing higher due to an increasing population. Sustainable use of water could maintain a balance between its demand and supply. Rainwater harvesting (RWH) is the most traditional and sustainable method, which could be easily used for potable and nonpotable purposes both in residential and commercial buildings. This could reduce the pressure on processed supply water which enhances the green living. This paper ensures the sustainability of this system through assessing several water-quality parameters of collected rainwater with respect to allowable limits. A number of parameters were included in the analysis: pH, fecal coliform, total coliform, total dissolved solids, turbidity, NH3–N, lead, BOD5, and so forth. The study reveals that the overall quality of water is quite satisfactory as per Bangladesh standards. RWH system offers sufficient amount of water and energy savings through lower consumption. Moreover, considering the cost for installation and maintenance expenses, the system is effective and economical.
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- 2014
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7. Experimental Study on Tsunami Risk Reduction on Coastal Building Fronted by Sea Wall
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Sadia Rahman, Shatirah Akib, M.T.R. Khan, and S. M. Shirazi
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Technology ,Medicine ,Science - Abstract
This experimental study was conducted to idealize the efficacy of sea wall in controlling the tsunami forces on onshore structures. Different types of sea walls were placed in front of the building model. The tsunami forces and the wave heights were measured with and without the sea wall conditions. Types of sea wall, wall height, and wall positions were varied simultaneously to quantify the force reductions. Maximum of 41% forces was reduced by higher sea wall, positioned closer proximity to the model whereas this reduction was about 27% when the wall height was half of the high wall. Experimental investigations revealed that wall with adequate height and placed closer to the structures enables a satisfactory predictor of the force reduction on onshore structures. Another set of tests were performed with perforated wall placing near the building model. Less construction cost makes the provision of perforated sea wall interesting. The overall results showed that the efficacy of perforated wall is almost similar to solid wall. Hence, it can be efficiently used instead of solid wall. Moreover, overtopped water that is stuck behind the wall is readily gone back to the sea through perforations releasing additional forces on the nearby structures.
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- 2014
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8. Why Do Some Homeless Succeed While Others Falter? A Network Science Perspective.
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Charalampos Chelmis and Khandker Sadia Rahman
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- 2024
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9. Bayesian Network Modeling and Prediction of Transitions Within the Homelessness System.
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Khandker Sadia Rahman, Daphney-Stavroula Zois, and Charalampos Chelmis
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- 2023
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10. Predictive Modeling of Homeless Service Assignment: A Representation Learning Approach.
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Khandker Sadia Rahman and Charalampos Chelmis
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- 2024
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11. Detecting Racist Text in Bengali: An Ensemble Deep Learning Framework.
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S. S. Saruar Jahan, Nusrat Jahan, and Sadia Rahman Priota
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- 2024
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12. Learning to Predict Transitions within the Homelessness System from Network Trajectories.
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Khandker Sadia Rahman and Charalampos Chelmis
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- 2022
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13. Ultrasound‐guided embolization for renal artery pseudoaneurysm in solitary kidney.
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Augustine, Sana, Patel, Mitwa, Inban, Pugazhendi, Synthia, Sk Sadia Rahman, Asfeen, Ummul Z, Yaqub, Aliza, Mahmood Khan, Aadil, and Singh, Mansi
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- 2025
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14. Peeking through the homelessness system with a network science lens.
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Charalampos Chelmis and Khandker Sadia Rahman
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- 2021
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15. Climate Change Impact and Comprehensive Disaster Management Approach in Bangladesh: A Review
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Islam, Md. Nazrul, Tamanna, Sahanaj, van Amstel, André, Noman, Md., Ali, Md. Sajid Saadat, Aparajita, Ditiya Malek, Roy, Prantanu, Tanha, Sadia Rahman, Sarkar, Nayem, Ashiquzzaman, Md., Ghosh, Sobuj Kumar, Hasnat, Syeda Raisa, Bhuiyan, Md. Farhanuzzaman, Sayef, Md., Saha, Protyaee, Hasan, Gazi Rokibul, Ghosh, Adipta, Dodson, John, Series Editor, Islam, Md. Nazrul, and van Amstel, André
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- 2021
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16. Modeling and predicting individual transitions within the homelessness system.
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Khandker Sadia Rahman and Charalampos Chelmis
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- 2023
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17. Detecting Racist Text in Bengali: An Ensemble Deep Learning Framework
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Saruar Jahan, S. S., primary, Jahan, Nusrat, additional, and Priota, Sadia Rahman, additional
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- 2023
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18. Study Comparing Between Surgical Evacuation and Medical Management with Vaginal Misoprostol for Early Pregnancy Loss
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Sadia Rahman, Rabeya Parvin, Most Nur A Sharmin, Md Nazmul Arefin, Md Ashraful Islam, Zillur Rahman, Md Aziz Ullah, Md Aminul Islam, and Afsana Begum
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General Medicine - Abstract
Background: Early pregnancy loss is one of the most common clinical problems that is encountered in dailygynaecological practice. The aim of this study is to assess the effectiveness and acceptability of using vaginalmisoprostol for management of first trimester spontaneous incomplete abortion as an alternative to direct vaginalsurgical evacuation in our setting. Methods: This prospective randomized study was carried out in the Department of Obstetrics and Gynaecology inShaheed Ziaur Rahman Medical College Hospital, Bogra. from January 2008 to December 2008. This study performedon 400 patients with first trimester incomplete abortion between 8 and 12 weeks requesting medical management. Theywere divided into two groups according to patients’ choice; group (I) received 800 microgram misprostol vaginally bydigital insertion into the posterior fornix while group (II) underwent surgical vaginal evacuation directly under generalanesthesia. Results: Although vaginal surgical evacuation was successful in solving the problem in 100% of cases, misoprostol wassuccessful in 70% after 1st dose and remained incomplete 30% after administration of 2nd dose. The overall satisfactionwas slightly higher in the surgical group. No serious side effects or complications were reported in the misoprostolgroup. The incidence of excessive post-abortive bleeding was more in the misoprostol group than in the surgicalevacuation group (p = 0.049). Conclusion: Although vaginal surgical evacuation is more effective than misoprostol in solving the problem stillmedical treatment is effective and acceptable especially when surgical management is not available or risky or patientsrefuse to do surgical management. Bangladesh Crit Care J March 2023; 11 (1): 19-23
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- 2023
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19. A Comparative Study between Metal Clip Application and Suture Ligation of Cystic Duct in Laparoscopic Cholecystectomy
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Mahmudul Hasan Chowdhury, Md Aziz Ullah, Md Zillur Rahman, Sadia Rahman, Nazmul Arefin, and Md Ashraful Islam
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General Medicine - Abstract
Introduction: Laparoscopic cholecystectomy has been performed for decades and is a fairly standardized procedure throughout the world. Occlusion of the cystic duct is popularly done with the help of metal clips. There are many other techniques described in the literature to deal with occlusion of the Cystic Duct. Suture ligation of the duct is one such way.To evaluate the effectiveness in term of cost, safety, and complication in occlusion of cystic duct with suture ligation compared to clip application. Materials and Methods: A prospective cross sectional comparative study was carried out From June 2020 to November 2020. Data were collected from 80 patients undergone laparoscopic cholecystectomy for Gall stone diseases. 40 patients were enrolled in each group by consecutive purposive sampling. Complete history was taken. Thorough clinical examination was done. Relevant investigations report was collected. Results: Female patients were predominant in both groups and most of the patients were underweight. Mean time for ligation was more in occlusion of cystic duct with clip application. Bile leakage was found and duration of drain in situ was more in occlusion with clip application. Cost was high in occlusion with clip application. Conclusion: : Time for ligation, Bile leakage, mean duration of drain in situ (days), and cost of Cystic Duct occlusion and port closure were significantly higher in Laparoscopic Cholecystectomy with conventional Clip application of Cystic Duct group in comparison to Laparoscopic Cholecystectomy with ligation of the Cystic duct with no-1vicryl by extra corporeal knotting group. Medicine Today 2023 Vol.35(1): 27-30
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- 2023
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20. Real time injecting device with automated robust vein detection using near infrared camera and live video.
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Tamim Ahmed, Khandker Sadia Rahman, Sk Subrina Shawlin, Mohammad Hasan, Arnab Bhattacharjee, Shaikh Anowarul Fattah, and Celia Shahnaz
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- 2017
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21. Uso profiláctico de apósitos de silicona para minimizar las lesiones por presión: revisión sistemática y metaanálisis
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Sk Sadia Rahman-Synthia, Sumeet Kumar, Sukhman Boparai, Swatika Gupta, Ali Mohtashim, and Danish Ali
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General Medicine ,General Nursing - Published
- 2023
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22. China’s Soft Power, Counter-Localisation, and the Role of Stateless Uyghurs in Turkey
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Sadia Rahman and Darren Byler
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General Medicine - Published
- 2022
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23. Melioidosis: A case of multiple subcutaneous abscesses with sepsis
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Mizanur Rahman Khan, Sadia Rahman, Chowdhury Adnan Sami, Hasan Mostafa Rashed, Abed Hussain Khan, and Shohael Mahmud Arafat
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General Medicine - Abstract
Melioidosis has lately expanded its endemic areas to encompass the Indian subcontinent, despite being well-known in Southeast Asia and Northern Australia.Though cases have been reported from Bangladesh, it might be a significantly underdiagnosed cause of infection & death in this agricultural country. We report a case of melioidosis with multiple abscesses & fulminant sepsis in a 55-year-old farmer diagnosed based on pus samples, which revealed gram-negative bacillus Burkholderiapseudomallei. Bangladesh J Medicine 2022; 33: 308-311
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- 2022
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24. Topical Cream Carrying Drug-Loaded Nanogels for Melanoma Treatment
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Sadia Rahman, Tasmima N. Haque, Vrashabh V. Sugandhi, Aishwarya L. Saraswat, Xiaoban Xin, and Hyunah Cho
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Pharmacology ,Organic Chemistry ,Pharmaceutical Science ,Molecular Medicine ,Pharmacology (medical) ,Biotechnology - Published
- 2023
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25. Performance evaluation of different seasonal adjustment techniques
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Salma, Nahid, primary, Lira, Sadia Rahman, additional, Alam, Md. Asraful, additional, and Mahmud, Shohel, additional
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- 2023
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26. Multicentric Castleman Disease: The Hyaline Vascular Type Without HIV Association in a Young Male With Cutaneous Manifestation and Renal Impairment
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Abed H Khan, Mohammad Ferdous Ur Rahaman, Sadia Rahman, Mizanur Rahman Khan, and Chowdhury Adnan Sami
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General Engineering - Published
- 2022
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27. Physical assessment of wave forces on bridge girder impacted by potential tsunami hazard
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Sadia Rahman and M. T. R. Khan
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Fluid Flow and Transfer Processes ,Environmental Engineering ,010504 meteorology & atmospheric sciences ,0208 environmental biotechnology ,02 engineering and technology ,01 natural sciences ,Bridge (interpersonal) ,020801 environmental engineering ,Tsunami hazard ,Girder ,Wave height ,Wave force ,Forensic engineering ,Geology ,0105 earth and related environmental sciences ,Water Science and Technology ,Civil and Structural Engineering - Abstract
Bridges are one of the most susceptible structural elements that can be viciously impacted by tsunami disaster. During the latest few tsunami hazards, a number of bridges were affected severely due...
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- 2020
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28. Synthesis and investigation of dyeing properties of 8-hydroxyquinoline-based azo dyes
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Khadija Begum, Md. Mustafizur Rahman, Abdullah Al Noman, Sadia Rahman, Tarek Md. Anamul Haque, Rony Mia, Nafish Sams Sourav, and Subrina Yesmin
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chemistry.chemical_classification ,Materials science ,010405 organic chemistry ,Salt (chemistry) ,Infrared spectroscopy ,8-Hydroxyquinoline ,General Chemistry ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Disperse dye ,Rubbing ,Polyester ,chemistry.chemical_compound ,chemistry ,Phenol ,Dyeing ,Nuclear chemistry - Abstract
A facile and well-known synthetic strategy has been used to prepare two novel 8-hydroxyquinoline-based azo dyes to apply as a disperse dye to polyester fabric. In this method, 8-hydroxyquinoline possessing a “privileged structure” which is made up of two rings, a phenol ring fused with pyridine ring, has been coupled with diazonium salt obtained from 2-amino-6-nitrotoluene (Dye-I) and with the diazonium salt obtained from 4-chloro-aniline (Dye-II). The structure of the dyes has been confirmed using nuclear magnetic resonance spectroscopy, Fourier-transform infrared spectroscopy, and elemental analysis. As-synthesized dyes are used as disperse to polyester fabric, and the dyed samples were characterized for color fastness to washing, light, rubbing, and perspiration. The fastness testing results indicate that the dyes have a good affinity to PET fabric as the dyed PET fabrics have moderate to excellent fastness to washing and light and very good fastness to rubbing and perspiration. The dyeing property of 8-hydroxyquinoline-based dyes is very promising and can be considered as the potential candidate to meet the actual demand of PET fabric dyeing in the textile industry.
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- 2020
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29. Psychological Features in Patients with Different Patterns of Irritable Bowel Syndrome
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Syed Alamgir Safwath, Fahmida Akter, Dilip Kumar Ghosh, and Sadia Rahman Chowdhury
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medicine.medical_specialty ,business.industry ,Hostility ,Context (language use) ,medicine.disease ,Diarrhea ,Internal medicine ,Psychoticism ,Medicine ,Anxiety ,Psychological testing ,medicine.symptom ,business ,Irritable bowel syndrome ,Depression (differential diagnoses) - Abstract
Context: Irritable bowel syndrome (IBS) is one of the most common chronic gastrointestinal (GI) disorders. Recently, many studies have found the association between irritable bowel syndrome (IBS) & the psychological factors. Aims: The study aimed to determine the relationship between psychological features and different subtypes and severity of irritable bowel syndrome. Settings and Design: This cross-sectional study was performed among 208 outpatients diagnosed as irritable bowel syndrome in two government medical college hospitals of Dhaka city from January, 2015 to December, 2015. The subtypes and severity of irritable bowel syndrome were assessed by Rome-III and ‘Irritable bowel syndrome severity scoring scale’ respectively. Psychological features were assessed by Brief Symptom Inventory consisting 53 items of psychological problems. Results: Global severity index of Brief Symptom Inventory, which is the best indicator of psychological distress, was found significantly higher in respondents with diarrhea predominant IBS (p< 0.001) and severe IBS patients (p< 0.001). Mean scores of other psychological problems among Brief Symptom Inventory -53 subscales (hostility, interpersonal sensitivity, paranoid ideation, psychoticism, depression, anxiety) were significantly higher in diarrhoea predominant IBS and severe IBS patients compared to the others (p
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- 2020
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30. Fluorescence Intensity Fluctuation Analysis of Protein Oligomerization in Cell Membranes
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Tom D, Killeen, Sadia, Rahman, Dammar N, Badu, Gabriel, Biener, Michael R, Stoneman, and Valerică, Raicu
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Diffusion ,Medical Laboratory Technology ,Spectrometry, Fluorescence ,Microscopy, Fluorescence ,General Immunology and Microbiology ,General Neuroscience ,Cell Membrane ,Proteins ,Health Informatics ,General Pharmacology, Toxicology and Pharmaceutics ,General Biochemistry, Genetics and Molecular Biology - Abstract
Fluorescence fluctuation spectroscopy (FFS) encompasses a bevy of techniques that involve analyzing fluorescence intensity fluctuations occurring due to fluorescently labeled molecules diffusing in and out of a microscope's focal region. Statistical analysis of these fluctuations may reveal the oligomerization (i.e., association) state of said molecules. We have recently developed a new FFS-based method, termed Two-Dimensional Fluorescence Intensity Fluctuation (2D FIF) spectrometry, which provides quantitative information on the size and stability of protein oligomers as a function of receptor concentration. This article describes protocols for employing FIF spectrometry to quantify the oligomerization of a membrane protein of interest, with specific instructions regarding cell preparation, image acquisition, and analysis of images given in detail. Application of the FIF Spectrometry Suite, a software package designed for applying FIF analysis on fluorescence images, is emphasized in the protocol. Also discussed in detail is the identification, removal, and/or analysis of inhomogeneous regions of the membrane that appear as bright spots. The 2D FIF approach is particularly suited to assess the effects of agonists and antagonists on the oligomeric size of membrane receptors of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of live cells expressing protein constructs Basic Protocol 2: Image acquisition and noise correction Basic Protocol 3: Drawing and segmenting regions of interest Basic Protocol 4: Calculating the molecular brightness and concentration of individual image segments Basic Protocol 5: Combining data subsets using a manual procedure (Optional) Alternate Protocol 1: Combining data subsets using the advanced FIF spectrometry suite (Optional; alternative to Basic Protocol 5) Basic Protocol 6: Performing meta-analysis of brightness spectrograms Alternate Protocol 2: Performing meta-analysis of brightness spectrograms (alternative to Basic Protocol 6) Basic Protocol 7: Spot extraction and analysis using a manual procedure or by writing a program (Optional) Alternate Protocol 3: Automated spot extraction and analysis (Optional; alternative to Protocol 7) Support Protocol: Monomeric brightness determination.
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- 2022
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31. Prophylactic use of silicone dressing to minimize pressure injuries: Systematic review and meta-analysis
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Sk Sadia Rahman-Synthia, Sumeet Kumar, Sukhman Boparai, Swatika Gupta, Ali Mohtashim, and Danish Ali
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General Medicine - Abstract
Preventing hospital-acquired pressure injuries (PI) in critically ill patients remains a significant clinical challenge because of its associated high risk for comorbid conditions. We assessed the preventive effectiveness of silicone dressings among patients admitted in intensive care units and non-intensive care units settings.A literature search was conducted across 3 electronic databases (MEDLINE, EMBASE, Cochrane Central) from inception through December 2021. Studies assessing the effectiveness of silicone dressing on the incidence of PI on the sacral area were included. Evaluations were reported as risk ratios (RRs) with 95% confidence interval, and analysis was performed using a random-effects model.Of the 1056 articles retrieved from the initial search, 11 studies were included in the final analysis. Silicone dressings significantly reduced the incidence of PI compared to usual care (RR: 0.30, 95% CI: 0.19-0.45, P0.01). We found no significant difference between results of studies conducted in intensive care settings (RR=0.25, 95% CI: 0.15-0.43, P0.01) and non-intensive care settings (RR=0.38, 95% CI: 0.17-0.83, P=0.01) (P-interaction: 0.39). Silicone dressings reduced the risk of developing PI among patients using five-layer foam Border dressing (Mepilex® Sacrum) (RR: 0.31, 95% CI: 0.20-0.48, P0.01), and dressing Allevyn Gentle Border® (RR: 0.10, 95% CI: 0.01-0.73, P=0.02) with no significant difference upon subgroup analysis (P-interaction: 0.27).The present meta-analysis suggests that silicone dressings consistently reduce the incidence of PI in intensive as well as in non-intensive care settings, regardless of the type of dressing used.
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- 2022
32. An IoT Based Integrated Health Monitoring System
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Salma Sultana, Sadia Rahman, Md. Atikur Rahman, Narayan Ranjan Chakraborty, and Tanveer Hasan
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- 2021
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33. Lured to Linger
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Sarah El Halwany, Nurul Hassan Mohammad, Minja Milanovic, Larry Bencze, Majd Zouda, and Sadia Rahman
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Pedagogy ,Science teachers ,Sociology ,Science education - Abstract
This article provides an overview of relationships among science teachers, school science students and science education researchers.
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- 2020
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34. China’s Hard-line Approach and Ethnic Unrest in Xinjiang: A Theoretical Understanding
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Sadia Rahman
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Radicalization ,Islamophobia ,media_common.quotation_subject ,05 social sciences ,Ethnic conflict ,Unrest ,050601 international relations ,Indigenous ,0506 political science ,State (polity) ,Political economy ,Political science ,050602 political science & public administration ,General Earth and Planetary Sciences ,China ,Legitimacy ,General Environmental Science ,media_common - Abstract
Ethnic conflicts issue has perturbed China for quite a long period, hence China is not a one-Unified nation, PRC is very clear that Xinjiang was and is part of China just like its other disputed territorial claims and it does not recognize the Uyghurs as the indigenous people of Xinjiang calling them settlers. In this paper, I have studied the PRC’s official history of Xinjiang and the historians’ history who are specialized in Xinjiang and the Silk Road history to understand the two different narratives that are fundamentally different and incompatible from each other. The framework used is the typology of qualitative studies as this is helpful to assess the situation theoretically and categorize accordingly. Beijing is very harsh towards the Uyghurs and has detained over one- million of the Uyghurs for ‘re-education’ to show its legitimacy and they are considered a threat to the state’s existence, post 9/11 China has been using this global Islamophobia wave justifying that all steps taken by the state are to combat radicalization. This paper is not about the Uyghurs trace being found connected to external non-state actors, whereas the study takes a dig in securitization discourse discussing that, the Uyghurs does not have a structured way of attacks like terrorists, its more of showing dissatisfaction against the authorities because neither they have the autonomy nor have any rights to exercise. The Chinese policies are countering them back in terms of attacks because the Uyghurs are relatively deprived and they are in a constant source of competition with the Han Chinese.
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- 2020
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35. A Randomised Control Trial Comparing the Efficacy of LMA-Supreme and I-Gel as Rescue Ventilatory Device in Patients with Simulated Difficult Airway Undergoing Anaesthesia with Controlled Ventilation
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Mona Swain, Swati Jain, Sushil Guria, Nidhi Agarwal, and Sadia Rahman
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extrication collar ,business.industry ,oropharyngeal leak pressure ,Clinical Biochemistry ,General Medicine ,Controlled ventilation ,Anesthesia ,Medicine ,laryngeal mask airway supreme ,In patient ,supraglottic airway devices ,business ,Difficult airway - Abstract
Introduction: In an unanticipated difficult airway or in an emergency situation of cannot-intubate-cannot-ventilate scenario, Supraglottic Airway Devices (SGD) are recommended as rescue devices for establishing airway quickly to prevent hypoxia. Aim: To compare efficacy of i-gel airway and Laryngeal Mask Airway supreme (LMA supreme) as ventilatory devices and the time taken for their insertion in anaesthetised and paralysed patients with simulated difficult airway. Materials and Methods: One hundred and eighty adult patients with simulated difficult airway were randomly allocated to two groups of 90 patients each. In group I: i-gel and in group S: LMA supreme was inserted. Primary outcome studied was time taken for insertion of SGD. Secondary outcomes were the number of attempts taken for insertion of device, oropharyngeal leak pressure, ease of gastric catheter insertion, fibreoptic bronchoscopic view of anatomical alignment of device with glottic opening. Quantitative variables were compared using unpaired t-test/Mann-Whitney Test, between the two groups. Qualitative variable were compared using Chi-Square test/Fisher’s-exact test. Results: Total time taken for successful insertion was significantly shorter with group i-gel as compared to group LMA supreme {median (IQR) {19 (18.25-21)} versus {24 (23-24)} with p-value ≤0.0001. Overall success rate of insertion (96.67% vs 97.78%, p=1.000) and oropharyngeal leak pressure (p-value=0.555) of i-gel and LMA-S were comparable. i-gel has better anatomic alignment with glottic opening as compared to LMA-S (p-value ≤0.0001). Gastric tube insertion was easy in all patients in both the groups. Conclusion: Shorter time for the insertion of i-gel was observed due to absence of inflatable cuff, although both LMA-S and i-gel are equally efficacious as ventilatory devices in patients with simulated difficult airway under general anaesthesia with controlled ventilation.
- Published
- 2021
36. Small Molecules Targeting Biological Clock; A Novel Prospective for Anti-Cancer Drugs
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Sadia Rahman, Karlo Wittine, Elitza Markova-Car, and Mirela Sedić
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circadian rhythm ,Biological clock ,Pharmaceutical Science ,Antineoplastic Agents ,biological clock ,Review ,Biology ,Analytical Chemistry ,Small Molecule Libraries ,03 medical and health sciences ,0302 clinical medicine ,Circadian Clocks ,Neoplasms ,Drug Discovery ,medicine ,cancer ,small molecules ,anticancer drugs ,Animals ,Humans ,Circadian rhythm ,Molecular Targeted Therapy ,Physical and Theoretical Chemistry ,030304 developmental biology ,0303 health sciences ,Organic Chemistry ,Cancer ,medicine.disease ,Small molecule ,Chemistry (miscellaneous) ,030220 oncology & carcinogenesis ,Anti cancer drugs ,Molecular Medicine ,Identification (biology) ,Neuroscience - Abstract
The circadian rhythms are an intrinsic timekeeping system that regulates numerous physiological, biochemical, and behavioral processes at intervals of approximately 24 h. By regulating such processes, the circadian rhythm allows organisms to anticipate and adapt to continuously changing environmental conditions. A growing body of evidence shows that disruptions to the circadian rhythm can lead to various disorders, including cancer. Recently, crucial knowledge has arisen regarding the essential features that underlie the overt circadian rhythm and its influence on physiological outputs. This knowledge suggests that specific small molecules can be utilized to control the circadian rhythm. It has been discovered that these small molecules can regulate circadian-clock-related disorders such as metabolic, cardiovascular, inflammatory, as well as cancer. This review examines the potential use of small molecules for developing new drugs, with emphasis placed on recent progress that has been made regarding the identification of small-molecule clock modulators and their potential use in treating cancer.
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- 2020
37. Evaluation of Socio-demographic and Lifestyle Factors Among Subtypes of Irritable Bowel Syndrome
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Dilip Kumar Ghosh, Sadia Rahman Chowdhury, Syed Alamgir Safwath, Madhusudan Saha, Mohammad Mahmuduzzaman, Muiz Uddin Ahmed Choudhury, and Jahangir Alam
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Gerontology ,Lifestyle factors ,business.industry ,Socio demographics ,medicine ,medicine.disease ,business ,Irritable bowel syndrome - Abstract
Background: Irritable bowel syndrome (IBS) is one of the most common functional gastrointestinal disorder with absence of organic damages to the intestine. The pathophysiology of IBS is still not completely understood, but in some cases psychological disorders may affect the onset and outcome of IBS. Some studies have found disparities between subtypes of irritable bowel syndrome (IBS) regarding socio-demographic characteristics and lifestyle factors.Methods: This cross-sectional study aimed to investigate whether there are differences in sociodemographic and lifestyle factors including smoking and physical activity between the subtypes of IBS. The study was performed on outpatients diagnosed as irritable bowel syndrome (from January 2015 to December 2015) in Dhaka Medical College Hospital and Shaheed Suhrawardy Medical College Hospital in Dhaka. A total of purposively selected 208 diagnosed IBS patients were interviewed by semi-structured questionnaire in which subtype of irritable bowel syndrome were measured by Rome-III criteria regarding stool consistency.Results: Mean age of the respondents was 32.3 (+ 10.32) years and majority of them were male (77%), married (66.8%), educated up to secondary level (35.6%), labour (skilled and unskilled) (30%), non- smoker (67.3%) and HEPA (health enhancing physical activity) active (65.9%). Diarrhea predominant irritable bowel syndrome (50%) was found the most common subtype among the irritable bowel syndrome respondents followed by mixed type irritable bowel syndrome (42%) and constipation predominant irritable bowel syndrome (8%) There were no statistical differences found between constipation predominant irritable bowel syndrome ( IBS-C), Diarrhea predominant irritable bowel syndrome (IBS-D), and mixed type irritable bowel syndrome (IBSM) patients regarding to socio-demographic characteristics and lifestyle factors (P
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- 2018
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38. Psychological Features in Patients with Different Patterns of Irritable Bowel Syndrome
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Chowdhury, Sadia Rahman, primary, Safwath, Syed Alamgir, primary, Ghosh, Dilip Kumar, primary, and Akter, Fahmida, primary
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- 2020
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39. Role of atd Angle of Palm in Diagnosis of Pulmonary Tuberculosis
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Sadia Rahman, Shamim Ara, Nadia Islam, Saida Rashed, KM Monjurul Alom, and Afrose Ahmed
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medicine.medical_specialty ,education.field_of_study ,Dermal ridges ,business.industry ,Population ,General Medicine ,Control subjects ,Surgery ,Pulmonary tuberculosis ,Internal medicine ,Early prediction ,medicine ,Vulnerable population ,In patient ,education ,business ,Palm - Abstract
Background: Dermtoglyphics are the lines and ridges forming a skin pattern, especially on the palm of the hands, fingertips and soles of feet. Differentiations of dermal ridges in early life are genetically determined1. Any disturbance by genetic factors causes development of unusual dermatoglyphics. On the other hand, deficiency of Mannose binding protein (MBP) gene and Interleukin-1 (IL-1) gene cause spread of pulmonary tuberculosis2. The dermatoglyphic pattern in patient with pulmonary tuberculosis can represent an anatomical, non-invasive, inexpensive tool for screening high-risk population, and facilitates early prediction of vulnerable population of PTB.Materials and Methods: A Cross-sectional, analytical type of study was conducted in Department of Anatomy, Dhaka Medical College, Dhaka, from January 2012 to December 2012. The study was performed in 100 patients suffering from pulmonary tuberculosis and 100 healthy individuals.Results: There was significant reduction in mean±SD of atd angle in pulmonary tuberculosis patients in comparison to control subjects. Mean±SD of atd angle was 37.87±3.403 in pulmonary tuberculosis patients and 49.77±4.628 in the control subjects. The difference was highly significant (P
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- 2017
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40. PREPARATION AND EVALUATION OF NAPROXEN SODIUM SUSTAINED RELEASE ENTERIC COATED TABLETS USING METHOCEL K15M CR AND INSTACOAT EN-II
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Parbon Mehmud Pantho, Kashfia Jalil, and Chaity, Sadia Rahman
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- 2020
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41. Circadian (De)regulation in Head and Neck Squamous Cell Carcinoma
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Sandra Kraljević Pavelić, Sadia Rahman, and Elitza Markova-Car
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circadian rhythm ,Circadian clock ,circadian clock genes ,Review ,Catalysis ,Inorganic Chemistry ,head and neck squamous cell carcinoma (HNSCC) ,lcsh:Chemistry ,stomatognathic system ,Biological Clocks ,Circadian Clocks ,medicine ,otorhinolaryngologic diseases ,Animals ,Humans ,cancer ,Physical and Theoretical Chemistry ,Molecular Biology ,lcsh:QH301-705.5 ,Spectroscopy ,business.industry ,Squamous Cell Carcinoma of Head and Neck ,Organic Chemistry ,Head and neck cancer ,Cancer ,General Medicine ,medicine.disease ,Head and neck squamous-cell carcinoma ,Computer Science Applications ,PER2 ,CLOCK ,Gene Expression Regulation, Neoplastic ,PER3 ,stomatognathic diseases ,lcsh:Biology (General) ,lcsh:QD1-999 ,Cancer research ,Disease Susceptibility ,business ,Biomarkers ,PER1 - Abstract
Head and neck cancer encompass different malignancies that develop in and around the throat, larynx, nose, sinuses and mouth. Most head and neck cancers are squamous cell carcinomas (HNSCC) that arise in the flat squamous cells that makeup the thin layer of tissue on the surface of anatomical structures in the head and neck. Each year, HNSCC is diagnosed in more than 600,000 people worldwide, with about 50,000 new cases. HNSCC is considered extremely curable if detected early. But the problem remains in treatment of inoperable cases, residues or late stages. Circadian rhythm regulation has a big role in developing various carcinomas, and head and neck tumors are no exception. A number of studies have reported that alteration in clock gene expression is associated with several cancers, including HNSCC. Analyses on circadian clock genes and their association with HNSCC have shown that expression of PER1, PER2, PER3, CRY1, CRY2, CKIε, TIM, and BMAL1 are deregulated in HNSCC tissues. This review paper comprehensively presents data on deregulation of circadian genes in HNSCC and critically evaluates their potential diagnostics and prognostics role in this type of pathology.
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- 2019
42. Elucidating the role of ATM in BER and MMR during B cell CSR
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Emily Sible, Mary Attaway, Tzippora Chwat, Giuseppe Fiorica, Sadia Rahman, Kristel Velez, and Bao Vuong
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Immunology ,Immunology and Allergy - Abstract
Secondary immunoglobulin isotypes are produced by class switch recombination (CSR), which requires AID-dependent DNA deamination of intronic switch (S) regions within the immunoglobulin heavy chain gene. Non-canonical repair of deaminated DNA by mismatch repair (MMR) or base excision repair (BER) creates staggered DNA breaks that promote recombination between S regions. ATM-dependent phosphorylation of AID at serine-38 (pS38-AID) promotes its interaction with APE1, a BER protein, suggesting that ATM regulates CSR through BER. However, pS38-AID may also play a role in MMR during CSR, although the mechanism remains unknown. To examine whether ATM participates in MMR-mediated CSR, ATM−/− mice were bred to mice deficient for the MMR gene MSH2. Surprisingly, the predicted Mendelian frequencies of ATM−/− MSH2−/− adult mice were not obtained. To bypass the observed lethality, ATM was conditionally deleted on an MSH2−/− background using a floxed ATM allele [ATMF] and B cell-specific Cre recombinase expression. These ATMd/dMSH2−/− mice and B cells display a hypomorphic CSR phenotype comparable to ATM−/− B cells, which suggests that ATM may function genetically upstream of MSH2 and implicates a role for ATM in both MMR and BER.
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- 2021
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43. Elucidating the role of ATM in BER and MMR during B cell CSR
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Emily Sible, Giuseppe Fiorica, Sadia Rahman, Mary Attaway, and Bao Q. Vuong
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Immunology ,Immunology and Allergy - Abstract
Secondary immunoglobulin isotypes are produced by class switch recombination (CSR), which requires AID-dependent DNA deamination of intronic switch (S) regions within the immunoglobulin heavy chain gene. Non-canonical repair of deaminated DNA by mismatch repair (MMR) or base excision repair (BER) creates staggered DNA breaks that promote recombination between S regions. ATM-dependent phosphorylation of AID at serine-38 (pS38-AID) promotes its interaction with a BER protein, suggesting that ATM regulates CSR through BER. However, the mechanism by which ATM participates in BER remains unknown. ATM−/− mice were bred to knockout mice of the MMR gene MSH2. Surprisingly, the predicted Mendelian frequencies of ATM−/−MSH2−/− adult mice were not obtained and preliminary data indicate a late embryonic lethal phenotype. To bypass the observed lethality, ATM was conditionally deleted on an MSH2−/− background using a floxed ATM allele [ATMF] and B cell-specific Cre recombinase expression. These ATMd/dMSH2−/− mice and B cells display a CSR phenotype comparable to ATM−/− B cells, which suggest that ATM may function genetically upstream of MSH2 and implicate a role for ATM in both MMR and BER.
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- 2020
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44. Contributors
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Md. Alauddin, Pradosh Prasad Chakrabarti, Nurhan Turgut Dunford, Nisi Gao, Umar Garba, Wei Han, Dongping He, Md Zakir Hossen Howlader, Jahidul Islam, Jörg J. Jacoby, Ram Chandra Reddy Jala, Yuanrong Jiang, Michio Komai, Oi-Ming Lai, Wee-Ting Lai, Wai-Fun Leong, Lingyi Liu, Sadia Rahman, Hitoshi Shirakawa, Riantong Singanusong, Yong Wang, Juan Wu, Tiankui Yang, Tie Yin, Baoru Yin, Xiaolin Zhang, Yan Zheng, Xuhui Zhuang, and Yanping Zou
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- 2019
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45. Identification of targetable BRAF ΔN486_P490 variant by whole-genome sequencing leading to dabrafenib-induced remission of a BRAF-mutant pancreatic adenocarcinoma
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Heather Geiger, Scott Powers, Sadia Rahman, Minsig Choi, A. Rao Chimpiri, Vanessa Felice, Vaidehi Jobanputra, Kazimierz O. Wrzeszczynski, Minita Shah, Mayu O. Frank, Dina Manaa, Vanessa V. Michelini, Kanika Arora, Esra Dikoglu, Robert B. Darnell, and Depinder Khaira
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Male ,Proto-Oncogene Proteins B-raf ,Lung Neoplasms ,Adenocarcinoma ,medicine.disease_cause ,03 medical and health sciences ,0302 clinical medicine ,CDKN2A ,Pancreatic cancer ,Carcinoma, Non-Small-Cell Lung ,Oximes ,medicine ,neoplasm of the pancreas ,Biomarkers, Tumor ,Humans ,neoplasms ,Protein Kinase Inhibitors ,030304 developmental biology ,Tumor marker ,Aged ,0303 health sciences ,Mutation ,Whole Genome Sequencing ,business.industry ,Remission Induction ,Imidazoles ,Dabrafenib ,General Medicine ,medicine.disease ,digestive system diseases ,3. Good health ,Pancreatic Neoplasms ,Protein kinase domain ,030220 oncology & carcinogenesis ,Cancer research ,business ,Rapid Cancer Communication ,V600E ,medicine.drug - Abstract
The tumor genome of a patient with advanced pancreatic cancer was sequenced to identify potential therapeutic targetable mutations after standard of care failed to produce any significant overall response. Matched tumor-normal whole-genome sequencing revealed somatic mutations in BRAF, TP53, CDKN2A, and a focal deletion of SMAD4. The BRAF variant was an in-frame deletion mutation (ΔN486_P490), which had been previously demonstrated to be a kinase-activating alteration in the BRAF kinase domain. Working with the Novartis patient assistance program allowed us to treat the patient with the BRAF inhibitor, dabrafenib. The patient's overall clinical condition improved dramatically with dabrafenib. Levels of serum tumor marker dropped immediately after treatment, and a subsequent CT scan revealed a significant decrease in the size of both primary and metastatic lesions. The dabrafenib-induced remission lasted for 6 mo. Preclinical studies published concurrently with the patient's treatment showed that the BRAF in-frame mutation (ΔNVTAP) induces oncogenic activation by a mechanism distinct from that induced by V600E, and that this difference dictates the responsiveness to different BRAF inhibitors. This study describes a dramatic instance of how high-level genomic technology and analysis was necessary and sufficient to identify a clinically logical treatment option that was then utilized and shown to be of clinical value for this individual.
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- 2019
46. Development of Rice Bran Functional Food and Evaluation of Its Healthful Properties
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Zakir Hossen Howlader, Sadia Rahman, Hitoshi Shirakawa, Md. Alauddin, Jahidul Islam, and Michio Komai
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chemistry.chemical_classification ,Bran ,Metabolic disorder ,food and beverages ,medicine.disease ,Lactic acid ,chemistry.chemical_compound ,Enzyme ,chemistry ,Functional food ,medicine ,Glucose homeostasis ,Fermentation ,Food science ,Polyunsaturated fatty acid - Abstract
Rice bran is used as a good source of proteins, oils, crude fibers, carbohydrates, energy, phenolic compounds, γ-oryzanols, and fatty acids (saturated fatty acids 16.59%–21%; monounsaturated fatty acids, 39.82%–49.95%; and polyunsaturated fatty acids, 33.23%–38.57%). Fermented rice bran (FRB) can be prepared by dual fermentation using fungi and lactic acid bacteria for improvement of its functional properties. FRB significantly reduced blood pressure elevation by inhibition of serum angiotensin-converting enzyme (ACE) activity and improved glucose impairment and insulin sensitivity, as well as leptin impairment and serum adiponectin level. FRB improved multifactorial metabolic disorder by the regulation of transcription factors and related gene expression to maintain glucose homeostasis. The anticolitis effect of FRB showed that FRB attenuated intestinal inflammation owing to elevated short-chain fatty acids (SCFAs) and tryptamine production, which might regulate tight junction barrier integrity and intestinal homeostasis. These results suggested that FRB could comprise an effective potential functional food agent for multifactorial metabolic disorder and inflammation.
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- 2019
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47. Retraction Note: Soft computing methodologies for estimation of bridge girder forces with perforations under tsunami wave loading
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Shatirah Akib, Sadia Rahman, Shahaboddin Shamshirband, and Dalibor Petković
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Geophysics ,Building and Construction ,Geotechnical Engineering and Engineering Geology ,Civil and Structural Engineering - Published
- 2020
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48. Sequencing and curation strategies for identifying candidate glioblastoma treatments
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Eli L. Diamond, Phaedra Agius, Minita Shah, Heather Geiger, Vaidehi Jobanputra, Anthony Calabro, Christian Grommes, Anne-Katrin Emde, Kahn Rhrissorrakrai, Ewa A. Bergmann, Jeffrey N. Bruce, Alice Fang, Andrew B. Lassman, Michael C. Zody, Alexis Demopoulos, Kazimierz O. Wrzeszczynski, Vanessa V. Michelini, Cecilia Esteves, Takahiko Koyama, Laxmi Parida, Catherine Reeves, John Anthony Kelly, Nicolas Robine, Mariza Daras, Vladimir Vacic, Christian Stolte, Peter Canoll, Dana E. Orange, Bo-Juen Chen, Antonio Omuro, Sadia Rahman, Julia L. Moore Vogel, Mayu O. Frank, Stephen J. Harvey, Elena Pentsova, Jerome B. Posner, Robert B. Darnell, Duyang Kim, Filippo Utro, Depinder Khaira, Ajay K. Royyuru, Michelle F. Lamendola-Essel, Kanika Arora, Vanessa Felice, John A. Boockvar, Cameron Brennan, Dimitris G. Placantonakis, John G. Golfinos, and Esra Dikoglu
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0301 basic medicine ,Adult ,Male ,lcsh:Internal medicine ,lcsh:QH426-470 ,MEDLINE ,Computational biology ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,Medicine ,Humans ,Molecular Targeted Therapy ,lcsh:RC31-1245 ,Genetics (clinical) ,Aged ,Whole genome sequencing ,Aged, 80 and over ,Potential impact ,Ploidies ,Whole Genome Sequencing ,business.industry ,Cancer ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,Correction ,Middle Aged ,Precision medicine ,medicine.disease ,Human genetics ,lcsh:Genetics ,030104 developmental biology ,030220 oncology & carcinogenesis ,Female ,DNA microarray ,business ,Glioblastoma - Abstract
Background Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare the ability of different sequencing assays and analysis methods to analyze glioblastoma tumors and generate real-time potential treatment options for physicians. Methods A consortium of seven institutions in New York City enrolled 30 patients with glioblastoma and performed tumor whole genome sequencing (WGS) and RNA sequencing (RNA-seq; collectively WGS/RNA-seq); 20 of these patients were also analyzed with independent targeted panel sequencing. We also compared results of expert manual annotations with those from an automated annotation system, Watson Genomic Analysis (WGA), to assess the reliability and time required to identify potentially relevant pharmacologic interventions. Results WGS/RNAseq identified more potentially actionable clinical results than targeted panels in 90% of cases, with an average of 16-fold more unique potentially actionable variants identified per individual; 84 clinically actionable calls were made using WGS/RNA-seq that were not identified by panels. Expert annotation and WGA had good agreement on identifying variants [mean sensitivity = 0.71, SD = 0.18 and positive predictive value (PPV) = 0.80, SD = 0.20] and drug targets when the same variants were called (mean sensitivity = 0.74, SD = 0.34 and PPV = 0.79, SD = 0.23) across patients. Clinicians used the information to modify their treatment plan 10% of the time. Conclusion These results present the first comprehensive comparison of technical and machine augmented analysis of targeted panel and WGS/RNA-seq to identify potential cancer treatments.
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- 2018
49. SAFT-γ Force Field for the Simulation of Molecular Fluids. 5. Hetero-Group Coarse-Grained Models of Linear Alkanes and the Importance of Intramolecular Interactions
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Sadia, Rahman, Olga, Lobanova, Guadalupe, Jiménez-Serratos, Carlos, Braga, Vasilios, Raptis, Erich A, Müller, George, Jackson, Carlos, Avendaño, and Amparo, Galindo
- Abstract
The SAFT-γ Mie group-contribution equation of state [ Papaioannou J. Chem. Phys. 2014 , 140 , 054107 ] is used to develop a transferable coarse-grained (CG) force-field suitable for the molecular simulation of linear alkanes. A heterogroup model is fashioned at the resolution of three carbon atoms per bead in which different Mie (generalized Lennard-Jones) interactions are used to characterize the terminal (CH
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- 2018
50. A recurrent novel
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Daniel, Diolaiti, Filemon S, Dela Cruz, Gunes, Gundem, Nancy, Bouvier, Mathieu, Boulad, Yanming, Zhang, Alexander J, Chou, Ira J, Dunkel, Rashesh, Sanghvi, Minita, Shah, Heather, Geiger, Sadia, Rahman, Vanessa, Felice, Kazimierz O, Wrzeszczynski, Robert B, Darnell, Cristina R, Antonescu, Christopher A, French, Elli, Papaemmanuil, Andrew L, Kung, and Neerav, Shukla
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Gene Rearrangement ,Male ,Recombination, Genetic ,Research Report ,NUTM1-rearranged tumor ,Oncogene Proteins, Fusion ,Whole Genome Sequencing ,Nuclear Proteins ,spindle cell carcinoma ,Cell Differentiation ,Sarcoma ,NUT carcinoma ,synovial sarcoma ,Immunohistochemistry ,Translocation, Genetic ,Neoplasm Proteins ,Sarcoma, Synovial ,Basic Helix-Loop-Helix Transcription Factors ,Biomarkers, Tumor ,Humans ,Female ,Gene Fusion ,Child ,MGA-NUT1 ,Transcription Factors - Abstract
NUTM1-rearranged tumors are defined by the presence of a gene fusion between NUTM1 and various gene partners and typically follow a clinically aggressive disease course with poor outcomes despite conventional multimodality therapy. NUTM1-rearranged tumors display histologic features of a poorly differentiated carcinoma with areas of focal squamous differentiation and typically express the BRD4–NUTM1 fusion gene defining a distinct clinicopathologic entity—NUT carcinoma (NC). NCs with mesenchymal differentiation have rarely been described in the literature. In this report, we describe the characterization of two cases of high-grade spindle cell sarcoma harboring a novel MGA–NUTM1 fusion. Whole-genome sequencing identified the presence of complex rearrangements resulting in a MGA–NUTM1 fusion gene in the absence of other significant somatic mutations. Genetic rearrangement was confirmed by fluorescence in situ hybridization, and expression of the fusion gene product was confirmed by transcriptomic analysis. The fusion protein was predicted to retain nearly the entire protein sequence of both MGA (exons 1–22) and NUTM1 (exons 3–8). Histopathologically, both cases were high-grade spindle cell sarcomas without specific differentiation markers. In contrast to typical cases of NC, these cases were successfully treated with aggressive local control measures (surgery and radiation) and both patients remain alive without disease. These cases describe a new subtype of NUTM1-rearranged tumors warranting expansion of diagnostic testing to evaluate for the presence of MGA–NUTM1 or alternative NUTM1 gene fusions in the diagnostic workup of high-grade spindle cell sarcomas or small round blue cell tumors of ambiguous lineage.
- Published
- 2018
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