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2. Brain Tumor Segmentation using Enhanced U-Net Model with Empirical Analysis

Author

Nasim, MD Abdullah Al, Munem, Abdullah Al, Islam, Maksuda, Palash, Md Aminul Haque, Haque, MD. Mahim Anjum, and Shah, Faisal Muhammad

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

Cancer of the brain is deadly and requires careful surgical segmentation. The brain tumors were segmented using U-Net using a Convolutional Neural Network (CNN). When looking for overlaps of necrotic, edematous, growing, and healthy tissue, it might be hard to get relevant information from the images. The 2D U-Net network was improved and trained with the BraTS datasets to find these four areas. U-Net can set up many encoder and decoder routes that can be used to get information from images that can be used in different ways. To reduce computational time, we use image segmentation to exclude insignificant background details. Experiments on the BraTS datasets show that our proposed model for segmenting brain tumors from MRI (MRI) works well. In this study, we demonstrate that the BraTS datasets for 2017, 2018, 2019, and 2020 do not significantly differ from the BraTS 2019 dataset's attained dice scores of 0.8717 (necrotic), 0.9506 (edema), and 0.9427 (enhancing)., Comment: 5 tables, 4 figures, 5 equations

Published
2022

4. Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh.

Author

Saha, Senjuti, Malaker, Roly, Sajib, Mohammad Saiful Islam, Hasanuzzaman, Md, Rahman, Hafizur, Ahmed, Zabed B, Islam, Mohammad Shahidul, Islam, Maksuda, Hooda, Yogesh, Ahyong, Vida, Vanaerschot, Manu, Batson, Joshua, Hao, Samantha, Kamm, Jack, Kistler, Amy, Tato, Cristina M, DeRisi, Joseph L, and Saha, Samir K

Abstract

The complete genome sequence of a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) isolate obtained from a nasopharyngeal swab from a patient with COVID-19 in Bangladesh is reported.

Published
2020

5. Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens

Author

Saha, Senjuti, Ramesh, Akshaya, Kalantar, Katrina, Malaker, Roly, Hasanuzzaman, Md, Khan, Lillian M, Mayday, Madeline Y, Sajib, MSI, Li, Lucy M, Langelier, Charles, Rahman, Hafizur, Crawford, Emily D, Tato, Cristina M, Islam, Maksuda, Juan, Yun-Fang, de Bourcy, Charles, Dimitrov, Boris, Wang, James, Tang, Jennifer, Sheu, Jonathan, Egger, Rebecca, De Carvalho, Tiago Rodrigues, Wilson, Michael R, Saha, Samir K, and DeRisi, Joseph L

Subjects
Pediatric, Prevention, Rare Diseases, Vaccine Related, Infectious Diseases, Emerging Infectious Diseases, Biodefense, Clinical Research, Infection, Good Health and Well Being, Bangladesh, Chikungunya virus, Communicable Diseases, Emerging, Disease Outbreaks, Female, Genome, Viral, Humans, Infant, Infant, Newborn, Male, Meningitis, Viral, Metagenomics, Phylogeny, Public Health Surveillance, idiopathic meningitis, metagenomics, etiology, cerebrospinal fluid, meningitis, virology, Microbiology
Abstract

The burden of meningitis in low-and-middle-income countries remains significant, but the infectious causes remain largely unknown, impeding institution of evidence-based treatment and prevention decisions. We conducted a validation and application study of unbiased metagenomic next-generation sequencing (mNGS) to elucidate etiologies of meningitis in Bangladesh. This RNA mNGS study was performed on cerebrospinal fluid (CSF) specimens from patients admitted in the largest pediatric hospital, a World Health Organization sentinel site, with known neurologic infections (n = 36), with idiopathic meningitis (n = 25), and with no infection (n = 30), and six environmental samples, collected between 2012 and 2018. We used the IDseq bioinformatics pipeline and machine learning to identify potentially pathogenic microbes, which we then confirmed orthogonally and followed up through phone/home visits. In samples with known etiology and without infections, there was 83% concordance between mNGS and conventional testing. In idiopathic cases, mNGS identified a potential bacterial or viral etiology in 40%. There were three instances of neuroinvasive Chikungunya virus (CHIKV), whose genomes were >99% identical to each other and to a Bangladeshi strain only previously recognized to cause febrile illness in 2017. CHIKV-specific qPCR of all remaining stored CSF samples from children who presented with idiopathic meningitis in 2017 (n = 472) revealed 17 additional CHIKV meningitis cases, exposing an unrecognized meningitis outbreak. Orthogonal molecular confirmation, case-based clinical data, and patient follow-up substantiated the findings. Case-control CSF mNGS surveys can complement conventional diagnostic methods to identify etiologies of meningitis, conduct surveillance, and predict outbreaks. The improved patient- and population-level data can inform evidence-based policy decisions.IMPORTANCE Globally, there are an estimated 10.6 million cases of meningitis and 288,000 deaths every year, with the vast majority occurring in low- and middle-income countries. In addition, many survivors suffer from long-term neurological sequelae. Most laboratories assay only for common bacterial etiologies using culture and directed PCR, and the majority of meningitis cases lack microbiological diagnoses, impeding institution of evidence-based treatment and prevention strategies. We report here the results of a validation and application study of using unbiased metagenomic sequencing to determine etiologies of idiopathic (of unknown cause) cases. This included CSF from patients with known neurologic infections, with idiopathic meningitis, and without infection admitted in the largest children's hospital of Bangladesh and environmental samples. Using mNGS and machine learning, we identified and confirmed an etiology (viral or bacterial) in 40% of idiopathic cases. We detected three instances of Chikungunya virus (CHIKV) that were >99% identical to each other and to a strain previously recognized to cause systemic illness only in 2017. CHIKV qPCR of all remaining stored 472 CSF samples from children who presented with idiopathic meningitis in 2017 at the same hospital uncovered an unrecognized CHIKV meningitis outbreak. CSF mNGS can complement conventional diagnostic methods to identify etiologies of meningitis, and the improved patient- and population-level data can inform better policy decisions.

Published
2019

6. Incidence of typhoid and paratyphoid fever in Bangladesh, Nepal, and Pakistan: results of the Surveillance for Enteric Fever in Asia Project

Author

Garrett, Denise O, Longley, Ashley T, Aiemjoy, Kristen, Yousafzai, Mohammad T, Hemlock, Caitlin, Yu, Alexander T, Vaidya, Krista, Tamrakar, Dipesh, Saha, Shampa, Bogoch, Isaac I, Date, Kashmira, Saha, Senjuti, Islam, Mohammad Shahidul, Sayeed, K M Ishtiaque, Bern, Caryn, Shakoor, Sadia, Dehraj, Irum F, Mehmood, Junaid, Sajib, Mohammad S I, Islam, Maksuda, Thobani, Rozina S, Hotwani, Aneeta, Rahman, Najeeb, Irfan, Seema, Naga, Shiva R, Memon, Ashraf M, Pradhan, Sailesh, Iqbal, Khalid, Shrestha, Rajeev, Rahman, Hafizur, Hasan, Md Mahmudul, Qazi, Saqib H, Kazi, Abdul M, Saddal, Nasir S, Jamal, Raza, Hunzai, Mohammed J, Hossain, Tanvir, Marks, Florian, Carter, Alice S, Seidman, Jessica C, Qamar, Farah N, Saha, Samir K, Andrews, Jason R, and Luby, Stephen P

Published
2022
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7. Effects of antibiotic resistance, drug target attainment, bacterial pathogenicity and virulence, and antibiotic access and affordability on outcomes in neonatal sepsis: an international microbiology and drug evaluation prospective substudy (BARNARDS)

Author

Saha, Samir, Islam, Maksuda, Bin-Ahmed, Zabed, Ahmed, Wazir, Begum, Taslima, Chowdhury, Mitu, Sharmin, Shaila, Rani Dey, Chumki, Uttam, Matin, Abdul, Chakraborty, Sowmitra Ranjan, Tasmin, Sadia, Rema, Dipa, Khatun, Rashida, Nath, Liza, Balkachew, Nigatu, Bekele, Delayehu, Schaughency, Katherine, Solomon, Semaria, Gebreyohanes, Zenebe, Ambachew, Rozina, Odumade, Oludare, Haileselassie, Misgana, Chan, Grace, Russo, Abigail, Workneh, Redeat, Metaferia, Gesit, Abayneh, Mahlet, Mohammed, Yahya Zekaria, Biteye, Tefera, Teklu, Alula, Gezahegn, Wendimagegn, Chakravorty, Partha Sarathi, Mukherjee, Anuradha, Nandy, Ranjan Kumar, Roy, Samarpan, Sinha, Anuradha, Naha, Sharmi, Malakar, Sukla Saha, Bose, Siddhartha, Majhi, Monaki, Sahoo, Subhasree, Mukherjee, Putul, Routa, Sumitra Kumari, Nandi, Chaitali, Basu, Sulagna, Saha, Bijan, Chattopadhyay, Pinaki, Modibbo, Fatima Zara Isa, Uwaezuoke, Stella, Meduekwe, Dilichukwu, Muhammad, Khairiyya, Nsude, Queen, Ukeh, Ifeoma, Okenu, Mary-Joe, Chinenye, Akpulu, Yakubu, Samuel, Asunugwo, Vivian, Aina, Folake, Issy, Isibong, Adekeye, Dolapo, Eunice, Adiele, Amina, Abdulmlik, Oyewole, R, Oloton, I, Nnaji, BC, Umejiego, M, Anoke, PN, Adebayo, S, Abegunrin, GO, Omotosho, OB, Ibrahim, R, Igwe, B, Abroko, M, Balami, K, Bayem, L, Anyanwu, C, Haruna, H, Okike, J, Goroh, K, Boi-Sunday, M, Ugafor, Augusta, Makama, Maryam, Ndukwe, Kaniba, Odama, Anastesia, Yusuf, Hadiza, Wachukwu, Patience, Yahaya, Kachalla, Kalade Colsons, Titus, Kura, Mercy, Orebiyi, Damilola, Iregbu, Kenneth C., Mmadueke, Chukwuemeka, Audu, Lamidi, Idris, Nura, Gambo, Safiya, Ibrahim, Jamila, Precious, Edwin, Hassan, Ashiru, Gwadabe, Shamsudden, Adeleye Falola, Adeola, Aliyu, Muhammad, Ibrahim, Amina, Mukaddas, Aisha Sani, Khalid, Rashida Yakubu, Alkali, Fatima Ibrahim, Muhammad, Maryam Yahaya, Tukur, Fatima Mohammad, Muhammad, Surayya Mustapha, Shittu, Adeola, Bello, Murjanatu, Hassan, Muhammad Abubakar, Sa ad, Fatima Habib, Kassim, Aishatu, Shirazi, Haider, Muhammad, Adil, Zahra, Rabaab, Ullah, Syed Najeeb, Hilal Jan, Muhammad, Kamran, Rubina, Sajana, Saeed, Jazba, Maqsood, Noreen, Zafar, Maria, Sadiq, Saraeen, Ahsan, Sumble, Tariq, Madiha, Sajid, Sidra, Mustafa, Hasma, Rehman, Anees-ur, Muhammad, Atif, Mehmood, Gahssan, Nisar, Mahnoor, Akif, Shermeen, Yasmeen, Tahira, Nawaz, Sabir, Atta, Anam Shanal, Laiq-ur-Rehman, Mian, Kousar, Robina, Bibi, Kalsoom, Waheed, Kosar, Majeed, Zainab, Jalil, Ayesha, Kajibwami, Espoir, Rucogoza, Aniceth, Nzabahimana, Innocent, Jean-Baptiste, Mazarati, Gaju, Lucie, Riziki, Kankundiye, Uwamahoro, Brigette, Uwera, Rachel, Nyiratuza, Eugenie, Muzungu, Kumwami, Uwitonze, Violette, Horanimpundu, Marie C, Nzeyimana, Francine, Mitima, Prince, Dramowski, Angela, Whitelaw, Andrew, Paterson, Lauren, Frans, Mary, Johnson, Marvina, Swanepoel, Eveline, Bojana, Zoleka, du Preez, Mieme, Mehtar, Shaheen, Bulabula, Andre, Liu, Feiyan, van Hasselt, Johan GC, Walsh, Timothy, Sands, Kirsty, Carvalho, Maria, Milton, Rebecca, Thomson, Kathryn, Portal, Edward, Mathias, Jordan, Dyer, Calie, Ferreira, Ana, Andrews, Robert, Watkins, John, Gillespie, David, Hood, Kerry, Taiyai, Katie, Kirby, Nigel, Nieto, Maria, Hender, Thomas, Hogan, Patrick, Saif, Habiba, Hassan, Brekhna, Jones, Ellis, Barrell, Matthew, Boostrom, Ian, Frayne, Francis, Rees, Jessica, Jones, Lim, Dunachie, Susanna, Spiller, Brad, Parkhill, Julian, Thomson, Kathryn M, Carvalho, Maria J, Farzana, Refath, Chan, Grace J, Mahlet, Abayneh, Nandy, Ranjan K, Iregbu, Kenneth, Modibbo, Fatima, Syed, Najeeb U, Mazarati, Jean-Baptiste, Bulabula, Andre N H, van Hasselt, Johan G C, and Walsh, Timothy R

Published
2021
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8. Impact of national introduction of ten-valent pneumococcal conjugate vaccine on invasive pneumococcal disease in Bangladesh: Case-control and time-trend studies

Author

Baqui, Abdullah H., Koffi, Alain K., McCollum, Eric D., Roy, Arunangshu D., Chowdhury, Nabidul H., Rafiqullah, Iftekhar, Ahmed, Zabed B., Mahmud, Arif, Begum, Nazma, Ahmed, Salahuddin, Khanam, Rasheda, Harrison, Meagan, Simmons, Nicole, Hossen, Shakir, Islam, Maksuda, Quaiyum, Abdul, Checkley, William, Santosham, Mathuram, Moulton, Lawrence H., and Saha, Samir K.

Published
2021
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9. Effectiveness of ten-valent pneumococcal conjugate vaccine on invasive pneumococcal disease among children <2 years old: A prospective population-based study in rural Bangladesh

Author

Malaker, Roly, primary, Hasanuzzaman, Md, additional, Hooda, Yogesh, additional, Rahman, Hafizur, additional, Chandra Das, Rajib, additional, Kanon, Naito, additional, Saha, Senjuti, additional, Tanmoy, Arif M., additional, Ranjan Chakraborty, Sowmitra, additional, Saha, Shampa, additional, Islam, Maksuda, additional, Darmstadt, Gary L., additional, Baqui, Abdullah H., additional, Sathosam, Mathuram, additional, El-Arifeen, Shams, additional, Whitney, Cynthia G., additional, and Saha, Samir K., additional

Published
2023
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10. Global burden of respiratory infections associated with seasonal influenza in children under 5 years in 2018: a systematic review and modelling study

Author

Nair, Harish, Campbell, Harry, Wang, Xin, Li, You, Chung, Alexandria, Rahi, Manveer, Abbas, Qalab, Ali, Asad, Bhutta, Zulfiqar A, Saeed, Bushra, Soofi, Sajid B, Yousafzai, Mohammad Tahir, Zaidi, Anita K, Amu, Alberta, Awini, Elizabeth, Azziz-Baumgartner, Eduardo, Baggett, Henry C, Chaves, Sandra S, Shang, Nong, Schrag, Stephanie J, Widdowson, Marc-Alain, Tempia, Stefano, Bassat, Quique, Lanaspa, Miguel, Acácio, Sozinho, Brooks, W Abdullah, Driscoll, Amanda, Knoll, Maria Deloria, O'Brien, Katherine L, Prosperi, Christine, Baqui, Abdullah H, Mullany, Luke, Byass, Peter, Cohen, Cheryl, von Gottberg, Anne, Hellferscee, Orienka, Treurnicht, Florette K, Walaza, Sibongile, Goswami, Doli, Rahman, Mustafizur, Connor, Nicholas E, El Arifeen, Shams, Echavarria, Marcela, Marcone, Débora N, Reyes, Noelia, Gutierrez, Andrea, Rodriguez, Ivan, Lopez, Olga, Ortiz, David, Gonzalez, Nathaly, Gentile, Angela, del Valle Juarez, Maria, Gordon, Aubree, Cutland, Clare, Groome, Michelle, Madhi, Shabir A, Nunes, Marta C, Nzenze, Susan, Heikkinen, Terho, Hirve, Siddhivinayak, Juvekar, Sanjay, Halasa, Natasha, Jara, Jorge H, Bernart, Chris, Katz, Mark A, Gofer, Ilan, Avni, Yonat Shemer, Khuri-Bulos, Najwa, Faori, Samir, Shehabi, Asem, Krishnan, Anand, Kumar, Rakesh, Amarchand, Ritvik, Contreras, Carmen L, de Leon, Oscar, Lopez, Maria R, McCracken, John P, Maldonado, Herberth, Samayoa, Antonio P, Gomez, Ana B, Lucero, Marilla G, Nillos, Leilani T, Lupisan, Socorro P, Nohynek, Hanna, Mira-Iglesias, Ainara, Puig-Barberà, Joan, Díez-Domingo, Javier, Gessner, Bradford D, Njanpop-Lafourcade, Berthe-Marie, Moïsi, Jennifer C, Tall, Haoua, Munywoki, Patrick K, Ngama, Mwanjuma, Nokes, D James, Omer, Saad B, Clark, Dayna R, Ourohiré, Millogo, Ali, Sié, Pascal, Zabré, Cheik, Bagagnan H, Caballero, Mauricio T, Libster, Romina, Polack, Fernando P, Rasmussen, Zeba A, Thomas, Elizabeth D, Baker, Julia M, Rath, Barbara A, Obermeier, Patrick E, Hassanuzzaman, MD., Islam, Maksuda, Islam, Mohammad S, Saha, Samir K, Panigrahi, Pinaki, Bose, Anuradha, Isaac, Rita, Murdoch, David, Nanda, Pritish, Qazi, Shamim A, Hessong, Danielle, Simőes, Eric AF, Sotomayor, Viviana, Thamthitiwat, Somsak, Chittaganpitch, Malinee, Dawood, Halima, Kyobutungi, Catherine, Wamukoya, Marylene, Ziraba, Abdhalah K, Yoshida, Lay-Myint, Yoshihara, Keisuke, Dand, Duc-Anh, Le, Minh-Nhat, Nicol, Mark P, Zar, Heather J, Broor, Shobha, Chadha, Mandeep, Madrid, Lola, Gresh, Lionel, Balmaseda, Angel, Kuan, Guillermina, Wairagkar, Niteen, Tapia, Milagritos D, Knobler, Stacey L, Barahona, Alfredo, Ferguson, Ericka, Schweiger, Brunhilde, Abdullah Brooks, W, Fasce, Rodrigo A, and Simões, Eric AF

Published
2020
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13. The Direct and Indirect Impact of SARS-CoV-2 Infections on Neonates: A Series of 26 Cases in Bangladesh

Author

Saha, Senjuti, Ahmed, ASM Nawshad Uddin, Sarkar, Probir Kumar, Bipul, Mohammed Rizwanul Ahsan, Ghosh, Kinkar, Rahman, Sheikh Wasik, Rahman, Hafizur, Hooda, Yogesh, Ahsan, Nafiz, Malaker, Roly, Sajib, Mohammad Saiful Islam, Islam, Mohammad Shahidul, Anik, Ataul Mustufa, Saha, Sudipta, Kanon, Naito, Islam, Maksuda, Hamer, Davidson H., Amin, Ruhul, Shahidullah, Mohammod, and Saha, Samir K.

Published
2020
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17. Safety and efficacy of alternative antibiotic regimens compared with 7 day injectable procaine benzylpenicillin and gentamicin for outpatient treatment of neonates and young infants with clinical signs of severe infection when referral is not possible: a randomised, open-label, equivalence trial

Author

Baqui, Abdullah H, Saha, Samir K, Ahmed, A S M Nawshad Uddin, Shahidullah, Mohammad, Quasem, Iftekhar, Roth, Daniel E, Samsuzzaman, A K M, Ahmed, Wazir, Tabib, S M Shahnawaz Bin, Mitra, Dipak K, Begum, Nazma, Islam, Maksuda, Mahmud, Arif, Rahman, Mohammad Hefzur, Moin, Mamun Ibne, Mullany, Luke C, Cousens, Simon, El Arifeen, Shams, Wall, Stephen, Brandes, Neal, Santosham, Mathuram, and Black, Robert E

Published
2015
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20. Risk factors for community-acquired bacterial infection among young infants in South Asia: a longitudinal cohort study with nested case–control analysis

Author

Connor, Nicholas E, primary, Islam, Mohammad Shahidul, additional, Mullany, Luke C, additional, Shang, Nong, additional, Bhutta, Zulfiqar A, additional, Zaidi, Anita K M, additional, Soofi, Sajid, additional, Nisar, Imran, additional, Panigrahi, Pinaki, additional, Panigrahi, Kalpana, additional, Satpathy, Radhanath, additional, Bose, Anuradha, additional, Isaac, Rita, additional, Baqui, Abdullah H, additional, Mitra, Dipak K, additional, Sadeq-ur Rahman, Qazi, additional, Hossain, Tanvir, additional, Schrag, Stephanie J, additional, Winchell, Jonas M, additional, Arvay, Melissa L, additional, Diaz, Maureen H, additional, Waller, Jessica L, additional, Weber, Martin W, additional, Hamer, Davidson H, additional, Hibberd, Patricia, additional, Nawshad Uddin Ahmed, A S M, additional, Islam, Maksuda, additional, Hossain, Mohammad Belal, additional, Qazi, Shamim A, additional, El Arifeen, Shams, additional, Darmstadt, Gary L, additional, and Saha, Samir K, additional

Published
2022
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22. Population-Based Incidence and Etiology of Community-Acquired Neonatal Bacteremia in Mirzapur, Bangladesh: An Observational Study

Author

Darmstadt, Gary L., Saha, Samir K., Choi, Yoonjoung, Arifeen, Shams El, Ahmed, Nawshad Uddin, Bari, Sanwarul, Rahman, Syed M., Mannan, Ishtiaq, Crook, Derrick, Fatima, Kaniz, Winch, Peter J., Seraji, Habibur Rahman, Begum, Nazma, Rahman, Radwanur, Islam, Maksuda, Rahman, Anisur, Black, Robert E., Santosham, Mathuram, Sacks, Emma, and Baqui, Abdullah H.

Published
2009

23. Invasive Pneumococcal Disease among Children in Rural Bangladesh: Results from a Population-Based Surveillance

Author

Arifeen, Shams E., Saha, Samir K., Rahman, Sayedur, Rahman, Kazi Mizanur, Rahman, Syed Moshfiqur, Bari, Sanwarul, Naheed, Aliya, Mannan, Ishtiaq, Seraji, M. Habibur R., Ahmed, Nawshad U., Hassan, M. Shameem, Huda, Nazmul, Siddik, Ashraf Uddin, Quasem, Iftekhar, Islam, Maksuda, Fatima, Kaniz, Al-Emran, Hassan, Brooks, W. Abdullah, Baqui, Abdullah H., Breiman, Robert F., Sack, David, and Luby, Stephen P.

Published
2009
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26. Nasopharyngeal pneumococcal carriage in South Asian infants: Results of observational cohort studies in vaccinated and unvaccinated populations

Author

Apte, Aditi, primary, Dayma, Girish, additional, Naziat, Hakka, additional, Williams, Linda, additional, Sanghavi, Sonali, additional, Uddin, Jamal, additional, Kawade, Anand, additional, Islam, Maksuda, additional, Kar, Sanchita, additional, Li, You, additional, Kyaw, Moe H, additional, Juvekar, Sanjay, additional, Campbell, Harry, additional, Nair, Harish, additional, Saha, Samir K, additional, and Bavdekar, Ashish, additional

Published
2021
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28. Incidence of Typhoid and Paratyphoid Fever in Bangladesh, Nepal, and Pakistan: Results of the Surveillance for Enteric Fever in Asia Project

Author

Garrett, Denise, primary, Longley, Ashley, additional, Aiemjoy, Kristen, additional, Qamar, Farah Naz, additional, Saha, Samir K., additional, Yousafzai, Mohammad Tahir, additional, Hemlock, Caitlin, additional, Yu, Alexander, additional, Vaidya, krista, additional, Tamrakar, Dipesh, additional, Saha, Shampa, additional, Bogoch, Isaac, additional, Bern, Caryn, additional, Date, Kashmira, additional, Saha, Senjuti, additional, Islam, Mohammad Shahidul, additional, Sayeed, Ishtiaque, additional, Shakoor, Sadia, additional, Dehraj, Irum, additional, Mehmood, Junaid, additional, Sajib, Mohammad, additional, Islam, Maksuda, additional, Thobani, Rozina, additional, Hotwani, Aneeta, additional, Rehman, Najeeb Ur, additional, Irfan, Seema, additional, Naga, Shiva, additional, Memon, Ashraf, additional, Pradhan, Sailesh, additional, Iqbal, Khalid, additional, Shrestha, Rajeev, additional, Rahman, Hafizur, additional, Hasan, Md Mahmudul, additional, Qazi, Saqib, additional, Kazi, Abdul M., additional, Saddal, Nasir, additional, Syed, Jamal R., additional, Hunzai, Mohammed, additional, Marks, Florian, additional, Seidman, Jessica, additional, Carter, Alice S., additional, Andrews, Jason R., additional, and Luby, Stephen, additional

Published
2021
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29. Impact of National Introduction of Ten-Valent Pneumococcal Conjugate Vaccine on Invasive Pneumococcal Diseases in Bangladesh: Case-Control and Time-Trend Studies

Author

Baqui, Abdullah H., primary, Koffi, Alain K., additional, McCollum, Eric D., additional, Roy, Arunangshu D., additional, Chowdhury, Nabidul H., additional, Rafiqullah, Iftekhar M., additional, Ahmed, Zabed B., additional, Mahmud, Arif, additional, Begum, Nazma, additional, Ahmed, Salahuddin, additional, Khanam, Rasheda, additional, Harrison, Meagan, additional, Simmons, Nicole, additional, Hossen, Shakir, additional, Islam, Maksuda, additional, Quaiyum, Abdul, additional, Checkley, William, additional, Santosham, Mathuram, additional, Moulton, Lawrence H., additional, Saha, Samir K., additional, and Group, Bangladesh, The Projahnmo Study Group in Bangla, additional

Published
2021
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30. Enteric Fever and Related Contextual Factors in Bangladesh

Author

Saha, Shampa, Saha, Senjuti, Das, Rajib Chandra, Faruque, A. S. G., Salam, M. Abdus, Islam, Maksuda, and Saha, Samir K.

Subjects
Adult, Aged, 80 and over, Bangladesh, Time Factors, Adolescent, Infant, Articles, Middle Aged, Young Adult, Risk Factors, Child, Preschool, Paratyphoid Fever, Humans, Typhoid Fever, Child, Aged, Retrospective Studies
Abstract

Enteric fever remains a major public health problem in the developing world. With the emergence of antimicrobial resistance, disease prevention is becoming essential. There is evidence that improvement of contextual factors, such as socioeconomic development and water supply and sanitation, reduce the burden of this disease. However, such positive results are not universal. This study describes enteric fever trends in Bangladesh along with these factors’ progress between 1990 and 2014. Retrospective enteric fever data were collected from Dhaka Shishu (children) Hospital (DSH), Shishu Shasthya Foundation Hospital (SSFH), International Center for Diarrheal Disease Research, Bangladesh, and Popular Diagnostic Center (PDC). Contextual factors data were gathered from relevant organizations and their websites and plotted against time to see trends. During 2001–2014, data for a total of 131,449 blood cultures were available at DSH, SSFH, and PDC. Of those, 7,100 (isolation rate 5.4%) yielded either Salmonella enterica serovar Typhi or Salmonella enterica serovar Paratyphi growth without visible change in isolation rate trends. Contextual factors data were reported from 1990 to 2014. There were significant developments for sanitation facilities, drinking water supply, female literacy, and reduction in poverty head count ratio. During this time period, population density also increased significantly. Despite improvements in these contextual factors in Bangladesh, the enteric fever trend seems steady, possibly because of high population density and unplanned development of water supply and sewerage system. Although proper development of these two factors is important, immunization with an effective vaccine is instrumental to prevent this disease immediately in endemic countries such as Bangladesh, specifically to overcome the challenge of emerging resistance to available antibiotics.

Published
2018

31. Hospitalization of Pediatric Enteric Fever Cases, Dhaka, Bangladesh, 2017–2019: Incidence and Risk Factors

Author

Saha, Shampa, primary, Sayeed, K M Ishtiaque, additional, Saha, Senjuti, additional, Islam, Md Shafiqul, additional, Rahaman, Afiour, additional, Islam, Maksuda, additional, Rahman, Hafizur, additional, Das, Raktim, additional, Hasan, Md Mahmudul, additional, Uddin, Mohammad Jamal, additional, Tanmoy, Arif Mohammad, additional, Ahmed, A S M Nawshad Uddin, additional, Luby, Stephen P, additional, Andrews, Jason R, additional, Garrett, Denise O, additional, and Saha, Samir K, additional

Published
2020
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33. Global burden of respiratory infections associated with seasonal influenza in children under 5 years in 2018: a systematic review and modelling study

Author

Wang, Xin, primary, Li, You, additional, O'Brien, Katherine L, additional, Madhi, Shabir A, additional, Widdowson, Marc-Alain, additional, Byass, Peter, additional, Omer, Saad B, additional, Abbas, Qalab, additional, Ali, Asad, additional, Amu, Alberta, additional, Azziz-Baumgartner, Eduardo, additional, Bassat, Quique, additional, Abdullah Brooks, W, additional, Chaves, Sandra S, additional, Chung, Alexandria, additional, Cohen, Cheryl, additional, Echavarria, Marcela, additional, Fasce, Rodrigo A, additional, Gentile, Angela, additional, Gordon, Aubree, additional, Groome, Michelle, additional, Heikkinen, Terho, additional, Hirve, Siddhivinayak, additional, Jara, Jorge H, additional, Katz, Mark A, additional, Khuri-Bulos, Najwa, additional, Krishnan, Anand, additional, de Leon, Oscar, additional, Lucero, Marilla G, additional, McCracken, John P, additional, Mira-Iglesias, Ainara, additional, Moïsi, Jennifer C, additional, Munywoki, Patrick K, additional, Ourohiré, Millogo, additional, Polack, Fernando P, additional, Rahi, Manveer, additional, Rasmussen, Zeba A, additional, Rath, Barbara A, additional, Saha, Samir K, additional, Simões, Eric AF, additional, Sotomayor, Viviana, additional, Thamthitiwat, Somsak, additional, Treurnicht, Florette K, additional, Wamukoya, Marylene, additional, Yoshida, Lay-Myint, additional, Zar, Heather J, additional, Campbell, Harry, additional, Nair, Harish, additional, Wang, Xin, additional, Bhutta, Zulfiqar A, additional, Saeed, Bushra, additional, Soofi, Sajid B, additional, Yousafzai, Mohammad Tahir, additional, Zaidi, Anita K, additional, Awini, Elizabeth, additional, Baggett, Henry C, additional, Shang, Nong, additional, Schrag, Stephanie J, additional, Tempia, Stefano, additional, Lanaspa, Miguel, additional, Acácio, Sozinho, additional, Brooks, W Abdullah, additional, Driscoll, Amanda, additional, Knoll, Maria Deloria, additional, Prosperi, Christine, additional, Baqui, Abdullah H, additional, Mullany, Luke, additional, von Gottberg, Anne, additional, Hellferscee, Orienka, additional, Walaza, Sibongile, additional, Goswami, Doli, additional, Rahman, Mustafizur, additional, Connor, Nicholas E, additional, El Arifeen, Shams, additional, Marcone, Débora N, additional, Reyes, Noelia, additional, Gutierrez, Andrea, additional, Rodriguez, Ivan, additional, Lopez, Olga, additional, Ortiz, David, additional, Gonzalez, Nathaly, additional, del Valle Juarez, Maria, additional, Cutland, Clare, additional, Nunes, Marta C, additional, Nzenze, Susan, additional, Juvekar, Sanjay, additional, Halasa, Natasha, additional, Bernart, Chris, additional, Gofer, Ilan, additional, Avni, Yonat Shemer, additional, Faori, Samir, additional, Shehabi, Asem, additional, Kumar, Rakesh, additional, Amarchand, Ritvik, additional, Contreras, Carmen L, additional, Lopez, Maria R, additional, Maldonado, Herberth, additional, Samayoa, Antonio P, additional, Gomez, Ana B, additional, Nillos, Leilani T, additional, Lupisan, Socorro P, additional, Nohynek, Hanna, additional, Puig-Barberà, Joan, additional, Díez-Domingo, Javier, additional, Gessner, Bradford D, additional, Njanpop-Lafourcade, Berthe-Marie, additional, Tall, Haoua, additional, Ngama, Mwanjuma, additional, Nokes, D James, additional, Clark, Dayna R, additional, Ali, Sié, additional, Pascal, Zabré, additional, Cheik, Bagagnan H, additional, Caballero, Mauricio T, additional, Libster, Romina, additional, Thomas, Elizabeth D, additional, Baker, Julia M, additional, Obermeier, Patrick E, additional, Hassanuzzaman, MD., additional, Islam, Maksuda, additional, Islam, Mohammad S, additional, Panigrahi, Pinaki, additional, Bose, Anuradha, additional, Isaac, Rita, additional, Murdoch, David, additional, Nanda, Pritish, additional, Qazi, Shamim A, additional, Hessong, Danielle, additional, Simőes, Eric AF, additional, Chittaganpitch, Malinee, additional, Dawood, Halima, additional, Kyobutungi, Catherine, additional, Ziraba, Abdhalah K, additional, Yoshihara, Keisuke, additional, Dand, Duc-Anh, additional, Le, Minh-Nhat, additional, Nicol, Mark P, additional, Broor, Shobha, additional, Chadha, Mandeep, additional, Madrid, Lola, additional, Gresh, Lionel, additional, Balmaseda, Angel, additional, Kuan, Guillermina, additional, Wairagkar, Niteen, additional, Tapia, Milagritos D, additional, Knobler, Stacey L, additional, Barahona, Alfredo, additional, Ferguson, Ericka, additional, and Schweiger, Brunhilde, additional

Published
2020
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34. Unbiased metagenomic sequencing for pediatric meningitis in Bangladesh reveals neuroinvasive Chikungunya virus outbreak and other unrealized pathogens

Author

Saha, Senjuti, primary, Ramesh, Akshaya, additional, Kalantar, Katrina, additional, Malaker, Roly, additional, Hasanuzzaman, Md, additional, Khan, Lillian M., additional, Mayday, Madeline Y, additional, Sajib, M S I, additional, Li, Lucy M., additional, Langelier, Charles, additional, Rahman, Hafizur, additional, Crawford, Emily D., additional, Tato, Cristina M., additional, Islam, Maksuda, additional, Juan, Yun-Fang, additional, Bourcy, Charles de, additional, Dimitrov, Boris, additional, Wang, James, additional, Tang, Jennifer, additional, Sheu, Jonathan, additional, Egger, Rebecca, additional, De Carvalho, Tiago Rodrigues, additional, Wilson, Michael R., additional, Saha, Samir K, additional, and DeRisi, Joseph L, additional

Published
2019
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35. Epidemiology of Typhoid and Paratyphoid: Implications for Vaccine Policy

Author

Saha, Senjuti, primary, Islam, Md Shfiqul, additional, Sajib, Mohammad Saiful Islam, additional, Saha, Shampa, additional, Uddin, Mohammad Jamal, additional, Hooda, Yogesh, additional, Hasan, Md, additional, Amin, Md Ruhul, additional, Hanif, Mohammed, additional, Shahidullah, Mohammad, additional, Islam, Maksuda, additional, Luby, Stephen P, additional, Andrews, Jason R, additional, and Saha, Samir K, additional

Published
2019
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36. Population-based incidence and serotype distribution of invasive pneumococcal disease prior to introduction of conjugate pneumococcal vaccine in Bangladesh.

Author

Baqui, Abdullah H., McCollum, Eric D., Mahmud, Arif, Roy, Arunangshu, Chowdhury, Nabidul H., Rafiqullah, Iftekhar, Rizvi, Syed Jafar Raza, Begum, Nazma, Mitra, Dipak K., Khanam, Rasheda, Harrison, Meagan, Ahmed, Salahuddin, Hasanuzzaman, Md, Rahman, Hafizur, Islam, Maksuda, Ahmed, Zabed B., Quaiyum, Md Abdul, Koffi, Alain, Simmons, Nicole, and Checkley, William

Subjects
PNEUMOCOCCAL vaccines, HAEMOPHILUS diseases, SEROTYPES, STREPTOCOCCUS pneumoniae, POLYMERASE chain reaction, CEREBROSPINAL fluid
Abstract

Background: Bangladesh introduced the 10-valent pneumococcal conjugate vaccine (PCV-10) in 2015. We measured population-based incidence of invasive pneumococcal disease (IPD) prior to introduction of PCV-10 to provide a benchmark against which the impact of PCV-10 can be assessed. Methods: We conducted population, facility and laboratory-based surveillance in children 0–59 months of age in three rural sub-districts of Sylhet district of Bangladesh from January 2014 to June 2015. All children received two-monthly home visits with one week recall for morbidity and care seeking. Children attending the three Upazilla Health Complexes (UHC, sub-district hospitals) in the surveillance area were screened for suspected IPD. Blood samples were collected from suspected IPD cases for culture and additionally, cerebrospinal fluid (CSF) was collected from suspected meningitis cases for culture and molecular testing. Pneumococcal isolates were serotyped by Quellung. Serotyping of cases detected by molecular testing was done by sequential multiplex polymerase chain reaction. Results: Children under surveillance contributed to 126,657 child years of observations. Sixty-three thousand three hundred eighty-four illness episodes were assessed in the UHCs. Blood specimens were collected from 8,668 suspected IPD cases and CSF from 177 suspected meningitis cases. Streptococcus pneumoniae was isolated from 46 cases; 32 (70%) were vaccine serotype. The population-based incidence of IPD was 36.3/100,000 child years of observations. About 80% of the cases occurred in children below two years of age. Discussion: IPD was common in rural Bangladesh suggesting the potential benefit of an effective vaccine. Measurement of the burden of IPD requires multiple surveillance modalities. [ABSTRACT FROM AUTHOR]

Published
2020
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37. Causes and incidence of community-acquired serious infections among young children in south Asia (ANISA): an observational cohort study

Author

Saha, Samir K, primary, Schrag, Stephanie J, additional, El Arifeen, Shams, additional, Mullany, Luke C, additional, Shahidul Islam, Mohammad, additional, Shang, Nong, additional, Qazi, Shamim A, additional, Zaidi, Anita K M, additional, Bhutta, Zulfiqar A, additional, Bose, Anuradha, additional, Panigrahi, Pinaki, additional, Soofi, Sajid B, additional, Connor, Nicholas E, additional, Mitra, Dipak K, additional, Isaac, Rita, additional, Winchell, Jonas M, additional, Arvay, Melissa L, additional, Islam, Maksuda, additional, Shafiq, Yasir, additional, Nisar, Imran, additional, Baloch, Benazir, additional, Kabir, Furqan, additional, Ali, Murtaza, additional, Diaz, Maureen H, additional, Satpathy, Radhanath, additional, Nanda, Pritish, additional, Padhi, Bijaya K, additional, Parida, Sailajanandan, additional, Hotwani, Aneeta, additional, Hasanuzzaman, M, additional, Ahmed, Sheraz, additional, Belal Hossain, Mohammad, additional, Ariff, Shabina, additional, Ahmed, Imran, additional, Ibne Moin, Syed Mamun, additional, Mahmud, Arif, additional, Waller, Jessica L, additional, Rafiqullah, Iftekhar, additional, Quaiyum, Mohammad A, additional, Begum, Nazma, additional, Balaji, Veeraraghavan, additional, Halen, Jasmin, additional, Nawshad Uddin Ahmed, A S M, additional, Weber, Martin W, additional, Hamer, Davidson H, additional, Hibberd, Patricia L, additional, Sadeq-ur Rahman, Qazi, additional, Mogan, Venkat Raghava, additional, Hossain, Tanvir, additional, McGee, Lesley, additional, Anandan, Shalini, additional, Liu, Anran, additional, Panigrahi, Kalpana, additional, Abraham, Asha Mary, additional, and Baqui, Abdullah H, additional

Published
2018
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39. Pneumococcal Conjugate Vaccine impact assessment in Bangladesh

Author

Baqui, Abdullah H., primary, McCollum, Eric D., additional, Saha, Samir K., additional, Roy, Arun K., additional, Chowdhury, Nabidul H., additional, Harrison, Meagan, additional, Hanif, Abu Abdullah Mohammad, additional, Simmons, Nicole, additional, Mahmud, Arif, additional, Begum, Nazma, additional, Ahmed, Salahuddin, additional, Khan, Ahad M., additional, Ahmed, Zabed Bin, additional, Islam, Maksuda, additional, Mitra, Dipak, additional, Quaiyum, Abdul, additional, Chavez, Miguel A., additional, Pervaiz, Farhan, additional, Miele, Catherine H., additional, Schuh, Holly B., additional, Khanam, Rasheda, additional, Checkley, William, additional, Moulton, Lawrence H., additional, and Santosham, Mathuram, additional

Published
2018
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40. Integration of enteric fever surveillance into the WHO-coordinated Invasive Bacterial-Vaccine Preventable Diseases (IB-VPD) platform: A low cost approach to track an increasingly important disease

Author

Saha, Senjuti, primary, Islam, Maksuda, additional, Uddin, Mohammad J., additional, Saha, Shampa, additional, Das, Rajib C., additional, Baqui, Abdullah H., additional, Santosham, Mathuram, additional, Black, Robert E., additional, Luby, Stephen P., additional, and Saha, Samir K., additional

Published
2017
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43. Prevalence, Serotype Distribution and Mortality Risk Associated With Group B Streptococcus Colonization of Newborns in Rural Bangladesh

Author

Islam, Mohammad Shahidul, primary, Saha, Samir K., additional, Islam, Maksuda, additional, Modak, Joyanta K., additional, Shah, Rashed, additional, Talukder, Radwanur R., additional, El Arifeen, Shams, additional, Baqui, Abdullah H., additional, Darmstadt, Gary L., additional, and Mullany, Luke C., additional

Published
2016
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44. Epidemiology and risk factors for pneumonia severity and mortality in Bangladeshi children <5 years of age before 10-valent pneumococcal conjugate vaccine introduction

Author

Saha, Shampa, primary, Hasan, Md, additional, Kim, Lindsay, additional, Farrar, Jennifer L., additional, Hossain, Belal, additional, Islam, Maksuda, additional, Ahmed, ASM Nawshad Uddin, additional, Amin, M. Ruhul, additional, Hanif, Mohammed, additional, Hussain, Manzoor, additional, El-Arifeen, Shams, additional, Whitney, Cynthia G., additional, and Saha, Samir K., additional

Published
2016
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45. Epidemiology of Invasive Pneumococcal Disease in Bangladeshi Children Before Introduction of Pneumococcal Conjugate Vaccine

Author

Saha, Samir K., primary, Hossain, Belal, additional, Islam, Maksuda, additional, Hasanuzzaman, Md, additional, Saha, Shampa, additional, Hasan, Mohammad, additional, Darmstadt, Gary L., additional, Chowdury, Mrittika, additional, Arifeen, Shams El, additional, Baqui, Abdullah H., additional, Breiman, Robert F., additional, Santosham, Mathuram, additional, Luby, Stephen P., additional, and Whitney, Cynthia G., additional

Published
2016
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47. Methods Employed in Monitoring and Evaluating Field and Laboratory Systems in the ANISA Study

Author

Connor, Nicholas E., primary, Islam, Mohammad Shahidul, additional, Arvay, Melissa L., additional, Baqui, Abdullah H., additional, Zaidi, Anita K., additional, Soofi, Sajid B., additional, Panigrahi, Pinaki, additional, Bose, Anuradha, additional, Islam, Maksuda, additional, Arifeen, Shams El, additional, Saha, Samir K., additional, and Qazi, Shamim A., additional

Published
2016
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49. Classification of Blood Culture Isolates Into Contaminants and Pathogens on the Basis of Clinical and Laboratory Data

Author

Hossain, Belal, primary, Weber, Martin W., additional, Hamer, Davidson H., additional, Hibberd, Patricia L., additional, Ahmed, A. S. M. Nawshad Uddin, additional, Marzan, Mahfuza, additional, Islam, Maksuda, additional, Connor, Nicholas E., additional, Islam, Mohammad Shahidul, additional, Zaidi, Anita K., additional, Baqui, Abdullah H., additional, Bhutta, Zulfiqar A., additional, Qureshi, Shahida M., additional, Rafiqullah, Iftekhar, additional, McGee, Lesley, additional, and Saha, Samir K., additional

Published
2016
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50. Understanding Bacterial Isolates in Blood Culture and Approaches Used to Define Bacteria as Contaminants

Author

Hossain, Belal, primary, Islam, Mohammad Shahidul, additional, Rahman, Atiqur, additional, Marzan, Mahfuza, additional, Rafiqullah, Iftekhar, additional, Connor, Nicholas E., additional, Hasanuzzaman, Mohammad, additional, Islam, Maksuda, additional, Hamer, Davidson H., additional, Hibberd, Patricia L., additional, and Saha, Samir K., additional

Published
2016
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