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1. Probing coalescence of light nuclei via femtoscopy and azimuthal anisotropies

Author

Bailung, Yoshini, Rode, Sudhir Pandurang, Shah, Neha, and Roy, Ankhi

Subjects
Nuclear Theory, High Energy Physics - Phenomenology
Abstract

The production mechanism of light nuclei in heavy-ion collisions is vital to understanding the intricate details of nucleon-nucleon interactions. The coalescence of nucleons is a well-known mechanism that attempts to explain the production mechanism of these light clusters. This work investigates the formation mechanism of these nucleon clusters with a combination of coalescence and femtoscopy of nucleons and nuclei. It is achieved by appending a coalescence and correlation afterburner (\texttt{CRAB}) to the \texttt{SMASH} transport model. To have a proper view of the anisotropy of light nuclei clusters, a mean-field approach to \texttt{SMASH} is applied. The anisotropic coefficients of various light nuclei clusters are calculated and compared to experimental measurements. To incorporate hydrodynamics into the picture, the anisotropic measurements are completed in a hybrid \texttt{SMASH}+\texttt{vHLLE} mode. In both approaches, the femtoscopy of nucleons and light nuclei is performed, reported with CRAB, and compared to the latest experimental measurements. An insight into cluster formation time is drawn by extracting the emission source size with the Lednick\'y-Lyuboshits (LL) model., Comment: 10 pages, 6 figures

Published
2024

2. Searching for enhancement in coalescence of in-jet (anti-)deuterons in proton-proton collisions

Author

Bailung, Yoshini, Shah, Neha, and Roy, Ankhi

Subjects
High Energy Physics - Phenomenology
Abstract

Recent measurements from ALICE report that $``$in-jet'' nucleons carry a higher probability of forming a deuteron via coalescence than the nucleons from the underlying event (UE). This study makes use of an event shape classifier to separate the $``$in-jet'' deuterons and the deuterons in the UE produced in high multiplicity proton-proton collisions at $\sqrt{s} = 13$ TeV. Event shape variables such as transverse spherocity allow the categorization of hard and soft components of an event, which can be divided into two respective classes; $``$jetty'' and $``$isotropic''. The $``$jetty'' deuterons minus the contribution of the deuterons from the $``$isotropic'' event are taken as $``$in-jet'' deuterons, and the coalescence mechanism is tested. The coalescence is performed with a Wigner function formalism, augmented as an afterburner to \textsc{pythia}8. The possible enhancement of the coalescence probability of $``$in-jet'' deuterons is investigated by calculating the coalescence parameter ($B_{2}$) in different spherocity classes in high-multiplicity $pp$ collisions., Comment: 11 pages, 9 figures, To appear in Physical Review C

Published
2024

3. Duvelisib plus romidepsin in relapsed/refractory T cell lymphomas: a phase 1b/2a trial

Author

Horwitz, Steven M., Nirmal, Ajit J., Rahman, Jahan, Xu, Ran, Drill, Esther, Galasso, Natasha, Ganesan, Nivetha, Davey, Theresa, Hancock, Helen, Perez, Leslie, Maccaro, Catherine, Bahgat, Alexandra, Marzouk, Evan, Cathcart, Elizabeth, Moskowitz, Alison, Noy, Ariela, Kumar, Anita, Jacobsen, Eric, Fisher, David C., Mehta-Shah, Neha, Kim, Youn H., Khodadoust, Michael, Kotlov, Nikita, Nikitina, Anastasia, Kudryashova, Olga, Zubareva, Valeria, Zornikova, Ksenia, Shin, Nara, Sorokina, Maria, Degryse, Sandrine, Postovalova, Ekaterina, Bagaev, Aleksander, Hosszu, Kinga, McAvoy, Devin, Boelens, Jaap J., Wu, Wenchao, Ciantra, Zoe, Appelt, Jackson W., Trevisani, Christopher, Amaka, Sam, Weinstock, David M., and Vardhana, Santosha A.

Published
2024
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5. Using Machine Learning to Optimize the Quality of Survey Data: Protocol for a Use Case in India

Author

Shah, Neha, Mohan, Diwakar, Bashingwa, Jean Juste Harisson, Ummer, Osama, Chakraborty, Arpita, and LeFevre, Amnesty E

Subjects
Medicine, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

BackgroundData quality is vital for ensuring the accuracy, reliability, and validity of survey findings. Strategies for ensuring survey data quality have traditionally used quality assurance procedures. Data analytics is an increasingly vital part of survey quality assurance, particularly in light of the increasing use of tablets and other electronic tools, which enable rapid, if not real-time, data access. Routine data analytics are most often concerned with outlier analyses that monitor a series of data quality indicators, including response rates, missing data, and reliability of coefficients for test-retest interviews. Machine learning is emerging as a possible tool for enhancing real-time data monitoring by identifying trends in the data collection, which could compromise quality. ObjectiveThis study aimed to describe methods for the quality assessment of a household survey using both traditional methods as well as machine learning analytics. MethodsIn the Kilkari impact evaluation’s end-line survey amongst postpartum women (n=5095) in Madhya Pradesh, India, we plan to use both traditional and machine learning–based quality assurance procedures to improve the quality of survey data captured on maternal and child health knowledge, care-seeking, and practices. The quality assurance strategy aims to identify biases and other impediments to data quality and includes seven main components: (1) tool development, (2) enumerator recruitment and training, (3) field coordination, (4) field monitoring, (5) data analytics, (6) feedback loops for decision making, and (7) outcomes assessment. Analyses will include basic descriptive and outlier analyses using machine learning algorithms, which will involve creating features from time-stamps, “don’t know” rates, and skip rates. We will also obtain labeled data from self-filled surveys, and build models using k-folds cross-validation on a training data set using both supervised and unsupervised learning algorithms. Based on these models, results will be fed back to the field through various feedback loops. ResultsData collection began in late October 2019 and will span through March 2020. We expect to submit quality assurance results by August 2020. ConclusionsMachine learning is underutilized as a tool to improve survey data quality in low resource settings. Study findings are anticipated to improve the overall quality of Kilkari survey data and, in turn, enhance the robustness of the impact evaluation. More broadly, the proposed quality assurance approach has implications for data capture applications used for special surveys as well as in the routine collection of health information by health workers. International Registered Report Identifier (IRRID)DERR1-10.2196/17619

Published
2020
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7. Author Correction: Duvelisib plus romidepsin in relapsed/refractory T cell lymphomas: a phase 1b/2a trial

Author

Horwitz, Steven M., Nirmal, Ajit J., Rahman, Jahan, Xu, Ran, Drill, Esther, Galasso, Natasha, Ganesan, Nivetha, Davey, Theresa, Hancock, Helen, Perez, Leslie, Maccaro, Catherine, Bahgat, Alexandra, Marzouk, Evan, Cathcart, Elizabeth, Moskowitz, Alison, Noy, Ariela, Kumar, Anita, Jacobsen, Eric, Fisher, David C., Mehta-Shah, Neha, Kim, Youn H., Khodadoust, Michael, Kotlov, Nikita, Nikitina, Anastasia, Kudryashova, Olga, Zubareva, Valeria, Zornikova, Ksenia, Shin, Nara, Sorokina, Maria, Degryse, Sandrine, Postovalova, Ekaterina, Bagaev, Aleksander, Hosszu, Kinga, McAvoy, Devin, Boelens, Jaap J., Wu, Wenchao, Ciantra, Zoe, Appelt, Jackson W., Trevisani, Christopher, Amaka, Sam, Weinstock, David M., and Vardhana, Santosha A.

Published
2024
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8. Gamma-hadron Separation in Imaging Atmospheric Cherenkov Telescopes using Quantum Classifiers

Author

S, Jashwanth, Ghosh, Sudeep, Shah, Neha, Yogaraj, Kavitha, and Roy, Ankhi

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - High Energy Astrophysical Phenomena
Abstract

In this paper we have introduced a novel method for gamma hadron separation in Imaging Atmospheric Cherenkov Telescopes (IACT) using Quantum Machine Learning. IACTs captures images of Extensive Air Showers (EAS) produced from very high energy gamma rays. We have used the QML Algorithms, Quantum Support Vector Classifier (QSVC) and Variational Quantum Classifier (VQC) for binary classification of the events into signals (Gamma) and background(hadron) using the image parameters. MAGIC Gamma Telescope dataset is used for this study which was generated from Monte Carlo Software Coriska. These quantum algorithms achieve performance comparable to standard multivariate classification techniques and can be used to solve variety of real-world problems. The classification accuracy is improved by hyper parameter tuning. We propose a new architecture for using QSVC efficiently on large datasets and found that clustering enhance the overall performance., Comment: It was supposed to be submitted as a Master Thesis and not as a paper. We need to withdraw this submission, so that we will able to submit this again as a Thesis

Published
2022

9. A multi-cohort phase 1b trial of rituximab in combination with immunotherapy doublets in relapsed/refractory follicular lymphoma

Author

Merryman, Reid W., Redd, Robert A., Freedman, Arnold S., Ahn, Inhye E., Brown, Jennifer R., Crombie, Jennifer L., Davids, Matthew S., Fisher, David C., Jacobsen, Eric D., Kim, Austin I., LaCasce, Ann S., Ng, Samuel, Odejide, Oreofe O., Parry, Erin M., Isufi, Iris, Kline, Justin, Cohen, Jonathon B., Mehta-Shah, Neha, Bartlett, Nancy L., Mei, Matthew, Kuntz, Thomas M., Wolff, Jacquelyn, Rodig, Scott J., Armand, Philippe, and Jacobson, Caron A.

Published
2024
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10. The Post-transplant Lymphoproliferative Disorders—Metagenomic Shotgun Microbial Sequencing (PTLD-MSMS) Study Methods and Protocol

Author

Dharnidharka, Vikas R., Wylie, Kristine M., Wylie, Todd N., Ruzinova, Marianna B., Goss, Charles W., Storch, Gregory A., Mehta-Shah, Neha, Byers, Derek, Walther, Leslie, Jaza, Lujain, Gu, Hongjie, Agarwal, Mansi, Green, Michael, Moore, Erika, Swerdlow, Steven H., Silveira, Fernanda, Marks, Lianna J., Gratzinger, Dita, Bagg, Adam, Law, Soi Cheng, and Gandhi, Maher

Published
2024
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11. Persistent low‐level viraemia is associated with non‐infectious comorbidities in an observational cohort in four African countries

Author

Esber, Allahna L., Colt, Suze, Jian, Ningbo, Dear, Nicole, Slike, Bonnie, Sing'Oei, Valentine, Maswai, Jonah, Iroezindu, Michael, Bahemana, Emmanuel, Kibuuka, Hannah, Polyak, Christina S., Streeck, Hendrik, Shah, Neha, Crowell, Trevor A., and Ake, Julie A.

Subjects
Comorbidity -- Analysis, Efavirenz -- Analysis, Highly active antiretroviral therapy -- Analysis, Hypercholesterolemia -- Analysis, Hyperglycemia -- Analysis, Health
Abstract

: Introduction: People living with HIV (PLWH) have higher rates of non‐infectious comorbid diseases (NCDs) than individuals without HIV. We characterized the risk of NCDs among PLWH with undetectable viral load and persistent low‐level viraemia (pLLV) in the African Cohort Study (AFRICOS). We secondarily quantified the role of immune activation in the association between LLV and NCDs. Methods: AFRICOS enrols participants in 12 clinics in Uganda, Kenya, Tanzania and Nigeria. Participants on antiretroviral therapy ≥ 6 months without an NCD at enrolment were included. PLLV was defined as at least two consecutive visits with a detectable viral load Results: From 23 January 2013 to 1 December 2022, 1755 participants met the inclusion criteria for these analyses. At the first eligible visit, the majority of participants had an undetectable viral load (n = 1375, 78.35%). Participants with pLLV had an increased rate of developing any NCD (aHR: 1.22, 95% CI: 1.02−1.47) compared to participants with an undetectable viral load. There was a statistically significant interaction between LLV and TNF‐α, CCL2/MCP‐1 and TNF‐RII in the association with any NCD. Conclusions: PLLV was significantly associated with NCDs and immune inflammation in this population. Aggressive management of LLV may positively impact NCDs in PLWH., INTRODUCTION Despite improved life expectancy with antiretroviral therapy (ART), people living with HIV (PLWH) have higher rates of non‐infectious comorbid diseases (NCDs) than do people living without HIV [1–5]. The [...]

Published
2024
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12. ASTCT and USCLC Clinical Practice Recommendations for Allogeneic Stem Cell Transplant in Mycosis Fungoides and Sézary Syndrome

Author

Goyal, Amrita, O'Leary, Daniel, Dabaja, Bouthaina, Weng, Wen-Kai, Zain, Jasmine, Cutler, Corey, Guitart, Joan, Kim, Youn H., Geskin, Larisa J., Hoppe, Richard T., Wilson, Lynn D., Beaven, Anne W., Horwitz, Steve, Allen, Pamela B., Barta, Stefan K., Bohjanen, Kimberly, Brammer, Jonathan E., Carter, Joi B., Comfere, Nneka, DeSimone, Jennifer A., Dusenbery, Kathryn, Duvic, Madeleine, Huen, Auris, Jagadeesh, Deepa, Kelsey, Chris R., Khodadoust, Michael S., Lechowicz, Mary Jo, Mehta-Shah, Neha, Moskowitz, Alison J., Olsen, Elise A., Poh, Christina, Pro, Barbara, Querfeld, Christiane, Sauter, Craig, Sokol, Lubomir, Sokumbi, Olayemi, Wilcox, Ryan A., Zic, John A., Hamadani, Mehdi, and Foss, Francine

Published
2024
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14. Neoantigen landscape supports feasibility of personalized cancer vaccine for follicular lymphoma

Author

Ramirez, Cody A., Becker-Hapak, Michelle, Singhal, Kartik, Russler-Germain, David A., Frenkel, Felix, Barnell, Erica K., McClain, Ethan D., Desai, Sweta, Schappe, Timothy, Onyeador, Onyinyechi C., Kudryashova, Olga, Belousov, Vladislav, Bagaev, Alexander, Ocheredko, Elena, Kiwala, Susanna, Hundal, Jasreet, Skidmore, Zachary L., Watkins, Marcus P., Mooney, Thomas B., Walker, Jason R., Krysiak, Kilannin, Gomez, Felicia, Fronick, Catrina C., Fulton, Robert S., Schreiber, Robert D., Mehta-Shah, Neha, Cashen, Amanda F., Kahl, Brad S., Ataullakhanov, Ravshan, Bartlett, Nancy L., Griffith, Malachi, Griffith, Obi L., and Fehniger, Todd A.

Published
2024
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15. The CNS relapse in T-cell lymphoma index predicts CNS relapse in patients with T- and NK-cell lymphomas

Author

Bhansali, Rahul S., Ellin, Fredrik, Relander, Thomas, Cao, Miao, Li, Wenrui, Long, Qi, Ganesan, Nivetha, Stuver, Robert, Horwitz, Steven M., Wudhikarn, Kitsada, Hwang, Steven R., Bennani, N. Nora, Chavez, Julio, Sokol, Lubomir, Saeed, Hayder, Duan, Frank, Porcu, Pierluigi, Pullarkat, Priyanka, Mehta-Shah, Neha, Zain, Jasmine M., Ruiz, Miguel, Brammer, Jonathan E., Prakash, Rishab, Iyer, Swaminathan P., Olszewski, Adam J., Major, Ajay, Riedell, Peter A., Smith, Sonali M., Goldin, Caroline, Haverkos, Bradley, Hu, Bei, Zhuang, Tony Z., Allen, Pamela B., Toama, Wael, Janakiram, Murali, Brooks, Taylor R., Jagadeesh, Deepa, Hariharan, Nisha, Goodman, Aaron M., Hartman, Gabrielle, Ghione, Paola, Fayyaz, Fatima, Rhodes, Joanna M., Chong, Elise A., Gerson, James N., Landsburg, Daniel J., Nasta, Sunita D., Schuster, Stephen J., Svoboda, Jakub, Jerkeman, Mats, and Barta, Stefan K.

Published
2024
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21. Sustaining HIV service delivery to key population clients using client‐centered models during the debate and enactment of the Anti‐Homosexuality Act in Uganda

Author

Vasireddy, Vamsi, Brown, Natalie E., Shah, Neha, and Crowell, Trevor A.

Subjects
HIV (Viruses) -- Laws, regulations and rules, Homosexuality -- Laws, regulations and rules, HIV testing -- Laws, regulations and rules, Security guards -- Sexual behavior, Gays -- Sexual behavior, Government regulation, Health
Abstract

Punitive and discriminatory laws against key populations (KP), particularly men who have sex with men (MSM), have been on the rise for over a decade [1, 2]. Studies have shown [...]

Published
2024
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22. Dynamic Silos: Increased Modularity in Intra-organizational Communication Networks during the Covid-19 Pandemic

Author

Zuzul, Tiona, Pahnke, Emily Cox, Larson, Jonathan, Bourke, Patrick, Caurvina, Nicholas, Shah, Neha Parikh, Amini, Fereshteh, Weston, Jeffrey, Park, Youngser, Vogelstein, Joshua, White, Christopher, and Priebe, Carey E.

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning
Abstract

Workplace communications around the world were drastically altered by Covid-19, related work-from-home orders, and the rise of remote work. To understand these shifts, we analyzed aggregated, anonymized metadata from over 360 billion emails within 4,361 organizations worldwide. By comparing month-to-month and year-over-year metrics, we examined changes in network community structures over 24 months before and after Covid-19. We also examined shifts across multiple communication media (email, instant messages, video calls, and calendaring software) within a single global organization, and compared them to communications shifts that were driven by changes in formal organizational structure. We found that, in 2020, organizations around the world became more siloed than in 2019, evidenced by increased modularity. This shift was concurrent with decreased stability within silos. Collectively, our analyses indicate that following the onset of Covid-19, employees began to shift more dynamically between subcommunities (teams, workgroups or functional areas). At the same time, once in a subcommunity, they limited their communication to other members of that community. We term these network changes dynamic silos. We provide initial insights into the meaning and implications of dynamic silos for the future of work., Comment: 48 pages, 15 figures

Published
2021

25. Golidocitinib, a selective JAK1 tyrosine-kinase inhibitor, in patients with refractory or relapsed peripheral T-cell lymphoma (JACKPOT8 Part B): a single-arm, multinational, phase 2 study

Author

Song, Yuqin, Malpica, Luis, Cai, Qingqing, Zhao, Weili, Zhou, Keshu, Wu, Jianqiu, Zhang, Huilai, Mehta-Shah, Neha, Ding, Kaiyang, Liu, Yao, Li, Zengjun, Zhang, Liling, Zheng, Meifang, Jin, Jie, Yang, Haiyan, Shuang, Yuerong, Yoon, Dok Hyun, Gao, Sujun, Li, Wenyu, Zhai, Zhimin, Zou, Liqun, Xi, Yaming, Koh, Youngil, Li, Fei, Prince, Miles, Zhou, Hui, Lin, Lie, Liu, Hui, Allen, Pamela, Roncolato, Fernando, Yang, Zhenfan, Kim, Won-Seog, and Zhu, Jun

Published
2024
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27. How Work From Home Affects Collaboration: A Large-Scale Study of Information Workers in a Natural Experiment During COVID-19

Author

Yang, Longqi, Jaffe, Sonia, Holtz, David, Suri, Siddharth, Sinha, Shilpi, Weston, Jeffrey, Joyce, Connor, Shah, Neha, Sherman, Kevin, Lee, CJ, Hecht, Brent, and Teevan, Jaime

Subjects
Computer Science - Computers and Society, Computer Science - Human-Computer Interaction, Computer Science - Software Engineering
Abstract

The COVID-19 pandemic has had a wide-ranging impact on information workers such as higher stress levels, increased workloads, new workstreams, and more caregiving responsibilities during lockdown. COVID-19 also caused the overwhelming majority of information workers to rapidly shift to working from home (WFH). The central question this work addresses is: can we isolate the effects of WFH on information workers' collaboration activities from all other factors, especially the other effects of COVID-19? This is important because in the future, WFH will likely to be more common than it was prior to the pandemic. We use difference-in-differences (DiD), a causal identification strategy commonly used in the social sciences, to control for unobserved confounding factors and estimate the causal effect of WFH. Our analysis relies on measuring the difference in changes between those who WFH prior to COVID-19 and those who did not. Our preliminary results suggest that on average, people spent more time on collaboration in April (Post WFH mandate) than in February (Pre WFH mandate), but this is primarily due to factors other than WFH, such as lockdowns during the pandemic. The change attributable to WFH specifically is in the opposite direction: less time on collaboration and more focus time. This reversal shows the importance of using causal inference: a simple analysis would have resulted in the wrong conclusion. We further find that the effect of WFH is moderated by individual remote collaboration experience prior to WFH. Meanwhile, the medium for collaboration has also shifted due to WFH: instant messages were used more, whereas scheduled meetings were used less. We discuss design implications -- how future WFH may affect focused work, collaborative work, and creative work.

Published
2020
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28. Workgroup Mapping: Visual Analysis of Collaboration Culture

Author

Edge, Darren, Larson, Jonathan, Trandev, Nikolay, Shah, Neha Parikh, Buractaon, Carolyn, Caurvina, Nicholas, Evans, Nathan, and White, Christopher M.

Subjects
Computer Science - Human-Computer Interaction, Computer Science - Social and Information Networks
Abstract

The digital transformation of work presents new opportunities to understand how informal workgroups organize around the dynamic needs of organizations, potentially in contrast to the formal, static, and idealized hierarchies depicted by org charts. We present a design study that spans multiple enabling capabilities for the visual mapping and analysis of organizational workgroups, including metrics for quantifying two dimensions of collaboration culture: the fluidity of collaborative relationships (measured using network machine learning) and the freedom with which workgroups form across organizational boundaries. These capabilities come together to create a turnkey pipeline that combines the analysis of a target organization, the generation of data graphics and statistics, and their integration in a template-based presentation that enables narrative visualization of results. Our metrics and visuals have supported hundreds of presentations to executives of major US-based and multinational organizations, while our engineering practices have created an ensemble of standalone tools with broad relevance to visualization and visual analytics. We present our work as an example of applied visual analytics research, describing the design iterations that allowed us to move from experimentation to production, as well as the perspectives of the research team and the customer-facing team at each stage in this process.

Published
2020

29. Implications of asymptomatic malaria infections on hematologic parameters in adults living with HIV in malaria-endemic regions with varying transmission intensities

Author

Kamau, Edwin, Maisiba, Risper, Dear, Nicole, Esber, Allahna, Parikh, Ajay P., Iroezindu, Michael, Bahemana, Emmanuel, Kibuuka, Hannah, Owuoth, John, Maswai, Jonah, Opot, Benjamin, Okoth, Raphael O., Abdi, Farid, Mwalo, Maureen, Juma, Dennis, Andagalu, Ben, Akala, Hoseah M., Shah, Neha, Crowell, Trevor A., Cowden, Jessica, Polyak, Christina S., and Ake, Julie A.

Published
2023
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30. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303

Author

Russler-Germain, David A., Krysiak, Kilannin, Ramirez, Cody, Mosior, Matthew, Watkins, Marcus P., Gomez, Felicia, Skidmore, Zachary L., Trani, Lee, Gao, Feng, Geyer, Susan, Cashen, Amanda F., Mehta-Shah, Neha, Kahl, Brad S., Bartlett, Nancy L., Alderuccio, Juan P., Lossos, Izidore S., Ondrejka, Sarah L., Hsi, Eric D., Martin, Peter, Leonard, John P., Griffith, Malachi, Griffith, Obi L., and Fehniger, Todd A.

Published
2023
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37. Tuberculosis Preventive Treatment Update--U.S. President's Emergency Plan for AIDS Relief, 36 Countries, 2016-2023

Author

Ajiboye, Aderonke S., O'Connor, Stephanie, Smith, Jonathan P., Ahmedov, Sevim, Coggin, William L., Charles, Macarthur, Ghosh, Smita, Pierre, Paul, Shah, Neha, Teran, Richard A., Moonan, Patrick K., and Date, Anand

Subjects
Medicine, Preventive -- Safety and security measures, Antiviral agents -- Safety and security measures, Highly active antiretroviral therapy -- Safety and security measures, Tuberculosis -- Safety and security measures, Preventive health services -- Safety and security measures, HIV patients -- Safety and security measures, AIDS (Disease) -- Safety and security measures, Rifapentine -- Safety and security measures, Emergency management -- Safety and security measures, Health, World Health Organization -- Safety and security measures
Abstract

Tuberculosis (TB) is the leading cause of death among persons with HIV. In 2022, an estimated 167,000 TB-related deaths occurred globally among persons with HIV. TB preventive treatment (TPT) helps [...]

Published
2024

38. Multicenter phase 2 study of oral azacitidine (CC-486) plus CHOP as initial treatment for PTCL

Author

Ruan, Jia, Moskowitz, Alison, Mehta-Shah, Neha, Sokol, Lubomir, Chen, Zhengming, Kotlov, Nikita, Nos, Grigorii, Sorokina, Maria, Maksimov, Vladislav, Sboner, Andrea, Sigouros, Michael, van Besien, Koen, Horwitz, Steven, Rutherford, Sarah C., Mulvey, Erin, Revuelta, Maria V., Xiang, Jenny, Alonso, Alicia, Melnick, Ari, Elemento, Olivier, Inghirami, Giorgio, Leonard, John P., Cerchietti, Leandro, and Martin, Peter

Published
2023
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42. Five cases of idiopathic sciatic mononeuropathy: Clinical, electrophysiological, radiological, and histological features

Author

Khadilkar, Satish, Kamat, Saurabh, Deshmukh, Narayan, Shah, Neha, Shetty, Vanaja, Shah, Swati, Halani, Hiral, and Mansukhani, Khushnuma

Subjects
Medical research, Medicine, Experimental, Health
Abstract

Byline: Satish. Khadilkar, Saurabh. Kamat, Narayan. Deshmukh, Neha. Shah, Vanaja. Shetty, Swati. Shah, Hiral. Halani, Khushnuma. Mansukhani Background: Common etiologies of sciatic mononeuropathy are compressive, infiltrative, traumatic, or diabetic. However, [...]

Published
2023

44. Treatment of Drug-Resistant Tuberculosis. An Official ATS/CDC/ERS/IDSA Clinical Practice Guideline

Author

Nahid, Payam, Mase, Sundari R, Migliori, Giovanni Battista, Sotgiu, Giovanni, Bothamley, Graham H, Brozek, Jan L, Cattamanchi, Adithya, Cegielski, J Peter, Chen, Lisa, Daley, Charles L, Dalton, Tracy L, Duarte, Raquel, Fregonese, Federica, Horsburgh, C Robert, Khan, Faiz Ahmad, Kheir, Fayez, Lan, Zhiyi, Lardizabal, Alfred, Lauzardo, Michael, Mangan, Joan M, Marks, Suzanne M, McKenna, Lindsay, Menzies, Dick, Mitnick, Carole D, Nilsen, Diana M, Parvez, Farah, Peloquin, Charles A, Raftery, Ann, Schaaf, H Simon, Shah, Neha S, Starke, Jeffrey R, Wilson, John W, Wortham, Jonathan M, Chorba, Terence, and Seaworth, Barbara

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Biodefense, Antimicrobial Resistance, Lung, Vaccine Related, Emerging Infectious Diseases, Rare Diseases, Prevention, Tuberculosis, Infectious Diseases, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Antitubercular Agents, Drug Administration Schedule, Drug Therapy, Combination, Humans, Tuberculosis, Multidrug-Resistant, Tuberculosis, Pulmonary, MDR-TB, tuberculosis, duration of treatment, drug treatment, treatment monitoring, Medical and Health Sciences, Respiratory System, Cardiovascular medicine and haematology, Clinical sciences
Abstract

Background: The American Thoracic Society, U.S. Centers for Disease Control and Prevention, European Respiratory Society, and Infectious Diseases Society of America jointly sponsored this new practice guideline on the treatment of drug-resistant tuberculosis (DR-TB). The document includes recommendations on the treatment of multidrug-resistant TB (MDR-TB) as well as isoniazid-resistant but rifampin-susceptible TB.Methods: Published systematic reviews, meta-analyses, and a new individual patient data meta-analysis from 12,030 patients, in 50 studies, across 25 countries with confirmed pulmonary rifampin-resistant TB were used for this guideline. Meta-analytic approaches included propensity score matching to reduce confounding. Each recommendation was discussed by an expert committee, screened for conflicts of interest, according to the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) methodology.Results: Twenty-one Population, Intervention, Comparator, and Outcomes questions were addressed, generating 25 GRADE-based recommendations. Certainty in the evidence was judged to be very low, because the data came from observational studies with significant loss to follow-up and imbalance in background regimens between comparator groups. Good practices in the management of MDR-TB are described. On the basis of the evidence review, a clinical strategy tool for building a treatment regimen for MDR-TB is also provided.Conclusions: New recommendations are made for the choice and number of drugs in a regimen, the duration of intensive and continuation phases, and the role of injectable drugs for MDR-TB. On the basis of these recommendations, an effective all-oral regimen for MDR-TB can be assembled. Recommendations are also provided on the role of surgery in treatment of MDR-TB and for treatment of contacts exposed to MDR-TB and treatment of isoniazid-resistant TB.

Published
2019

47. Improving eligibility criteria for first-line trials for patients with DLBCL using a US-based Delphi-method survey

Author

Harkins, R. Andrew, Patel, Sharvil P., Lee, Michelle J., Switchenko, Jeffrey M., Ansell, Stephen M., Bartlett, Nancy L., Blum, Kristie A., Cashen, Amanda F., Casulo, Carla, Friedberg, Jonathan W., Johnston, Patrick B., Kahl, Brad S., Leonard, John P., Link, Brian K., Lossos, Izidore S., Martin, Peter, Maurer, Matt J., Mehta-Shah, Neha, Reagan, Patrick M., Westin, Jason R., Koff, Jean L., and Flowers, Christopher R.

Published
2022
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49. Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout.

Author

Parekh, Udit, Wu, Yan, Zhao, Dongxin, Worlikar, Atharv, Shah, Neha, Zhang, Kun, and Mali, Prashant

Subjects
Cell Line, Humans, Transcription Factors, Gene Expression Profiling, Sequence Analysis, RNA, Male, Gene Regulatory Networks, Epithelial-Mesenchymal Transition, Single-Cell Analysis, Cellular Reprogramming, ORF overexpression, cellular reprogramming, pluripotent stem cells, single-cell screens, Sequence Analysis, RNA, Human Genome, Stem Cell Research, Regenerative Medicine, Biotechnology, Genetics, Generic Health Relevance, Biochemistry and Cell Biology
Abstract

Understanding the effects of genetic perturbations on the cellular state has been challenging using traditional pooled screens, which typically rely on the delivery of a single perturbation per cell and unidimensional phenotypic readouts. Here, we use barcoded open reading frame overexpression libraries coupled with single-cell RNA sequencing to assay cell state and fitness, a technique we call SEUSS (scalable functional screening by sequencing). Using SEUSS, we perturbed hPSCs with a library of developmentally critical transcription factors (TFs) and assayed the impact of TF overexpression on fitness and transcriptomic states. We further leveraged the versatility of the ORF library approach to assay mutant genes and whole gene families. From the transcriptomic responses, we built genetic co-regulatory networks to identify altered gene modules and found that KLF4 and SNAI2 drive opposing effects along the epithelial-mesenchymal transition axis. From the fitness responses, we identified ETV2 as a driver of reprogramming toward an endothelial-like state.

Published
2018

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