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7,024 results on '"Wagner, John"'

1. Vaccination for Patients Receiving Dialysis.

Author

Sam, Ramin, Rankin, Laura, Ulasi, Ifeoma, Frantzen, Luc, Nitsch, Dorothea, Henner, David, Molony, Donald, Wagner, John, Chen, Jing, Agarwal, Sanjay, Howard, Andrew, Atkinson, Ralph, Landry, Daniel, Pastan, Stephen, and Kalantar-Zadeh, Kamyar

Subjects
Dialysis, SARS-CoV2, influenza, pneumococcus, vaccination
Abstract

Vaccinating patients receiving dialysis may prevent morbidity and mortality in this vulnerable population. The National Forum of End-Stage Renal Disease Networks (the Forum) published a revised vaccination toolkit in 2021 to update evidence and recommendations on vaccination for patients receiving dialysis. Significant changes in the last 10 years include more data supporting the use of a high-dose influenza vaccine, the introduction of the Heplisav-B vaccine for hepatitis B, and changes in pneumococcal vaccines, including the approval of the PCV15 and PCV20 to replace the PCV13 and PPSV23 vaccines. Additional key items include the introduction of vaccines against severe acute respiratory syndrome coronavirus 2, the virus that causes coronavirus disease 2019 (COVID-19), and a new vaccine to prevent respiratory syncytial virus disease. Historically, influenza and pneumococcal vaccinations were routinely administered by dialysis facilities, and because of possible risks of hematogenous spread of hepatitis B, dialysis providers often have detailed hepatitis B vaccine protocols. In March 2021, COVID-19 vaccines were made available for dialysis facilities to administer, although with the end of the public health emergency, vaccine policies by dialysis facilities against COVID-19 remains uncertain. The respiratory syncytial virus vaccine was authorized in 2023, and how dialysis facilities will approach this vaccine also remains uncertain. This review summarizes the Forums vaccination toolkit and discusses the role of the dialysis facility in vaccinating patients to reduce the risk of severe infections.

Published
2024

2. Impact of pre-transplant induction and consolidation cycles on AML allogeneic transplant outcomes: a CIBMTR analysis in 3113 AML patients.

Author

Boyiadzis, Michael, Zhang, Mei-Jie, Chen, Karen, Abdel-Azim, Hisham, Abid, Muhammad, Aljurf, Mahmoud, Bacher, Ulrike, Badar, Talha, Badawy, Sherif, Battiwalla, Minoo, Bejanyan, Nelli, Bhatt, Vijaya, Brown, Valerie, Castillo, Paul, Cerny, Jan, Copelan, Edward, Craddock, Charles, Dholaria, Bhagirathbhai, Perez, Miguel, Ebens, Christen, Gale, Robert, Ganguly, Siddhartha, Gowda, Lohith, Grunwald, Michael, Hashmi, Shahrukh, Hildebrandt, Gerhard, Iqbal, Madiha, Jamy, Omer, Kharfan-Dabaja, Mohamed, Khera, Nandita, Lazarus, Hillard, Lin, Richard, Modi, Dipenkumar, Nathan, Sunita, Nishihori, Taiga, Patel, Sagar, Pawarode, Attaphol, Saber, Wael, Sharma, Akshay, Solh, Melhem, Wagner, John, Wang, Trent, Williams, Kirsten, Wirk, Baldeep, Zeidan, Amer, Hourigan, Christopher, Litzow, Mark, Kebriaei, Partow, de Lima, Marcos, Page, Kristin, Weisdorf, Daniel, and Winestone, Lena

Subjects
Adult, Humans, Transplantation, Homologous, Transplantation Conditioning, Neoplasm Recurrence, Local, Hematopoietic Stem Cell Transplantation, Leukemia, Myeloid, Acute, Retrospective Studies
Abstract

We investigated the impact of the number of induction/consolidation cycles on outcomes of 3113 adult AML patients who received allogeneic hematopoietic cell transplantation (allo-HCT) between 2008 and 2019. Patients received allo-HCT using myeloablative (MAC) or reduced-intensity (RIC) conditioning in first complete remission (CR) or with primary induction failure (PIF). Patients who received MAC allo-HCT in CR after 1 induction cycle had 1.3-fold better overall survival (OS) than 2 cycles to CR and 1.47-fold better than ≥3 cycles. OS after CR in 2 or ≥3 cycles was similar. Relapse risk was 1.65-fold greater in patients receiving ≥3 cycles to achieve CR. After RIC allo-HCT, the number of induction cycles to CR did not affect OS. Compared to CR in 1 cycle, relapse risk was 1.24-1.41-fold greater in patients receiving 2 or ≥3 cycles. For patients receiving only 1 cycle to CR, consolidation therapy prior to MAC allo-HCT was associated with improved OS vs. no consolidation therapy. Detectable MRD at the time of MAC allo-HCT did not impact outcomes while detectable MRD preceding RIC allo-HCT was associated with an increased risk of relapse. For allo-HCT in PIF, OS was significantly worse than allo-HCT in CR after 1-3 cycles.

Published
2023

18. Alloengraftment without significant toxicity or GVHD in CD45 antibody-drug conjugate–conditioned Fanconi anemia mice

Author

Saha, Asim, Palchaudhuri, Rahul, Lanieri, Leanne, Hyzy, Sharon, Riddle, Megan J., Panthera, Jamie, Eide, Cindy R., Tolar, Jakub, Panoskaltsis-Mortari, Angela, Gorfinkel, Lev, Tkachev, Victor, Gerdemann, Ulrike, Alvarez-Calderon, Francesca, Palato, Elisa Rojas, MacMillan, Margaret L., Wagner, John E., Kean, Leslie S., Osborn, Mark J., Kiem, Hans-Peter, Scadden, David T., Olson, Lisa M., and Blazar, Bruce R.

Published
2024
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23. American Society of Hematology 2021 guidelines for sickle cell disease: stem cell transplantation

Author

Kanter, Julie, Liem, Robert I, Bernaudin, Françoise, Bolaños-Meade, Javier, Fitzhugh, Courtney D, Hankins, Jane S, Murad, M Hassan, Panepinto, Julie A, Rondelli, Damiano, Shenoy, Shalini, Wagner, John, Walters, Mark C, Woolford, Teonna, Meerpohl, Joerg J, and Tisdale, John

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Stem Cell Research - Nonembryonic - Human, Rare Diseases, Clinical Research, Stem Cell Research, Hematology, Sickle Cell Disease, Transplantation, Pain Research, Regenerative Medicine, Clinical Trials and Supportive Activities, Anemia, Sickle Cell, Hematopoietic Stem Cell Transplantation, Humans, Quality of Life, Stem Cell Transplantation, United States, Cardiovascular medicine and haematology
Abstract

BackgroundSickle cell disease (SCD) is a life-limiting inherited hemoglobinopathy that results in significant complications and affects quality of life. Hematopoietic stem cell transplantation (HSCT) is currently the only curative intervention for SCD; however, guidelines are needed to inform how to apply HSCT in clinical practice.ObjectiveThese evidence-based guidelines of the American Society of Hematology (ASH) are intended to support patients, clinicians, and health professionals in their decisions about HSCT for SCD.MethodsThe multidisciplinary guideline panel formed by ASH included 2 patient representatives and was balanced to minimize potential bias from conflicts of interest. The Mayo Evidence-Based Practice Research Program supported the guideline development process, including performing systematic evidence reviews (through 2019). The panel prioritized clinical questions and outcomes according to their importance for clinicians and patients. The panel used the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach, including GRADE Evidence-to-Decision frameworks, to assess evidence and make recommendations, which were subject to public comment.ResultsThe panel agreed on 8 recommendations to help patients and providers assess how individuals with SCD should consider the timing and type of HSCT.ConclusionsThe evidence review yielded no randomized controlled clinical trials for HSCT in SCD; therefore, all recommendations are based on very low certainty in the evidence. Key recommendations include considering HSCT for those with neurologic injury or recurrent acute chest syndrome at an early age and to improve nonmyeloablative regimens. Future research should include the development of a robust SCD registry to serve as a comparator for HSCT studies.

Published
2021

26. Towards a Predictive Patent Analytics and Evaluation Platform

Author

Alam, Nebula, Tran, Khoi-Nguyen, Chen, Sue Ann, Wagner, John, Andres, Josh, and Mohania, Mukesh

Subjects
Computer Science - Digital Libraries, Computer Science - Machine Learning
Abstract

The importance of patents is well recognised across many regions of the world. Many patent mining systems have been proposed, but with limited predictive capabilities. In this demo, we showcase how predictive algorithms leveraging the state-of-the-art machine learning and deep learning techniques can be used to improve understanding of patents for inventors, patent evaluators, and business analysts alike. Our demo video is available at http://ibm.biz/ecml2019-demo-patent-analytics, Comment: ECML-PKDD 2019 - Demo Track

Published
2019

27. Allogeneic hematopoietic cell transplantation for blastic plasmacytoid dendritic cell neoplasm: a CIBMTR analysis

Author

Murthy, Hemant S., Zhang, Mei-Jie, Chen, Karen, Ahmed, Sairah, Deotare, Uday, Ganguly, Siddhartha, Kansagra, Ankit, Michelis, Fotios V., Nishihori, Taiga, Patnaik, Mrinal, Abid, Muhammad Bilal, Aljurf, Mahmoud, Arai, Yasuyuki, Bacher, Ulrike, Badar, Talha, Badawy, Sherif M., Ballen, Karen, Battiwalla, Minoo, Beitinjaneh, Amer, Bejanyan, Nelli, Bhatt, Vijaya Raj, Brown, Valerie I., Martino, Rodrigo, Cahn, Jean-Yves, Castillo, Paul, Cerny, Jan, Chhabra, Saurabh, Copelan, Edward, Daly, Andrew, Dholaria, Bhagirathbhai, Diaz Perez, Miguel Angel, Freytes, César O., Grunwald, Michael R., Hashmi, Shahrukh, Hildebrandt, Gerhard C., Jamy, Omer, Joseph, Jacinth, Kanakry, Christopher G., Khera, Nandita, Krem, Maxwell M., Kuwatsuka, Yachiyo, Lazarus, Hillard M., Lekakis, Lazaros J., Liu, Hongtao, Modi, Dipenkumar, Munshi, Pashna N., Mussetti, Alberto, Palmisiano, Neil, Patel, Sagar S., Rizzieri, David A., Seo, Sachiko, Shah, Mithun Vinod, Sharma, Akshay, Sohl, Melhm, Solomon, Scott R., Ulrickson, Matthew, Ustun, Celalettin, van der Poel, Marjolein, Verdonck, Leo F., Wagner, John L., Wang, Trent, Wirk, Baldeep, Zeidan, Amer, Litzow, Mark, Kebriaei, Partow, Hourigan, Christopher S., Weisdorf, Daniel J., Saber, Wael, and Kharfan-Dabaja, Mohamed A.

Published
2023
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28. Uncertainty in Diversity: Language Shift and Language Planning in Papua New Guinea, a Kala Case Study

Author

Schreyer, Christine and Wagner, John

Abstract

Since independence in 1975, Papua New Guinea, the most linguistically diverse country in the world, has had both unofficial and official policies of mother-tongue education. However, limited resources and support for mother-tongue education has led communities to incorporate bottom-up language planning as well. In particular, this paper examines the language planning efforts of the Kala Language Committee (KLC). The Kala language, which has four distinct dialects, is spoken in six villages in the Morobe province. In 2010, the KLC developed an orthography for their traditionally oral language leading to the expansion of mother-tongue education programmes in each of the six villages. Each village has different levels of language shift and during meetings in 2013 had developed their own individual language plans, which best suit their community's needs. This paper compares the choices of each village to the wider choices of the KLC and to the demands of the national mother-tongue education policies.

Published
2022
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29. The Influence of Unpublished Studies on Results of Recent Meta-Analyses: Publication Bias, the File Drawer Problem, and Implications for the Replication Crisis

Author

Wagner, John A., III

Abstract

The replication crisis in the social and psychological sciences is said to be due in part to publication bias and the resulting file drawer problem. Meta-analysis is often advocated as a means of resolving this crisis but is prone to the same publication bias and file drawer effects. A study of 23 meta-analyses examined the consequences of correcting for these effects through the inclusion of unpublished research. Results indicated that the inclusion of unpublished data led to smaller meta-analytic means in some instances, consistent with the primary theorized effects of the file drawer problem and publication bias, but led to larger meta-analytic means in nearly as many instances, suggesting the presence and influence of other, unknown artifacts in unpublished research. These findings suggest that meta-analysis is limited in its ability to resolve the replication crisis and instead may introduce unexplained effects that render cumulative science problematic.

Published
2022
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30. Characteristics and Outcomes of Individuals With Pre-existing Kidney Disease and COVID-19 Admitted to Intensive Care Units in the United States

Author

Flythe, Jennifer E, Assimon, Magdalene M, Tugman, Matthew J, Chang, Emily H, Gupta, Shruti, Shah, Jatan, Sosa, Marie Anne, Renaghan, Amanda DeMauro, Melamed, Michal L, Wilson, F Perry, Neyra, Javier A, Rashidi, Arash, Boyle, Suzanne M, Anand, Shuchi, Christov, Marta, Thomas, Leslie F, Edmonston, Daniel, Leaf, David E, Walther, Carl P, Anumudu, Samaya J, Arunthamakun, Justin, Kopecky, Kathleen F, Milligan, Gregory P, McCullough, Peter A, Nguyen, Thuy-Duyen, Shaefi, Shahzad, Krajewski, Megan L, Shankar, Sidharth, Pannu, Ameeka, Valencia, Juan D, Waikar, Sushrut S, Kibbelaar, Zoe A, Athavale, Ambarish M, Hart, Peter, Upadhyay, Shristi, Vohra, Ishaan, Green, Adam, Rachoin, Jean-Sebastien, Schorr, Christa A, Shea, Lisa, Edmonston, Daniel L, Mosher, Christopher L, Shehata, Alexandre M, Cohen, Zaza, Allusson, Valerie, Bambrick-Santoyo, Gabriela, Bhatti, Noor ul aain, Mehta, Bijal, Williams, Aquino, Brenner, Samantha K, Walters, Patricia, Go, Ronaldo C, Rose, Keith M, Chan, Lili, Mathews, Kusum S, Coca, Steven G, Altman, Deena R, Saha, Aparna, Soh, Howard, Wen, Huei Hsun, Bose, Sonali, Leven, Emily A, Wang, Jing G, Mosoyan, Gohar, Nadkarni, Girish N, Pattharanitima, Pattharawin, Gallagher, Emily J, Friedman, Allon N, Guirguis, John, Kapoor, Rajat, Meshberger, Christopher, Kelly, Katherine J, Parikh, Chirag R, Garibaldi, Brian T, Corona-Villalobos, Celia P, Wen, Yumeng, Menez, Steven, Malik, Rubab F, Cervantes, Carmen Elena, Gautam, Samir C, Mallappallil, Mary C, Ouyang, Jie, John, Sabu, Yap, Ernie, Melaku, Yohannes, Mohamed, Ibrahim, Bajracharya, Siddhartha, Puri, Isha, Thaxton, Mariah, Bhattacharya, Jyotsna, Wagner, John, Boudourakis, Leon, Nguyen, H Bryant, Ahoubim, Afshin, Kashani, Kianoush, Tehranian, Shahrzad, Sirganagari, Dheeraj Reddy, Guru, Pramod K, and Zhou, Yan

Subjects
Clinical Research, Cardiovascular, Clinical Trials and Supportive Activities, Kidney Disease, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Renal and urogenital, Good Health and Well Being, Aged, COVID-19, Comorbidity, Critical Illness, Female, Hospital Mortality, Humans, Intensive Care Units, Kidney Function Tests, Male, Renal Dialysis, Renal Insufficiency, Chronic, Retrospective Studies, Risk Factors, SARS-CoV-2, Treatment Outcome, United States, STOP-COVID Investigators, COVID-19 outcome, Coronavirus disease 2019, altered mental status, chronic kidney disease, clinical course, clinical trajectory, critical illness, dialysis, end-stage kidney disease, end-stage renal disease, glomerular filtration rate, in-hospital mortality, intensive care unit, prognosis, renal function, severe COVID-19, severe acute respiratory syndrome coronavirus 2, Clinical Sciences, Public Health and Health Services, Urology & Nephrology
Abstract

Rationale & objectiveUnderlying kidney disease is an emerging risk factor for more severe coronavirus disease 2019 (COVID-19) illness. We examined the clinical courses of critically ill COVID-19 patients with and without pre-existing chronic kidney disease (CKD) and investigated the association between the degree of underlying kidney disease and in-hospital outcomes.Study designRetrospective cohort study.Settings & participants4,264 critically ill patients with COVID-19 (143 patients with pre-existing kidney failure receiving maintenance dialysis; 521 patients with pre-existing non-dialysis-dependent CKD; and 3,600 patients without pre-existing CKD) admitted to intensive care units (ICUs) at 68 hospitals across the United States.Predictor(s)Presence (vs absence) of pre-existing kidney disease.Outcome(s)In-hospital mortality (primary); respiratory failure, shock, ventricular arrhythmia/cardiac arrest, thromboembolic events, major bleeds, and acute liver injury (secondary).Analytical approachWe used standardized differences to compare patient characteristics (values>0.10 indicate a meaningful difference between groups) and multivariable-adjusted Fine and Gray survival models to examine outcome associations.ResultsDialysis patients had a shorter time from symptom onset to ICU admission compared to other groups (median of 4 [IQR, 2-9] days for maintenance dialysis patients; 7 [IQR, 3-10] days for non-dialysis-dependent CKD patients; and 7 [IQR, 4-10] days for patients without pre-existing CKD). More dialysis patients (25%) reported altered mental status than those with non-dialysis-dependent CKD (20%; standardized difference=0.12) and those without pre-existing CKD (12%; standardized difference=0.36). Half of dialysis and non-dialysis-dependent CKD patients died within 28 days of ICU admission versus 35% of patients without pre-existing CKD. Compared to patients without pre-existing CKD, dialysis patients had higher risk for 28-day in-hospital death (adjusted HR, 1.41 [95% CI, 1.09-1.81]), while patients with non-dialysis-dependent CKD had an intermediate risk (adjusted HR, 1.25 [95% CI, 1.08-1.44]).LimitationsPotential residual confounding.ConclusionsFindings highlight the high mortality of individuals with underlying kidney disease and severe COVID-19, underscoring the importance of identifying safe and effective COVID-19 therapies in this vulnerable population.

Published
2021

31. Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer

Author

Webster, Andrew L. H., Sanders, Mathijs A., Patel, Krupa, Dietrich, Ralf, Noonan, Raymond J., Lach, Francis P., White, Ryan R., Goldfarb, Audrey, Hadi, Kevin, Edwards, Matthew M., Donovan, Frank X., Hoogenboezem, Remco M., Jung, Moonjung, Sridhar, Sunandini, Wiley, Tom F., Fedrigo, Olivier, Tian, Huasong, Rosiene, Joel, Heineman, Thomas, Kennedy, Jennifer A., Bean, Lorenzo, Rosti, Rasim O., Tryon, Rebecca, Gonzalez, Ashlyn-Maree, Rosenberg, Allana, Luo, Ji-Dung, Carroll, Thomas S., Shroff, Sanjana, Beaumont, Michael, Velleuer, Eunike, Rastatter, Jeff C., Wells, Susanne I., Surrallés, Jordi, Bagby, Grover, MacMillan, Margaret L., Wagner, John E., Cancio, Maria, Boulad, Farid, Scognamiglio, Theresa, Vaughan, Roger, Beaumont, Kristin G., Koren, Amnon, Imielinski, Marcin, Chandrasekharappa, Settara C., Auerbach, Arleen D., Singh, Bhuvanesh, Kutler, David I., Campbell, Peter J., and Smogorzewska, Agata

Published
2022
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33. Risk Factors for Graft-versus-Host Disease in Haploidentical Hematopoietic Cell Transplantation Using Post-Transplant Cyclophosphamide.

Author

Im, Annie, Rashidi, Armin, Wang, Tao, Hemmer, Michael, MacMillan, Margaret, Pidala, Joseph, Jagasia, Madan, Pavletic, Steven, Majhail, Navneet, Weisdorf, Daniel, Abdel-Azim, Hisham, Agrawal, Vaibhav, Al-Homsi, A, Aljurf, Mahmoud, Askar, Medhat, Auletta, Jeffery, Bashey, Asad, Beitinjaneh, Amer, Bhatt, Vijaya, Byrne, Michael, Cahn, Jean-Yves, Cairo, Mitchell, Castillo, Paul, Cerny, Jan, Chhabra, Saurabh, Choe, Hannah, Ciurea, Stefan, Daly, Andrew, Perez, Miguel, Farhadfar, Nosha, Gadalla, Shahinaz, Gale, Robert, Ganguly, Siddhartha, Gergis, Usama, Hanna, Rabi, Hematti, Peiman, Herzig, Roger, Hildebrandt, Gerhard, Lad, Deepesh, Lee, Catherine, Lehmann, Leslie, Lekakis, Lazaros, Kamble, Rammurti, Kharfan-Dabaja, Mohamed, Khandelwal, Pooja, Martino, Rodrigo, Murthy, Hemant, Nishihori, Taiga, OBrien, Tracey, Olsson, Richard, Patel, Sagar, Perales, Miguel-Angel, Prestidge, Tim, Qayed, Muna, Romee, Rizwan, Schoemans, Hélène, Seo, Sachiko, Sharma, Akshay, Solh, Melhem, Strair, Roger, Teshima, Takanori, Urbano-Ispizua, Alvaro, Van der Poel, Marjolein, Vij, Ravi, Wagner, John, William, Basem, Wirk, Baldeep, Yared, Jean, Spellman, Steve, Arora, Mukta, and Hamilton, Betty

Subjects
Adult, Cyclophosphamide, Graft vs Host Disease, Hematopoietic Stem Cell Transplantation, Humans, Risk Factors, Transplantation Conditioning
Abstract

Post-transplant cyclophosphamide (PTCy) has significantly increased the successful use of haploidentical donors with a relatively low incidence of graft-versus-host disease (GVHD). Given its increasing use, we sought to determine risk factors for GVHD after haploidentical hematopoietic cell transplantation (haplo-HCT) using PTCy. Data from the Center for International Blood and Marrow Transplant Research on adult patients with acute myeloid leukemia, acute lymphoblastic leukemia, myelodysplastic syndrome, or chronic myeloid leukemia who underwent PTCy-based haplo-HCT (2013 to 2016) were analyzed and categorized into 4 groups based on myeloablative (MA) or reduced-intensity conditioning (RIC) and bone marrow (BM) or peripheral blood (PB) graft source. In total, 646 patients were identified (MA-BM = 79, MA-PB = 183, RIC-BM = 192, RIC-PB = 192). The incidence of grade 2 to 4 acute GVHD at 6 months was highest in MA-PB (44%), followed by RIC-PB (36%), MA-BM (36%), and RIC-BM (30%) (P = .002). The incidence of chronic GVHD at 1 year was 40%, 34%, 24%, and 20%, respectively (P < .001). In multivariable analysis, there was no impact of stem cell source or conditioning regimen on grade 2 to 4 acute GVHD; however, older donor age (30 to 49 versus

Published
2020

34. SBML Level 3: an extensible format for the exchange and reuse of biological models.

Author

Keating, Sarah M, Waltemath, Dagmar, König, Matthias, Zhang, Fengkai, Dräger, Andreas, Chaouiya, Claudine, Bergmann, Frank T, Finney, Andrew, Gillespie, Colin S, Helikar, Tomáš, Hoops, Stefan, Malik-Sheriff, Rahuman S, Moodie, Stuart L, Moraru, Ion I, Myers, Chris J, Naldi, Aurélien, Olivier, Brett G, Sahle, Sven, Schaff, James C, Smith, Lucian P, Swat, Maciej J, Thieffry, Denis, Watanabe, Leandro, Wilkinson, Darren J, Blinov, Michael L, Begley, Kimberly, Faeder, James R, Gómez, Harold F, Hamm, Thomas M, Inagaki, Yuichiro, Liebermeister, Wolfram, Lister, Allyson L, Lucio, Daniel, Mjolsness, Eric, Proctor, Carole J, Raman, Karthik, Rodriguez, Nicolas, Shaffer, Clifford A, Shapiro, Bruce E, Stelling, Joerg, Swainston, Neil, Tanimura, Naoki, Wagner, John, Meier-Schellersheim, Martin, Sauro, Herbert M, Palsson, Bernhard, Bolouri, Hamid, Kitano, Hiroaki, Funahashi, Akira, Hermjakob, Henning, Doyle, John C, Hucka, Michael, and SBML Level 3 Community members

Subjects
SBML Level 3 Community members, Animals, Humans, Logistic Models, Systems Biology, Models, Biological, Software, computational modeling, file format, interoperability, reproducibility, systems biology, Bioengineering, Networking and Information Technology R&D, Bioinformatics, Biochemistry and Cell Biology, Other Biological Sciences
Abstract

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

Published
2020

35. Effect of donor type and conditioning regimen intensity on allogeneic transplantation outcomes in patients with sickle cell disease: a retrospective multicentre, cohort study

Author

Eapen, Mary, Brazauskas, Ruta, Walters, Mark C, Bernaudin, Françoise, Bo-Subait, Khalid, Fitzhugh, Courtney D, Hankins, Jane S, Kanter, Julie, Meerpohl, Joerg J, Bolaños-Meade, Javier, Panepinto, Julie A, Rondelli, Damiano, Shenoy, Shalini, Williamson, Joi, Woolford, Teonna L, Gluckman, Eliane, Wagner, John E, and Tisdale, John F

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Immunology, Transplantation, Hematology, Regenerative Medicine, Stem Cell Research, Rare Diseases, Orphan Drug, Clinical Research, Adolescent, Adult, Anemia, Sickle Cell, Blood Donors, Bone Marrow Transplantation, Child, Female, Fetal Blood, Graft vs Host Disease, Histocompatibility Testing, Humans, Male, Middle Aged, Peripheral Blood Stem Cell Transplantation, Progression-Free Survival, Proportional Hazards Models, Retrospective Studies, Survival Rate, Transplantation, Homologous, Young Adult, Cardiorespiratory Medicine and Haematology, Clinical Sciences, Cardiovascular medicine and haematology
Abstract

BackgroundDonors other than matched siblings and low-intensity conditioning regimens are increasingly used in haematopoietic stem cell transplantation. We aimed to compare the relative risk of donor type and conditioning regimen intensity on the transplantation outcomes of in patients with sickle cell disease.MethodsFor this retrospective cohort study, we collected data from 90 US centres reported to the Center for International Blood and Marrow Transplant Research. Eligible patients were younger than 50 years, had genetically confirmed sickle cell disease (Hb SS) or sickle beta thalassemia (Hb Sβ), and underwent allogeneic haematopoietic cell transplantation between Jan 15, 2008, and Dec 28, 2017. We considered transplants from donor-recipient pairs matched at the allele-level (HLA-A, HLA-B, HLA-C, and HLA-DRB1), including HLA-matched sibling donors, haploidentical related donors, matched unrelated donors, or mismatched unrelated donors. The main outcome was event-free survival. The effect of donor type, conditioning regimen intensity (myeloablative, non-myeloablative, and reduced-intensity regimens), age (≤12 or 13-49 years), sex, performance score, comorbidity index, recipient cytomegalovirus serostatus, graft type (bone marrow, peripheral blood, or umbilical cord blood), and transplantation period (2008-12 and 2013-17) on outcomes was studied using Cox regression models.FindingsOf 996 patients with sickle cell disease and who underwent transplantation in 2008-17, 910 (91%) were included (558 [61%] patients had HLA-matched sibling donors, 137 [15%] haploidentical related donors, 111 [12%] matched unrelated donors, and 104 [11%] mismatched unrelated donors). The median follow-up was 36 months (IQR 18-60) after transplantation from HLA-matched siblings, 25 months (12-48) after transplantation from haploidentical related donors, 37 months (23-60) after transplantation from HLA-matched unrelated donors, and 47 months (24-72) after transplantation from mismatched unrelated donors. Event-free survival was worse in recipients aged 13 years or older than in those younger than 13 years (hazard ratio 1·74, 95% CI 1·24-2·45; p=0·0014) and in those who received a transplant from haploidentical related donors (5·30, 3·17-8·86; p

Published
2019

36. Prevention of acute GVHD using an orthogonal IL-2/IL-2Rβ system to selectively expand regulatory T cells in vivo

Author

Ramos, Teresa L., Bolivar-Wagers, Sara, Jin, Sujeong, Thangavelu, Govindarajan, Simonetta, Federico, Lin, Po-Yu, Hirai, Toshihito, Saha, Asim, Koehn, Brent, Su, Leon L., Picton, Lora K., Baker, Jeanette, Lohmeyer, Juliane K., Riddle, Megan, Eide, Cindy, Tolar, Jakub, Panoskaltsis-Mortari, Angela, Wagner, John E., Garcia, K. Christopher, Negrin, Robert S., and Blazar, Bruce R.

Published
2023
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40. A prospective study of posttransplant cyclophosphamide for unrelated donor peripheral blood stem cell transplant with special attention to graft content and the impact of a higher γδ T cell dose

Author

Jeurkar, Chetan, primary, Leiby, Benjamin, additional, Rashid, Shaik, additional, Gergis, Usama, additional, Grossso, Dolores, additional, Carabasi, Matthew, additional, Filicko‐O'Hara, Joanne, additional, O'Hara, William, additional, Klumpp, Thomas, additional, Porcu, Pierluigi, additional, Flomenberg, Neal, additional, and Wagner, John L., additional

Published
2024
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44. Outcomes of haploidentical vs matched sibling transplantation for acute myeloid leukemia in first complete remission.

Author

Rashidi, Armin, Hamadani, Mehdi, Zhang, Mei-Jie, Wang, Hai-Lin, Abdel-Azim, Hisham, Aljurf, Mahmoud, Assal, Amer, Bajel, Ashish, Bashey, Asad, Battiwalla, Minoo, Beitinjaneh, Amer, Bejanyan, Nelli, Bhatt, Vijaya, Bolaños-Meade, Javier, Byrne, Michael, Cahn, Jean-Yves, Cairo, Mitchell, Ciurea, Stefan, Copelan, Edward, Cutler, Corey, Daly, Andrew, Diaz, Miguel-Angel, Farhadfar, Nosha, Gale, Robert, Ganguly, Siddhartha, Grunwald, Michael, Hahn, Theresa, Hashmi, Shahrukh, Hildebrandt, Gerhard, Holland, H, Hossain, Nasheed, Kanakry, Christopher, Kharfan-Dabaja, Mohamed, Khera, Nandita, Koc, Yener, Lazarus, Hillard, Lee, Jong-Wook, Maertens, Johan, Martino, Rodrigo, McGuirk, Joseph, Munker, Reinhold, Murthy, Hemant, Nakamura, Ryotaro, Nathan, Sunita, Nishihori, Taiga, Palmisiano, Neil, Patel, Sagar, Pidala, Joseph, Olin, Rebecca, Olsson, Richard, Oran, Betul, Ringden, Olov, Rizzieri, David, Rowe, Jacob, Savoie, Mary, Schultz, Kirk, Seo, Sachiko, Shaffer, Brian, Singh, Anurag, Solh, Melhem, Stockerl-Goldstein, Keith, Verdonck, Leo, Wagner, John, Waller, Edmund, De Lima, Marcos, Sandmaier, Brenda, Litzow, Mark, Weisdorf, Dan, Romee, Rizwan, and Saber, Wael

Subjects
Adolescent, Adult, Aged, Blood Donors, Bone Marrow Transplantation, Calcineurin Inhibitors, Chronic Disease, Cyclophosphamide, Disease-Free Survival, Female, Graft vs Host Disease, Hematopoietic Stem Cell Transplantation, Humans, Immunosuppressive Agents, Incidence, Leukemia, Myeloid, Acute, Male, Middle Aged, Recurrence, Remission Induction, Retrospective Studies, Siblings, Survival Analysis, Transplantation Conditioning, Transplantation, Haploidentical, Young Adult
Abstract

HLA-haploidentical hematopoietic cell transplantation (Haplo-HCT) using posttransplantation cyclophosphamide (PT-Cy) has improved donor availability. However, a matched sibling donor (MSD) is still considered the optimal donor. Using the Center for International Blood and Marrow Transplant Research database, we compared outcomes after Haplo-HCT vs MSD in patients with acute myeloid leukemia (AML) in first complete remission (CR1). Data from 1205 adult CR1 AML patients (2008-2015) were analyzed. A total of 336 patients underwent PT-Cy-based Haplo-HCT and 869 underwent MSD using calcineurin inhibitor-based graft-versus-host disease (GVHD) prophylaxis. The Haplo-HCT group included more reduced-intensity conditioning (65% vs 30%) and bone marrow grafts (62% vs 7%), consistent with current practice. In multivariable analysis, Haplo-HCT and MSD groups were not different with regard to overall survival (P = .15), leukemia-free survival (P = .50), nonrelapse mortality (P = .16), relapse (P = .90), or grade II-IV acute GVHD (P = .98). However, the Haplo-HCT group had a significantly lower rate of chronic GVHD (hazard ratio, 0.38; 95% confidence interval, 0.30-0.48; P < .001). Results of subgroup analyses by conditioning intensity and graft source suggested that the reduced incidence of chronic GVHD in Haplo-HCT is not limited to a specific graft source or conditioning intensity. Center effect and minimal residual disease-donor type interaction were not predictors of outcome. Our results indicate a lower rate of chronic GVHD after PT-Cy-based Haplo-HCT vs MSD using calcineurin inhibitor-based GVHD prophylaxis, but similar other outcomes, in patients with AML in CR1. Haplo-HCT is a viable alternative to MSD in these patients.

Published
2019

49. A CD45-targeted antibody-drug conjugate successfully conditions for allogeneic hematopoietic stem cell transplantation in mice

Author

Saha, Asim, Hyzy, Sharon, Lamothe, Tahirih, Hammond, Katelyn, Clark, Nicholas, Lanieri, Leanne, Bhattarai, Prashant, Palchaudhuri, Rahul, Gillard, Geoffrey O., Proctor, Jennifer, Riddle, Megan J., Panoskaltsis-Mortari, Angela, MacMillan, Margaret L., Wagner, John E., Kiem, Hans-Peter, Olson, Lisa M., and Blazar, Bruce R.

Published
2022
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50. Kidney Recovery and Death in Critically Ill Patients With COVID-19–Associated Acute Kidney Injury Treated With Dialysis: The STOP-COVID Cohort Study

Author

Gupta, Hsu, Faugno, Goyal, Raichoudhury, Tariq, Meyer, Sharma, Leaf, Kshirsagar, Walther, Carl P., Anumudu, Samaya J., Arunthamakun, Justin, Kopecky, Kathleen F., Milligan, Gregory P., McCullough, Peter A., Nguyen, Thuy-Duyen, Shaefi, Shahzad, Krajewski, Megan L., Shankar, Sidharth, Pannu, Ameeka, Valencia, Juan D., Bauer, Kenneth A., Waikar, Sushrut S., Kibbelaar, Zoe A., Athavale, Ambarish M., Hart, Peter, Upadhyay, Shristi, Vohra, Ishaan, Oyintayo, Ajiboye, Green, Adam, Rachoin, Jean-Sebastien, Schorr, Christa A., Shea, Lisa, Edmonston, Daniel L., Mosher, Christopher L., Shehata, Alexandre M., Cohen, Zaza, Allusson, Valerie, Bambrick-Santoyo, Gabriela, Bhatti, Noor ul aain, Mehta, Bijal, WilliamsSamantha K. Brenner, Aquino, Walters, Patricia, Go, Ronaldo C., Rose, Keith M., Hernán, Miguel A., Zhou, Amy M., Kim, Ethan C., Lisk, Rebecca, Chan, Lili, Mathews, Kusum S., Coca, Steven G., Altman, Deena R., Saha, Aparna, Soh, Howard, Wen, Huei Hsun, Bose, Sonali, Leven, Emily A., Wang, Jing G., Mosoyan, Gohar, Pattharanitima, Pattharawin, Gallagher, Emily J., Friedman, Allon N., Guirguis, John, Kapoor, Rajat, Meshberger, Christopher, Kelly, Katherine J., Parikh, Chirag R., Garibaldi, Brian T., Corona-Villalobos, Celia P., Wen, Yumeng, Menez, Steven, Malik, Rubab F., Cervantes, Carmen Elena, Gautam, Samir C., Mallappallil, Mary C., Ouyang, Jie, John, Sabu, Yap, Ernie, Melaku, Yohannes, Mohamed, Ibrahim, Bajracharya, Siddhartha, Puri, Isha, Thaxton, Mariah, Bhattacharya, Jyotsna, Wagner, John, Boudourakis, Leon, Nguyen, H. Bryant, Ahoubim, Afshin, Thomas, Leslie F., Sirganagari, Dheeraj Reddy, Guru, Pramod K., Kashani, Kianoush, Tehranian, Shahrzad, Zhou, Yan, Bergl, Paul A., Rodriguez, Jesus, Shah, Jatan A., Gupta, Mrigank S., Kumar, Princy N., Lazarous, Deepa G., Kassaye, Seble G., Melamed, Michal L., Johns. Ryan Mocerino, Tanya S., Prudhvi, Kalyan, Zhu, Denzel, Levy, Rebecca V., Azzi, Yorg, Fisher, Molly, Yunes, Milagros, Sedaliu, Kaltrina, Golestaneh, Ladan, Brogan, Maureen, Thakkar, Jyotsana, Kumar, Neelja, Ross, Michael J., Chang, Michael, Athreya, Akshay, Farag, Mohamed, Schenck, Edward J., Cho, Soo Jung, Plataki, Maria, Alvarez-Mulett, Sergio L., Gomez-Escobar, Luis G., Pan, Di, Lee, Stefi, Krishnan, Jamuna, Whalen, William, Charytan, David, Macina, Ashley, Srivastava, Anand, Leidner, Alexander S., Martinez, Carlos, Kruser, Jacqueline M., Wunderink, Richard G., Hodakowski, Alexander J., Velez, Juan Carlos Q., Price-Haywood, Eboni G., Matute-Trochez, Luis A., Hasty, Anna E., Mohamed, Muner M.B., Avasare, Rupali S., Zonies, David, Al-Samkari, Hanny, Leaf, Rebecca Karp, Rosovsky, Rachel, Sise, Meghan E., Newman, Erik T., Omar, Samah Abu, Pokharel, Kapil K., Sharma, Shreyak, Singh, Harkarandeep, Correa, Simon, Shaukat, Tanveer, Kamal, Omer, Wang, Wei, Lee, Meghan, Strohbehn, Ian A., Li, Jiahua, Mueller, Ariel L., Redfern, Roberta E., Cairl, Nicholas S., Naimy, Gabriel, Abu-Saif, Abeer, Hall, Danyell, Bickley, Laura, Rowan, Chris, Madhani-Lovely, Farah, Peev, Vasil, Reiser, Jochen, Byun, John J., Vissing, Andrew, Kapania, Esha M., Post, Zoe, Patel, Nilam P., Hermes, Joy-Marie, Sutherland, Anne K., Patrawalla, Amee, Finkel, Diana G., Danek, Barbara A., Arikapudi, Sowminya, Paer, Jeffrey M., Cangialosi, Peter, Liotta, Mark, Radbel, Jared, Puri, Sonika, Sunderram, Jag, Scharf, Matthew T., Ahmed, Ayesha, Berim, Ilya, Vatson, Jayanth S., Karp, George, Anand, Shuchi, Levitt, Joseph E., Garcia, Pablo, Boyle, Suzanne M., Song, Rui, Zhang, Jingjing, Woo, Sang Hoon, Deng, Xiaoying, Katz-Greenberg, Goni, Sharshir, Moh’d A., Rusnak, Vadym V., Bansal, Anip, Podoll, Amber S., Chonchol, Michel, Sharma, Sunita, Burnham, Ellen L., Rashidi, Arash, Hejal, Rana, Judd, Eric, Latta, Laura, Tolwani, Ashita, Albertson, Timothy E., Adams, Jason Y., Chang, Steven Y., Beutler, Rebecca M., Schulze, Carl E., Macedo, Etienne, RheeKa, Harin, thleen D. Liu, Jotwani, Vasantha K., Koyner, Jay L., Shah, Chintan V., Jaikaransingh, Vishal, Toth-Manikowski, Stephanie M., Joo, Min J., Lash, James P., Neyra, Javier A., Chaaban, Nourhan, Elias, Madona, Ahmad, Yahya, Dy, Rajany, Iardino, Alfredo, Au, Elizabeth H., Sosa, Marie Anne, Taldone, Sabrina, Contreras, Gabriel, De La Zerda, David, Gershengorn, Hayley B., Fornoni, Alessia, Hayek, Salim S., Blakely, Pennelope, Berlin, Hanna, Azam, Tariq U., Shadid, Husam, Pan, Michael, O’Hayer, Patrick, Meloche, Chelsea, Feroze, Rafey, Padalia, Kishan J., Leya, Jeff, Donnelly, John P., Admon, Andrew J., Flythe, Jennifer E., Tugman, Matthew J., Chang, Emily H., Brown, Brent R., Leonberg-Yoo, Amanda K., Spiardi, Ryan C., Miano, Todd A., Roche, Meaghan S., Vasquez, Charles R., Bansal, Amar D., Ernecoff, Natalie C., Kapoor, Sanjana, Verma, Siddharth, Chen, Huiwen, Kovesdy, Csaba P., Molnar, Miklos Z., Azhar, Ambreen, Hedayati, S. Susan, Nadamuni, Mridula V., Shastri, Shani, Willett, Duwayne L., Short, Samuel A.P., Renaghan, Amanda D., Enfield, Kyle B., Bhatraju, Pavan K., Malik, A. Bilal, Semler, Matthew W., Vijayan, Anitha, Joy, Christina Mariyam, Li, Tingting, Goldberg, Seth, Kao, Patricia F., Schumaker, Greg L., Christov, Marta, Griffiths, Jennifer, Gupta, Sanjeev, Kapoor, Aromma, Chugh, Savneek, Wilson, Perry, Arora, Tanima, Ugwuowo, Ugochukwu, Hsu, Caroline M., Gupta, Shruti, Tighiouart, Hocine, Goyal, Nitender, Faugno, Anthony J., Tariq, Asma, Raichoudhury, Ritesh, Sharma, Jill H., Meyer, Leah, Kshirsagar, Ravi K., Jose, Aju, Leaf, David E., and Weiner, Daniel E.

Published
2022
Full Text
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