tbuckley/cabot-search huggingface dataset:
Communicating the components of informed treatment decision-making in patients with pancreatic cancer receiving preoperative therapy.
Authors: Howard J. Lee, Carolyn L. Qian, Sophia L. Landay, Deirdre O'Callaghan, Emilia Kaslow-Zieve, Chinenye C. Azoba, Charn-Xin Fuh, Brandon Temel, Zhi Ven Fong, Joseph A. Greer, Areej El-Jawahri, Jennifer S. Temel, Lara Traeger, Ryan David Nipp
Journal: Journal of Clinical Oncology (2020)

147 Background: Preoperative therapy for localized pancreatic cancer represents an emerging treatment paradigm with the potential to provide significant benefits, yet with complex risks. Research is lacking about whether clinicians effectively communicate key components of informed decision-making for patients considering this treatment. Methods: From 2017-2019, we conducted a two-part, mixed methods study. In part 1, we conducted interviews with clinicians (medical/radiation/surgical oncology, n = 13) and patients with pancreatic cancer who had received preoperative therapy (n = 18) to explore perceptions of information needed to make informed decisions about preoperative therapy, from which we generated a list of key elements. In part 2, we audio recorded the initial multidisciplinary visits of patients with pancreatic cancer eligible for preoperative therapy (n = 20). Two coders (94% concordance) independently identified whether clinicians discussed key elements from part 1. Patients also completed a post-visit survey reporting whether clinicians discussed the key elements. We explored discordance between audio recordings and patient reports using qualitative, explanatory themes. Results: In part 1, we identified 13 key elements of informed treatment decision-making, including treatment logistics, alternatives, and potential risks/benefits. In part 2, recordings showed that most visits included discussions about logistics, such as the chemotherapy schedule (n = 20) and use of a port-a-cath (n = 20), whereas few included discussions about risks, such as the potential for hospitalizations (n = 7), urgent visits (n = 6), or needing help with daily tasks (n = 6). Patients reported hearing about potential benefits, such as likelihood of achieving surgery (n = 10) and cure (n = 7), even when these were not discussed. Qualitative themes across these discordant cases included clinician optimism regarding present day results versus historical findings and mentions of positive outcomes from prior patients without citing specific data or potential adverse outcomes. Conclusions: We identified key elements of information patients with pancreatic cancer need to make informed decisions about preoperative therapy. Although clinicians frequently disclosed much of this information, we found multiple cases of patient-clinician discordance for certain key elements, which underscores the need for interventions to enhance patient-clinician communication regarding pancreatic cancer treatment decisions.
Hemagglutinin Traits Determine Transmission of Avian A/H10N7 Influenza Virus between Mammals
Authors: Sander Herfst, Jie Zhang, Mathilde Richard, Ryan McBride, Pascal Lexmond, Theo M. Bestebroer, Monique I.J. Spronken, Dennis de Meulder, Judith M. van den Brand, Miruna E. Rosu, Stephen R. Martin, Steve J. Gamblin, Xiaoli Xiong, Wenjie Peng, Rogier Bodewes, Erhard van der Vries, Albert D.M.E. Osterhaus, James C. Paulson, John J. Skehel, Ron A.M. Fouchier
Journal: Cell Host & Microbe (2020)
Capturing the financial hardship of cancer in military adolescent and young adult patients: A conceptual framework.
Authors: Christabel K. Cheung, Thuli Katerere-Virima, Laura E. Helbling, Bria N. Thomas, Reginald Tucker-Seeley
Journal: Journal of Clinical Oncology (2020)

163 Background: Cancer can be a setback for young active-duty military patients, with potential implications for their financial well-being, early career paths, and young families. Despite the assumption of sufficient material support for military patients, cancer and its treatments still result in substantial out-of-pocket expenses and lost-opportunity costs that can lead to financial hardship. Although prior cancer survivorship studies have put forth a material, psychosocial, and behavioral conceptual framework for describing financial hardship following a cancer diagnosis, it is unknown whether this framework adequately depicts the experience of financial hardship among military adolescent and young adult (AYA) patients. The primary aim of the current study was to extend this conceptual model of financial hardship following a cancer diagnosis for application among military AYA patients. Methods: Using Gale and colleagues’ Framework Method for qualitative multi-disciplinary health research, the investigator team conducted focus groups and key informant interviews (n=24) with active-duty AYA cancer patients, cancer care providers, and commanding officers at both a military medical center and a military post in Hawaii. Subsequently, content analysis and thematic abstraction produced results that were sorted to characterize the material, psychosocial, and behavioral domains of financial hardship. Finally, investigators employed health behavioral change theories to construct a conceptual framework. Results: Data analysis revealed that young active-duty military patients’ experiences of financial hardship following a cancer diagnosis occur within material, psychosocial, and behavioral domains that are uniquely situated within the environments of AYA development and military culture. Hence, we elaborated upon an existing conceptual framework of the financial hardship of cancer, by extending it to capture two meso-level contexts that emerged from our findings: (1) life course development and (2) occupational culture. Conclusions: Differentiating individual experiences of financial hardship within the contexts of life course development and occupational culture, may enable the development of interventions that are informed by the aspect of financial hardship most impacted by cancer care for this special population. Future research should further explicate the meso-level contexts in our study, and investigate the associations among and between factors within these social and environmental contexts.
Discovery of Ongoing Selective Sweeps within<i>Anopheles</i>Mosquito Populations Using Deep Learning
Authors: Alexander T Xue, Daniel R Schrider, Andrew D Kern, Alessandra della Torre, Andrew Kern, Beniamino Caputo, Bilali Kabula, Bradley White, Charles Godfray, Constant Edi, Craig Wilding, Dan Neafsey, Daniel Schrider, David Conway, David Weetman, Diego Ayala, Dominic Kwiatkowski, Igor Sharakhov, Janet Midega, Jiannong (John) Xu, João Pinto, John Essandoh, Johnson Matowo, Ken Vernick, Luc S Djogbenou, Mamadou Coulibaly, Mara Lawniczak, Martin Donnelly, Matthew Hahn, Michaël Fontaine, Michelle Riehle, Nora Besansky, Omar Cornejo, Robert McCann, Sam O’Loughlin, Vincent Robert, Alexander Xue, Alistair Miles, Chris Clarkson, CJ Battey, Cody Champion, Frederic Labbe, Giordano Bottà, Jeffrey Adrion, Joel Nelson, Nick Harding, Richard Wang, Scott T Small, Seth Redmond, Tiago Antão
Journal: Molecular Biology and Evolution (2020)

Abstract Identification of partial sweeps, which include both hard and soft sweeps that have not currently reached fixation, provides crucial information about ongoing evolutionary responses. To this end, we introduce partialS/HIC, a deep learning method to discover selective sweeps from population genomic data. partialS/HIC uses a convolutional neural network for image processing, which is trained with a large suite of summary statistics derived from coalescent simulations incorporating population-specific history, to distinguish between completed versus partial sweeps, hard versus soft sweeps, and regions directly affected by selection versus those merely linked to nearby selective sweeps. We perform several simulation experiments under various demographic scenarios to demonstrate partialS/HIC’s performance, which exhibits excellent resolution for detecting partial sweeps. We also apply our classifier to whole genomes from eight mosquito populations sampled across sub-Saharan Africa by the Anopheles gambiae 1000 Genomes Consortium, elucidating both continent-wide patterns as well as sweeps unique to specific geographic regions. These populations have experienced intense insecticide exposure over the past two decades, and we observe a strong overrepresentation of sweeps at insecticide resistance loci. Our analysis thus provides a list of candidate adaptive loci that may be relevant to mosquito control efforts. More broadly, our supervised machine learning approach introduces a method to distinguish between completed and partial sweeps, as well as between hard and soft sweeps, under a variety of demographic scenarios. As whole-genome data rapidly accumulate for a greater diversity of organisms, partialS/HIC addresses an increasing demand for useful selection scan tools that can track in-progress evolutionary dynamics.
Strategies for comprehensive implementation of survivorship care: A qualitative analysis of CoC-accredited cancer programs.
Authors: Soohyun Hwang, Burcu Bozkurt, Tamara Huson, Sarah Asad, Lauren Richardson, Joseph Ogbansiegbe, Laura Viera, Caroline Buse, Deborah Mayer, Lawrence N. Shulman, Sarah A. Birken
Journal: Journal of Clinical Oncology (2020)

209 Background: The Commission on Cancer (CoC) seeks to promote comprehensive approaches to implementing survivorship programs among accredited cancer programs. In practice, cancer programs’ approaches range from cursory (e.g., developing care plans without robust services) to comprehensive (e.g., facilitating follow-up care). This study identified strategies that were unique to cancer programs with comprehensive approaches to implementing survivorship programs. Methods: We sampled 39 CoC-accredited cancer programs with approaches to survivorship program implementation ranging from cursory to comprehensive, as reported in CoC annual surveys. Within sampled cancer programs, we conducted in-depth semi-structured interviews with a total of 42 healthcare professionals (1-2/program). We identified strategies unique to cancer programs with comprehensive approaches by comparing them to cancer programs with cursory approaches. Results: Cancer programs with comprehensive approaches to implementing survivorship programs had formal committees with ample opportunities to evaluate the progress, revise roles, and acquire multiple stakeholders’ support. Keeping a good record system enabled these cancer programs to meet accreditation requirements and improve processes. Buy-in from upper management and key physicians was deemed crucial in leveraging cancer program resources. These programs also had clear roles with shared accountability among multidisciplinary groups. Like cancer programs with comprehensive approaches to implementing survivorship programs, many cancer programs with cursory approaches also had formal committees; however, cancer programs with cursory approaches lacked buy-in from key stakeholders, relying on few staff or a champion for implementation. Cancer programs with cursory approaches had limited resources, cumbersome processes, and team members with unclear roles. Conclusions: Cancer programs with comprehensive approaches to survivorship program implementation gained broad stakeholder buy-in and established clear team member roles with shared accountability. Study findings will inform more than 1500 CoC-accredited US cancer programs’ approaches to implementing survivorship programs. At the conference, we will have results from quantitative and measures validation companion studies.
Utilization of circulating cell-free DNA profiling to guide first-line chemotherapy in advanced lung squamous cell carcinoma
Authors: Tao Jiang, Liyan Jiang, Xiaorong Dong, Kangsheng Gu, Yueyin Pan, Qin Shi, Guojun Zhang, Huijuan Wang, Xiaochun Zhang, Nong Yang, Yuping Li, Jianping Xiong, Tienan Yi, Min Peng, Yong Song, Yun Fan, Jiuwei Cui, Gongyan Chen, Wei Tan, Aimin Zang, Qisen Guo, Guangqiang Zhao, Ziping Wang, Jianxing He, Wenxiu Yao, Xiaohong Wu, Kai Chen, Xiaohua Hu, Chunhong Hu, Lu Yue, Da Jiang, Guangfa Wang, Junfeng Liu, Guohua Yu, Junling Li, Henghui Zhang, Lihong Wu, Lu Fang, Dandan Liang, Yi Zhao, Weihong Zhao, Wenmin Xie, Shengxiang Ren, Caicun Zhou
Journal: Theranostics (2020)

Rationale: Platinum-based chemotherapy is one of treatment mainstay for patients with advanced lung squamous cell carcinoma (LUSC) but it is still a "one-size fits all" approach. Here, we aimed to investigate the predictive and monitoring role of circulating cell-free DNA (cfDNA) profiling for the outcome of first-line chemotherapy in patients with advanced LUSC. Methods: Peripheral blood samples of 155 patients from a phase IV trial and 42 cases from an external real-world cohort were prospectively collected. We generated a copy number variations-based classifier via machine learning algorithm to integrate molecular profiling of cfDNA, named RESPONSE SCORE (RS) to predict the treatment outcome. To monitor the treatment efficacy, cfDNA samples collected at different time points were subjected to an ultra-deep sequencing platform. Results: The results showed that patients with high RS showed substantially higher objective response rate than those with low RS in training set (P < 0.001), validation set (P < 0.001) and real-world cohort (P = 0.019). Furthermore, a significant difference was observed in both progression-free survival (training set, P < 0.001; validation set: P < 0.001; real-world cohort: P = 0.019) and overall survival (training set, P < 0.001; validation set: P = 0.037) between high and low RS group. Notably, variant allele frequency (VAF) calculated from an ultra-deep sequencing platform significantly reduced in patients experienced a complete or partial response after 2 cycles of chemotherapy (P < 0.001), while it significantly increased in these of non-responder (P < 0.001). Moreover, VAF undetectable after 2 cycles of chemotherapy was correlated with markedly better objective response rate (P < 0.001) and progression-free survival (P < 0.001) than those with detectable VAF. Conclusions: These findings indicated that the RS, a circulating cfDNA sequencing-based stratification index, could help to guide first-line chemotherapy in advanced LUSC. The change of VAF is valuable to monitor the treatment response.
Feasibility and Outcome of Late Intensification with Native L-Asparaginase for Acute Lymphoblastic Leukemia in the Elderly: A Single Center Experience
Authors: Francois Xavier Gros, Pierre-Yves Dumas, Edouard Forcade, Claire Calmettes, Margot Robles, Vincent Servant, Nicolas Lechevalier, Audrey Bidet, Noel Milpied, Arnaud Pigneux, Thibaut Leguay
Journal: Blood (2017)
Financial and employment toxicity related to breast reconstruction following mastectomy in a diverse population-based cohort.
Authors: Nicholas L. Berlin, Adeyiza O. Momoh, Paul Abrahamse, Steven J. Katz, Reshma Jagsi, Sarah T. Hawley
Journal: Journal of Clinical Oncology (2020)

78 Background: Despite mandated private insurance coverage for breast reconstruction following mastectomy, health care costs are increasingly passed onto women who seek these procedures through cost-sharing arrangements and high-deductible health plans. In this population-based study, we sought to characterize financial and employment toxicities related to pursuing breast reconstruction following mastectomy. Methods: Women (white, African American, and Latina-English and Spanish speaking) with early stage breast cancer (stages 0-II) diagnosed between July 2013 to September 2014 and who underwent mastectomy were identified through the Georgia and Los Angeles Surveillance, Epidemiology, and End Results (SEER) registries and surveyed. Primary outcome measures included patient-reported appraisal of financial toxicity and employment status following breast cancer treatment using previously developed measures. Multivariable models evaluated the association between breast reconstruction and self-reported financial and employment status. Results: Among 868 breast cancer patients who underwent mastectomy, 43.5% (n = 378) did not undergo breast reconstruction and 56.5% (n = 490) underwent reconstruction. 43.4% of the cohort reported being worse off financially since their diagnosis (49.4% with reconstruction vs. 35.0% without reconstruction, P&lt; .001). Among women who were employed at time of breast cancer diagnosis (n = 535), 70.2% who underwent reconstruction reported being worse off regarding employment status compared to 51.1% who did not undergo reconstruction ( P&lt; .001). Receipt of reconstruction was independently associated with a self-reported decline in financial status (Odds Ratio (OR) 2.1, 95% Confidence Interval (CI) 1.4-3.4, P= .001). Similarly, reports of being worse off regarding employment status were also higher in those who underwent reconstruction vs. not (OR 2.2, 95% CI 1.2-3.8, P= .006). Spanish-speaking Latina women more often reported being worse off regarding employment status (OR 4.3, 95% CI 2.1-9.0, P&lt; .001) than white women. Conclusions: In this diverse cohort of women who underwent mastectomy for early stage breast cancer, women who elected to undergo reconstruction experienced more self-reported financial and employment toxicities. Patients should be counseled regarding the potential costs related to these procedures. Policy-makers should be aware of the financial barriers for women who undergo reconstruction despite mandatory insurance coverage in the United States.
Correspondence on ‘Long-term outcome of a randomised controlled trial comparing tacrolimus with mycophenolate mofetil as induction therapy for active lupus nephritis’
Authors: Chuanhui Xu
Journal: Annals of the Rheumatic Diseases (2020)

Correspondence on 'Long-term outcome of a randomised controlled trial comparing tacrolimus with mycophenolate mofetil as induction therapy for active lupus nephritis' I read with great interest the recently published long-term outcome of a randomised controlled trial comparing tacrolimus with mycophenolate mofetil as induction therapy for active lupus nephritis. 12][3][4][5] However, I am concerned about the risks of thrombotic microangiopathy (TMA) and posterior reversible encephalopathy syndrome (PRES) when CNIs were given for patients with systemic lupus erythematosus (SLE) with concomitant antiphospholipid syndrome (APS).The anticardiolipin or lupus anticoagulant was present in 48 out of 150 patients (28%) in the study by Mok et al, 3 which was not reported in other studies. 2 4 5 There were about 17.6% patients with TMA in a cohort of 341 patients with stable lupus nephritis, who had the poorest renal outcome. 6The use of CNIs in patients with SLE/APS should be prudent because both CNI and APS are risk factors for the occurrence of TMA, 7 especially for whom with the presence of histological features of TMA.PRES is contributed by endothelial cell dysfunction.SLE/APS, renal impairment and CNIs are known risk factors for PRES. 8There were 4 out of 177 cases reported PRES in the voclosporin group regardless of the dosage, whereas none in the placebo group from the Aurinia Urinary Protein Reduction Active -Lupus With Voclosporin (AURA-LV) study. 4I also noted one case developed epilepsy in the group of multitarget therapy, but none in the group of cyclophosphamide from the study by Liu et al. 2 The use of CNIs in patients with SLE/APS may confer a higher risk of PRES.In summary, the risks of TMA and PRES should not be neglected when CNIs are used for patient with SLE/APS.The authors should be encouraged to report the outcomes of CNIs use in patients with SLE and APS, which would shed light on the management of these patients.
Notch activity characterizes a common hepatocellular carcinoma subtype with unique molecular and clinicopathologic features
Authors: Changyu Zhu, Yu-Jui Ho, Marcela A. Salomao, Dianne H. Dapito, Alberto Bartolome, Robert F. Schwabe, Ju-Seog Lee, Scott W. Lowe, Utpal B. Pajvani
Journal: Journal of Hepatology (2020)
Retraction Notice to: The Cancer-Associated FGFR4-G388R Polymorphism Enhances Pancreatic Insulin Secretion and Modifies the Risk of Diabetes
Authors: Shereen Ezzat, Lei Zheng, Jose C. Florez, Norbert Stefan, Thomas Mayr, Maw Maw Hliang, Kathleen Jablonski, Maegan Harden, Alena Stanĉáková, Markku Laakso, Hans-Ulrich Haring, Axel Ullrich, Sylvia L. Asa
Journal: Cell Metabolism (2020)
Persistence of serum and saliva antibody responses to SARS-CoV-2 spike antigens in COVID-19 patients
Authors: Baweleta Isho, Kento T. Abe, Michelle Zuo, Alainna J. Jamal, Bhavisha Rathod, Jenny H. Wang, Zhijie Li, Gary Chao, Olga L. Rojas, Yeo Myong Bang, Annie Pu, Natasha Christie-Holmes, Christian Gervais, Derek Ceccarelli, Payman Samavarchi-Tehrani, Furkan Guvenc, Patrick Budylowski, Angel Li, Aimee Paterson, Feng Yun Yue, Lina M. Marin, Lauren Caldwell, Jeffrey L. Wrana, Karen Colwill, Frank Sicheri, Samira Mubareka, Scott D. Gray-Owen, Steven J. Drews, Walter L. Siqueira, Miriam Barrios-Rodiles, Mario Ostrowski, James M. Rini, Yves Durocher, Allison J. McGeer, Jennifer L. Gommerman, Anne-Claude Gingras
Journal: Science Immunology (2020)

While the antibody response to SARS-CoV-2 has been extensively studied in blood, relatively little is known about the antibody response in saliva and its relationship to systemic antibody levels. Here, we profiled by enzyme-linked immunosorbent assays (ELISAs) IgG, IgA and IgM responses to the SARS-CoV-2 spike protein (full length trimer) and its receptor-binding domain (RBD) in serum and saliva of acute and convalescent patients with laboratory-diagnosed COVID-19 ranging from 3-115 days post-symptom onset (PSO), compared to negative controls. Anti-SARS-CoV-2 antibody responses were readily detected in serum and saliva, with peak IgG levels attained by 16-30 days PSO. Longitudinal analysis revealed that anti-SARS-CoV-2 IgA and IgM antibodies rapidly decayed, while IgG antibodies remained relatively stable up to 105 days PSO in both biofluids. Lastly, IgG, IgM and to a lesser extent IgA responses to spike and RBD in the serum positively correlated with matched saliva samples. This study confirms that serum and saliva IgG antibodies to SARS-CoV-2 are maintained in the majority of COVID-19 patients for at least 3 months PSO. IgG responses in saliva may serve as a surrogate measure of systemic immunity to SARS-CoV-2 based on their correlation with serum IgG responses.