tbuckley/cabot-search huggingface dataset:
Utilizing volunteer, nonclinical navigators (NCN) as extenders of the breast nurse navigator (BNN) to provide patient education and support.
Authors: Judy B Koutlas, Debra C Mascarenhas
Journal: Journal of Clinical Oncology (2019)

128 Background: The role of the BNN during the treatment phase of the care continuum involves educating patients and families and assisting them with overcoming barriers to care by linking them to appropriate resources. Our BNN provides education to approximately 15 new patients per month. Additional navigation services are provided to 114 patients per month with an annual caseload of 580. The caseload volume limits the number of patients she can see in one day. With our existing volunteer NCN program, we decided to conduct a 3-month pilot project utilizing NCN in our breast clinic to provide navigation services while the BNN was on medical leave. Methods: Three NCN were trained by BNN to provide breast navigation services. Each NCN received a minimum of 10 hours of training, which included education regarding breast cancer, common barriers to care, and resources. The BNN created a navigation tool indicating the education to be provided at diagnosis, pre-and post-surgery, and systemic therapy. NCN provided education by utilizing videos and written materials. Patient medical questions were deferred to nursing staff and physicians. BNN provided training and resource guide to aide NCN to identify and link patients with appropriate resources and support staff. Results: NCN provided services to 78 patients including approximately 10 new patients per month. A total of 24 surveys were completed by healthcare team and patients. Results revealed 94% of patients agreed/strongly agreed NCN helped them feel better and reduced fears, 100% reported helpfulness in linking to resources and support programs, and 50% viewed a video and reported better understanding. Healthcare team overwhelmingly reported the emotional support provided was beneficial and that NCN were helpful in providing resources and recommended continuing. Conclusions: NCN are effective in providing additional navigation services. Our breast navigation program had a 29% increase in new patient encounters and 27% increase in returning patient encounters compared to the previous year prior to the addition of NCN. We plan to expand this model into other multidisciplinary clinics.
Oncology urgent care to decrease unnecessary emergency room visits.
Authors: Maura Abbott, Laureen Hill, Deepa Kumaraiah, Christina Russomanno, Yelena Ustoyev, Danielle Drimer Katayen, Kate Kaley, Kristina Howard, Maria Negron, Gary K. Schwartz
Journal: Journal of Clinical Oncology (2019)

212 Background: In March 2019, Columbia University Irving Medical Center (CUIMC)/New York Presbyterian (NYP) piloted an oncology urgent care center, Oncology Care Initiation Unit (OCIU). Patients currently on therapy were referred to OCIU Nurse Practitioners (NP) by primary Oncology Teams for acute, non-life threatening complaints for management. We evaluated the impact of the OCIU on preventing unnecessary emergency room (ER) visits, patient wait times, and patient satisfaction. Prior to the OCIU, 52% of oncology patients presenting to the ER were discharged indicating that an ER visit most likely was not needed. Average wait time for evaluation in ERs for non-critical patients is 7 to 9 hours and can be another 7 to 9 hours for intervention. Methods: We opened the 8-week OCIU pilot to Thoracic and Gastrointestinal (GI) Oncology, and Sarcoma patients who had an acute, non-life threatening complaint from, 8AM to 6PM, Monday to Friday. We collected data on all OCIU patient referrals from 3/7/2019 to 5/2/2019, including patient demographics, primary cancer diagnosis, chief complaint, wait times, interventions, disposition and patient satisfaction using a validated 5 question satisfaction survey. Results: During the pilot, we received 51 referrals, 44 (86%) were considered OCIU appropriate and evaluated; 25 (57%) had a GI cancer diagnosis, 14 (32%) Thoracic cancer diagnosis, and 5 (11%) Sarcoma. Primary chief complaints in order of frequency were pain, GI distress, and dyspnea. 44 (100%) had no wait to be evaluated by the OCIU NP. 33 (75%) of OCIU patients were discharged home, 9 (20%) were directly admitted, and 2 (5%) were transferred to the ER. Patients not requiring invasive intervention were discharged home within thirty minutes of their appointment. Patients requiring infusions, radiology services, and/or paracentesis or thoracentesis were discharged within 4 hours of appointment time. 100% patient satisfaction was reported. Conclusions: Implementation of the OCIU has led to decreased ER visits, wait times for evaluation and management, and increased patient satisfaction. These findings support the need for the OCIU, as well as increasing access to the OCIU by extending to additional HICCC patients.
Reconstructing the Clonal and Mutational Architecture of Myeloma through Avian Leukosis Virus (ALV)-Mediated Genome Editing
Authors: Zachary Morrow, Alexander Cicala, Evan Flietner, Athanasios Papadas, Adam Pagenkopf, Zhi Wen, Adhithi Rajagopalan, Poulikos Poulikakos, Natalie Scott Callander, Marta Chesi, P. Leif Bergsagel, Jing Zhang, Fotios Asimakopoulos
Journal: Blood (2018)
Abstract 450: Adipose Tissue Browning Induced by Natriuretic Peptide Exerts Thermogenic Actions and Improves Insulin Resistance in an in vivo Model of Diet-Induced Obese Mice
Authors: Haruka Kimura, Tomohisa Nagoshi, Akira Yoshii, Yoshiro Tanaka, Yuhei Oi, Michihiro Yoshimura
Journal: Circulation Research (2019)

Although natriuretic peptides (NPs) classically act on renal and cardiovascular systems, increasing evidence suggest that NPs also largely coordinate inter-organ metabolic cross-talk with adipose tissues. We recently reported that A-type NP (ANP) raises intracellular temperature in cultured adipocytes in a low-temperature sensitive manner. We herein investigated whether ANP exerts a significant impact on adipose tissues in vivo, using diet-induced obese mice. C57BL/6 mice were exposed to high-fat diet (HFD) or normal-fat diet (NFD) for 13 weeks, and treated with or without ANP infusion for 3 weeks (0.5 ug/kg/min via osmotic-pump). The ANP infusion significantly increased its serum concentration both in NFD and HFD group. Histological analyses revealed that HFD induced increased brown adipose tissue (BAT) cell size with accumulation of lipid droplets (whitening). ANP treatment significantly suppressed this whitening response (re-browning). Similarly, HFD induced enlarged inguinal white adipose tissue (WAT) lipid droplets, which was significantly reduced by ANP. This was associated with a substantial increase in uncoupling protein-1(UCP1) expression in WAT confirmed by immunohistochemical analysis (browning, n=3 each) and UCP1mRNA analysis (NFD+NP 2.7±0.4 fold vs NFD, P&lt;0.01; HFD+NP 6.4±2.2 fold vs HFD, P&lt;0.05, n=5 each). To determine the functional significance of browning effects of ANP, intraperitoneal glucose tolerance test (IPGTT) and insulin tolerance test (ITT) were performed and showed that ANP treatment substantially improved insulin resistance in HFD (p&lt;0.05, n=9 each). Moreover, cold tolerance test (at 4°C for 4 hours) demonstrated that the ANP-treated mice were tolerant to cold exposure, which was more salient in HFD with ANP (Decrease in rectal temperature from baseline [°C]: NFD+ANP –2.4±0.6, HFD –2.5±0.4, HFD+ANP –2.1±0.4, versus NFD –9.2±2.2, P&lt;0.01 each, n=9 each). In conclusion, ANP induces WAT browning and preserves BAT function in obese models, leading to in vivo thermogenesis as well as improvement in insulin resistance. These findings reveal the compensatory roles of natriuretic peptides against the core body temperature fall and insulin resistance in a state of heart failure.
Clinical Studies of Cell Therapy in Cardiovascular Medicine
Authors: Monisha N. Banerjee, Roberto Bolli, Joshua M. Hare
Journal: Circulation Research (2018)

Given the rising prevalence of cardiovascular disease worldwide and the limited therapeutic options for severe heart failure, novel technologies that harness the regenerative capacity of the heart are sorely needed. The therapeutic use of stem cells has the potential to reverse myocardial injury and improve cardiac function, in contrast to most current medical therapies that only mitigate heart failure symptoms. Nearly 2 decades and >200 trials for cardiovascular disease have revealed that most cell types are safe; however, their efficacy remains controversial, limiting the transition of this therapy from investigation to practice. Lessons learned from these initial studies are driving the design of new clinical trials; higher fidelity of cell isolation techniques, standardization of conditions, more consistent use of state of the art measurement techniques, and assessment of multiple end points to garner insights into the efficacy of stem cells. Translation to clinical trials has almost outpaced our mechanistic understanding, and individual patient factors likely play a large role in stem cell efficacy. Therefore, careful analysis of dosing, delivery methods, and the ideal patient populations is necessary to translate cell therapy from research to practice. We are at a pivotal stage in the field in which information from many relatively small clinical trials must guide carefully executed efficacy trials. Larger efficacy trials are being launched to answer questions about older, first-generation stem cell therapeutics, while novel, second-generation products are being introduced into the clinical realm. This review critically examines the current state of clinical research on cell-based therapies for cardiovascular disease, highlighting the controversies in the field, improvements in clinical trial design, and the application of exciting new cell products.
Abstract 448: Predicting Blood Pressure Response to Fluid Bolus Therapy Using Neural Networks with Clinical Interpretability
Authors: Uma Girkar, Ryo Uchimido, Li-wei H Lehman, Peter Szolovits, Leo Celi, Wei-Hung Weng
Journal: Circulation Research (2019)

Background: Fluid bolus therapy (FBT), the rapid infusion of fluid, has been recommended as the primary-line treatment for acute hypotensive episode (AHE) that occurs in about 41% of patients in ICU. However, previous studies have reported that approximately one-third of the acute hypotensive patients do not successfully respond to FBT treatment. Avoiding the administration of FBT that will not successfully resolve AHE might prevent an inappropriate increase of the total fluid volume administered to ICU patients, potentially reducing their risk for severe organ dysfunction and increased mortality. Methods: Our study utilized regression models and attention-based recurrent neural network (RNN) algorithms and two large-scale information system databases, the multi-clinical MIMIC-ICU one and the multi-center Philips eICU CRD one, to predict the successful response to FBT among hypotensive patients in ICUs. We investigated both time-aggregated modeling and time-series modeling using RNN with the attention mechanism (AM) for clinical interpretability. The successful FBT is defined by intensive care experts as the presence of the maximum mean atrial pressure (MAP) &gt; 1.15 * average (MAP) at least once, where maximum(MAP) is the maximal MAP from the FBT starting time to two hours after FBT, and average (MAP) is the average MAP from 30 minutes before FBT until 10 minutes after FBT. Results: The stacked RNN with AM yielded the highest accuracy of 0.852 and area under the curve (AUC) value of 0.925 when trained and tested on the MIMIC-ICU dataset. The top features learned from regression include the patient's respiratory rate, diastolic pressure, temperature, and bicarbonate and base excess levels in blood. Preliminary results from training and testing the RNN on the Philips eICU-CRD database yielded an accuracy of 0.812 and AUC value of 0.769. We were also able to identify timesteps close to the time of FBT administration as clinically meaningful using the RNN models with AM. Conclusion: This is the first study that utilizes machine learning for identifying hypotensive patients in ICUs who will have sufficient blood pressure recovery after FBT. Utilizing AM and identifying the top features learned also provided clinical interpretability to the models we used.
Methods of implementation for an electronic ongoing professional practice evaluation system.
Authors: Woo Yeon Park, Dhruvkumar Patel, Patrick Samedy, Alicia Li
Journal: Journal of Clinical Oncology (2019)

313 Background: Hospitals accredited by the Joint Commission are required to provide Ongoing Professional Practice Evaluation (OPPE) for all privileged providers. Historically, OPPE reports had been created and completed by a peer review process on a paper-based system, where the data was managed in spreadsheets. The Division of Quality and Safety (DQS) developed an electronic system of collecting clinical and administrative data, with the goal of assessing quality of care in an impartial, modernized, and efficient process. Methods: Electronic implementation of the OPPE process can be divided into three main parts: metric development using electronic medical records (EMR), report automation, and application development for review. We designed queries to extract EMR data to validate the quality measures developed in collaboration with clinical leadership. Data pulls are then automated to populate outcomes to a table, from which the OPPE reports are populated according to selected parameters such as provider’s unique ID and OPPE period. Reports are then accessed by supervisors and providers directly through a web application developed by DQS. After verifying the data, clinicians can sign off in the application to complete the OPPE review process. Results: We have distributed 8,630 electronic OPPE report since 2012, and 1,486 distinct physicians had received reports. We evaluated engagement of the process by looking at engagement rate (number of OPPE signed reports divided by the total number of OPPE reports). The engagement rate varies by department, but the median of engagement rates of the OPPE process is 100%. Conclusions: Moving from paper chart reviews to an electronic process enables the institution to scale, lower the burden on employees, and improve the convenience of OPPE for busy providers. It also provides opportunities to evaluate quality of care on the provider level by analyzing outliers using the OPPE measure outcomes and finding the correlation of engagement rate and the quality outcomes.
Vβ Spectratype-guided Separation of Graft-Versus-Host Disease and Graft-Versus-Leukemia Effects in a MHC-Matched miHA-Mismatched Mouse Model of Hematopoietic Stem Cell Transplantation
Authors: Stacey L Fanning, Stephanie A Berger, Kristin Vazzana, Loise N Gichuru, Robert Korngold, Thea M Friedman
Journal: Blood (2008)
DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data
Authors: Cédric Arisdakessian, Olivier Poirion, Breck Yunits, Xun Zhu, Lana X. Garmire
Journal: Genome biology (2019)

Single-cell RNA sequencing (scRNA-seq) offers new opportunities to study gene expression of tens of thousands of single cells simultaneously. We present DeepImpute, a deep neural network-based imputation algorithm that uses dropout layers and loss functions to learn patterns in the data, allowing for accurate imputation. Overall, DeepImpute yields better accuracy than other six publicly available scRNA-seq imputation methods on experimental data, as measured by the mean squared error or Pearson's correlation coefficient. DeepImpute is an accurate, fast, and scalable imputation tool that is suited to handle the ever-increasing volume of scRNA-seq data, and is freely available at https://github.com/lanagarmire/DeepImpute .
Feasibility study for implementation of the AI-powered Internet+ Primary Care Model (AiPCM) across hospitals and clinics in Gongcheng county, Guangxi, China
Authors: Anjun Chen, Zhiyong Zhang, Qinghua Li, Wei Jiang, Qiyu Zheng, Zhiming He, Hui Chen, Ruobing Han, Han-Zhu Qian
Journal: The Lancet (2019)
Abstract 910: Identification of Novel Cardiac Sarcomere Interactions Using BioID Proximity-labeling
Authors: Anthony M PETTINATO, Feria Ladha, Ketan Thakar, Travis Hinson
Journal: Circulation Research (2019)

Mutations in components of the sarcomere, the contractile unit of cardiomyocytes, are a leading cause of genetic cardiomyopathies, such as dilated cardiomyopathy (DCM), which is an important contributor to heart failure burden. Using human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), our work has previously shown that DCM-causing mutations in titin, a major structural and functional component of the sarcomere, lead to diminished cardiac force production and impaired sarcomerogenesis. A classical model of sarcomerogenesis suggests that sarcomere assembly begins with pre-myofibrils containing beaded Z-disks composed of alpha-actinin, actin, and non-muscle myosin, with further assembly marked by addition of muscle myosin and titin. Once assembled, sarcomeres exhibit linear Z-disks and distinct protein markers. We are interested in understanding this stepwise process by probing sarcomere protein-protein interactions, with the objective of identifying novel developmental mediators and structural components of the sarcomere. More specifically, we would like to identify proteins that interact or localize near alpha-actinin at the Z-disk of the sarcomere. To do this, we have combined CRISPR/Cas9 genome-editing with BioID proximity-labeling to produce isogenic iPSC-CMs that express alpha-actinin fused with BirA, a promiscuous biotin ligase that biotinylates vicinal proteins. We have also generated a sarcomere-deficient iPSC-CM model that can readily reform sarcomeres on-demand, which we will use to further understand stage-specific interactions of sarcomere structure and development. Our results will not only provide novel insights into human sarcomere biology, but may also uncover novel targets for heart failure drug development.
Abstract 643: Integrated Systems Genetics Analysis of Tmem43 Mouse Model and Murine Genetic Reference Population of Bxd Strains Defines Novel Genetic Modifiers and Pathogenic Mechanisms in Arrhythmogenic Cardiomyopathy
Authors: Undral Munkhsaikhan, Qingqing Gu, Ramona Sabau, Joseph F Pierre, Joseph F Pierre, Deli Dong, Jeffrey A Towbin, Lu Lu, Enkhsaikhan Purevjav
Journal: Circulation Research (2019)

Background: Arrhythmogenic cardiomyopathies (ACMs) are heritable diseases characterized by arrhythmias, related sudden death, fibro-fatty infiltration and progressive heart failure. Although the pathogenic variant p.S358L in TMEM43/ LUMA causes fully penetrant ACM (ARVC5) in patients, little in vivo evidence has been reported and the roles of Tmem43 in normal cardiac function and disease remain obscure and controversial. This study explored Tmem43-associated genetic modifiers using forward, reverse, and systems genetics analyses in vivo . Methods: Microarray of cardiac and jejunal tissues were performed in a newly created Tmem43 S358L knock-in mouse and in forty BXD strains, used as a murine genetic reference population (GRP). Levels of plasma and fecal lipids and Pparγ activities were defined in heart and jejunum of Tmem43 animals. Immunohistochemistry was performed in the myocardium of patients with non-TMEM43 origin ACM. Results: BXD strain cardiac tissues demonstrated high levels of Tmem43 expression that was significantly negatively correlated with heart mass and heart rate, while positively correlated with plasma HDL and LDL levels. Expression of Tmem43 was also significantly (r&gt;0.5, p&lt;0.00075) correlated with Ppargc1a ( Pcg1a ) in the heart and intestine of BXDs and Tmem43 mutants. In the Tmem43 S358L mouse heart, Tmem43 and Ppargc1a were downregulated resulting in reduced Pparγ activities. Conversely, Tmem43 and Ppars- regulated genes, including Mogat2, responsible for cholesterol, bile acid, and lipid absorption and re-esterification, were upregulated in the jejunum, resulting in elevated lipid absorption in the gut lumen and hyperlipidemia in Tmem43 S358L mutants. Expression of TMEM43 was disrupted in cardiomyocyte intercalated disks in ACM patients’ myocardium in contrast to normal controls. Conclusions: Tmem43 is an essential gene for cardiac and small intestine signaling and function. The S358L-Tmem43 pathogenic variant is significantly associated with downregulation of Tmem43 , Ppagc1a and Ppar γ in the myocardium and upregulation of Pparγ and Pparα signaling in small intestine in vivo . Testing plasma lipid levels and TMEM43 expression in ACM patients may provide critical information for personalized predictive care.
Democratizing Evidence Production — A 51-Year-Old Man with Sudden Onset of Dense Hemiparesis
Authors: Shaheen Chowdhury, Timothy Laux, Michelle Morse, Angela Jenks, Scott Stonington, Yogesh Jain
Journal: New England Journal of Medicine (2019)

Interview with Dr. Yogesh Jain on the production of medical evidence that can benefit people in lower-resource settings. (07:37)Download A 51-year-old farmer in rural India presents with dense right hemiparesis, facial droop, and inability to speak. With the closest CT scanner 45 minutes away, his doctors realize that there’s no pragmatic standard of care for acute ischemic stroke in their setting.
Development of a Predictive Model of Multiple Myeloma (MM) Patient (pt) Outcomes Based on Treatment Class Transitions Using the Connect® MMpatient Registry
Authors: Sundar Jagannath, Robert M. Rifkin, Cristina J. Gasparetto, Kathleen Toomey, Brian G. M. Durie, James W. Hardin, Howard R. Terebelo, Lynne Wagner, Mohit Narang, Shankar Srinivasan, Ahmed YoussefAgha, Amani Kitali, Gail Larkins, Amit Agarwal, Rafat Abonour
Journal: Blood (2017)
Robotics Against the Evidence
Authors: Wouter J. Bom, Marja A. Boermeester
Journal: JAMA Surgery (2019)

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Phosphorylation-Regulated Activation of the Arabidopsis RRS1-R/RPS4 Immune Receptor Complex Reveals Two Distinct Effector Recognition Mechanisms
Authors: Hailong Guo, Hee-Kyung Ahn, Jan Sklenar, Jianhua Huang, Yan Ma, Pingtao Ding, Frank L.H. Menke, Jonathan D.G. Jones
Journal: Cell Host & Microbe (2020)
Abstract 15928: Supplementation of L-Alanyl Glutamine and Fish Oil Improves Body Composition and Quality of Life in Patients With Advanced Heart Failure
Authors: Christina Wu, Tomoko S Kato, Cynthia F Zizola, Hirokazu Akashi, Daniel Foreman, Hilary Armstrong, Mathew Bartels, Raymond Givens, David Seres, Paul Christian Schulze
Journal: Circulation (2013)

Introduction: Reduced skeletal muscle mass, strength and exercise capacity have been described in subjects with heart failure (HF). Prior studies suggest beneficial effects of ω-3 polyunsaturated f...