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https://www.readbyqxmd.com/read/28532962/from-snomed-ct-to-uberon-transferability-of-evaluation-methodology-between-similarly-structured-ontologies
#1
Gai Elhanan, Christopher Ochs, Jose L V Mejino, Hao Liu, Christopher J Mungall, Yehoshua Perl
OBJECTIVE: To examine whether disjoint partial-area taxonomy, a semantically-based evaluation methodology that has been successfully tested in SNOMED CT, will perform with similar effectiveness on Uberon, an anatomical ontology that belongs to a structurally similar family of ontologies as SNOMED CT. METHOD: A disjoint partial-area taxonomy was generated for Uberon. One hundred randomly selected test concepts that overlap between partial-areas were matched to a same size control sample of non-overlapping concepts...
May 19, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28515149/pyruvate-kinase-inhibits-proliferation-during-postnatal-cerebellar-neurogenesis-and-suppresses-medulloblastoma-formation
#2
Katherine Tech, Andrey P Tikunov, Hamza Farooq, A Sorana Morrissy, Jessica Meidinger, Taylor Fish, Sarah C Green, Hedi Liu, Yisu Li, Andrew J Mungall, Richard A Moore, Yussanne Ma, Steven Jm Jones, Marco A Marra, Matthew G Vander Heiden, Michael D Taylor, Jeffrey MacDonald, Timothy R Gershon
Aerobic glycolysis supports proliferation through unresolved mechanisms. We have previously shown that aerobic glycolysis is required for the regulated proliferation of cerebellar granule neuron progenitors (CGNPs), and for the growth of CGNP-derived medulloblastoma. Blocking the initiation of glycolysis via deletion of Hexokinase-2 (Hk2) disrupts CGNP proliferation and restricts medulloblastoma growth. Here, we assessed whether disrupting Pyruvate kinase-M (Pkm), an enzyme that acts in the terminal steps of glycolysis, would alter CGNP metabolism, proliferation and tumorigenesis...
May 17, 2017: Cancer Research
https://www.readbyqxmd.com/read/28514723/genomic-profiling-of-pelvic-genital-type-leiomyosarcoma-in-a-woman-with-a-germline-chek2-c-1100delc-mutation-and-a-concomitant-diagnosis-of-metastatic-invasive-ductal-breast-carcinoma
#3
My Linh Thibodeau, Caralyn Reisle, Eric Zhao, Lee Ann Martin, Yazeed Alwelaie, Karen L Mungall, Carolyn Ch'ng, Ruth Thomas, Tony Ng, Stephen Yip, Howard Lim, Sophie Sun, Sean S Young, Aly Karsan, Yongjun Zhao, Andrew J Mungall, Richard A Moore, Daniel Renouf, Karen Gelmon, Yussanne P Ma, Malcolm Hayes, Janessa Laskin, Marco A Marra, Kasmintan A Schrader, Steven J M Jones
INTRODUCTION: We describe a woman with the known pathogenic germline variant CHEK2:c.1100delC and synchronous diagnoses of both pelvic genital type leiomyosarcoma and metastatic invasive ductal breast carcinoma. CHEK2 (checkpoint kinase 2) is a tumour suppressor gene encoding a serine/threonine-protein kinase (CHEK2) involved in double-strand DNA break repair and cell cycle arrest. The CHEK2:c.1100delC variant is a moderate penetrance allele resulting in an approximate 2-fold increase in breast cancer risk...
May 16, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28486579/biomake-a-gnu-make-compatible-utility-for-declarative-workflow-management
#4
Ian H Holmes, Christopher J Mungall
. The Unix "make" program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modification times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program. . We present BioMake, a make-like utility that is compatible with most features ofGNUMake and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog...
May 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28436987/genomic-consequences-of-aberrant-dna-repair-mechanisms-stratify-ovarian-cancer-histotypes
#5
Yi Kan Wang, Ali Bashashati, Michael S Anglesio, Dawn R Cochrane, Diljot S Grewal, Gavin Ha, Andrew McPherson, Hugo M Horlings, Janine Senz, Leah M Prentice, Anthony N Karnezis, Daniel Lai, Mohamed R Aniba, Allen W Zhang, Karey Shumansky, Celia Siu, Adrian Wan, Melissa K McConechy, Hector Li-Chang, Alicia Tone, Diane Provencher, Manon de Ladurantaye, Hubert Fleury, Aikou Okamoto, Satoshi Yanagida, Nozomu Yanaihara, Misato Saito, Andrew J Mungall, Richard Moore, Marco A Marra, C Blake Gilks, Anne-Marie Mes-Masson, Jessica N McAlpine, Samuel Aparicio, David G Huntsman, Sohrab P Shah
We studied the whole-genome point mutation and structural variation patterns of 133 tumors (59 high-grade serous (HGSC), 35 clear cell (CCOC), 29 endometrioid (ENOC), and 10 adult granulosa cell (GCT)) as a substrate for class discovery in ovarian cancer. Ab initio clustering of integrated point mutation and structural variation signatures identified seven subgroups both between and within histotypes. Prevalence of foldback inversions identified a prognostically significant HGSC group associated with inferior survival...
April 24, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28403581/correction-mir-509-3p-is-clinically-significant-and-strongly-attenuates-cellular-migration-and-multi-cellular-spheroids-in-ovarian-cancer
#6
Yinghong Pan, Gordon Robertson, Lykke Pedersen, Emilia Lim, Anadulce Hernandez-Herrera, Amy C Rowat, Sagar L Patil, Clara K Chan, Yunfei Wen, Xinna Zhang, Upal Basu-Roy, Alka Mansukhani, Andy Chu, Payal Sipahimalani, Reanne Bowlby, Denise Brooks, Nina Thiessen, Cristian Coarfa, Yussanne Ma, Richard A Moore, Jacquie E Schein, Andrew J Mungall, Jinsong Liu, Chad V Pecot, Anil K Sood, Steven J M Jones, Marco A Marra, Preethi H Gunaratne
No abstract text is available yet for this article.
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28394352/spatial-heterogeneity-in-medulloblastoma
#7
A Sorana Morrissy, Florence M G Cavalli, Marc Remke, Vijay Ramaswamy, David J H Shih, Borja L Holgado, Hamza Farooq, Laura K Donovan, Livia Garzia, Sameer Agnihotri, Erin N Kiehna, Eloi Mercier, Chelsea Mayoh, Simon Papillon-Cavanagh, Hamid Nikbakht, Tenzin Gayden, Jonathon Torchia, Daniel Picard, Diana M Merino, Maria Vladoiu, Betty Luu, Xiaochong Wu, Craig Daniels, Stuart Horswell, Yuan Yao Thompson, Volker Hovestadt, Paul A Northcott, David T W Jones, John Peacock, Xin Wang, Stephen C Mack, Jüri Reimand, Steffen Albrecht, Adam M Fontebasso, Nina Thiessen, Yisu Li, Jacqueline E Schein, Darlene Lee, Rebecca Carlsen, Michael Mayo, Kane Tse, Angela Tam, Noreen Dhalla, Adrian Ally, Eric Chuah, Young Cheng, Patrick Plettner, Haiyan I Li, Richard D Corbett, Tina Wong, William Long, James Loukides, Pawel Buczkowicz, Cynthia E Hawkins, Uri Tabori, Brian R Rood, John S Myseros, Roger J Packer, Andrey Korshunov, Peter Lichter, Marcel Kool, Stefan M Pfister, Ulrich Schüller, Peter Dirks, Annie Huang, Eric Bouffet, James T Rutka, Gary D Bader, Charles Swanton, Yusanne Ma, Richard A Moore, Andrew J Mungall, Jacek Majewski, Steven J M Jones, Sunit Das, David Malkin, Nada Jabado, Marco A Marra, Michael D Taylor
Spatial heterogeneity of transcriptional and genetic markers between physically isolated biopsies of a single tumor poses major barriers to the identification of biomarkers and the development of targeted therapies that will be effective against the entire tumor. We analyzed the spatial heterogeneity of multiregional biopsies from 35 patients, using a combination of transcriptomic and genomic profiles. Medulloblastomas (MBs), but not high-grade gliomas (HGGs), demonstrated spatially homogeneous transcriptomes, which allowed for accurate subgrouping of tumors from a single biopsy...
May 2017: Nature Genetics
https://www.readbyqxmd.com/read/28245243/serelaxin-as-a-potential-treatment-for-renal-dysfunction-in-cirrhosis-preclinical-evaluation-and-results-of-a-randomized-phase-2-trial
#8
Victoria K Snowdon, Neil J Lachlan, Anna M Hoy, Patrick W F Hadoke, Scott I Semple, Dilip Patel, Will Mungall, Timothy J Kendall, Adrian Thomson, Ross J Lennen, Maurits A Jansen, Carmel M Moran, Antonella Pellicoro, Prakash Ramachandran, Isaac Shaw, Rebecca L Aucott, Thomas Severin, Rajnish Saini, Judy Pak, Denise Yates, Neelesh Dongre, Jeremy S Duffield, David J Webb, John P Iredale, Peter C Hayes, Jonathan A Fallowfield
BACKGROUND: Chronic liver scarring from any cause leads to cirrhosis, portal hypertension, and a progressive decline in renal blood flow and renal function. Extreme renal vasoconstriction characterizes hepatorenal syndrome, a functional and potentially reversible form of acute kidney injury in patients with advanced cirrhosis, but current therapy with systemic vasoconstrictors is ineffective in a substantial proportion of patients and is limited by ischemic adverse events. Serelaxin (recombinant human relaxin-2) is a peptide molecule with anti-fibrotic and vasoprotective properties that binds to relaxin family peptide receptor-1 (RXFP1) and has been shown to increase renal perfusion in healthy human volunteers...
February 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28223492/role-of-degassing-of-the-noril-sk-nickel-deposits-in-the-permian-triassic-mass-extinction-event
#9
Margaux Le Vaillant, Stephen J Barnes, James E Mungall, Emma L Mungall
The largest mass extinction event in Earth's history marks the boundary between the Permian and Triassic Periods at circa 252 Ma and has been linked with the eruption of the basaltic Siberian Traps large igneous province (SLIP). One of the kill mechanisms that has been suggested is a biogenic methane burst triggered by the release of vast amounts of nickel into the atmosphere. A proposed Ni source lies within the huge Noril'sk nickel ore deposits, which formed in magmatic conduits widely believed to have fed the eruption of the SLIP basalts...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28201737/effectiveness-of-a-screening-programme-in-identifying-individuals-with-increased-risk-of-cardiovascular-disease-in-south-africa
#10
Nasheeta Peer, Yusentha Balakrishna, Anniza de Villiers, Christelle Crickmore, Vash Mungal-Singh
No abstract text is available yet for this article.
February 14, 2017: Journal of Public Health
https://www.readbyqxmd.com/read/27972707/an-updated-cost-effectiveness-analysis-of-synflorix-universal-mass-vaccination-implementation-in-new-zealand
#11
L Varghese, L Talbot, A Govender, B Mungall
No abstract text is available yet for this article.
November 2016: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/27959929/histological-transformation-and-progression-in-follicular-lymphoma-a-clonal-evolution-study
#12
Robert Kridel, Fong Chun Chan, Anja Mottok, Merrill Boyle, Pedro Farinha, King Tan, Barbara Meissner, Ali Bashashati, Andrew McPherson, Andrew Roth, Karey Shumansky, Damian Yap, Susana Ben-Neriah, Jamie Rosner, Maia A Smith, Cydney Nielsen, Eva Giné, Adele Telenius, Daisuke Ennishi, Andrew Mungall, Richard Moore, Ryan D Morin, Nathalie A Johnson, Laurie H Sehn, Thomas Tousseyn, Ahmet Dogan, Joseph M Connors, David W Scott, Christian Steidl, Marco A Marra, Randy D Gascoyne, Sohrab P Shah
BACKGROUND: Follicular lymphoma (FL) is an indolent, yet incurable B cell malignancy. A subset of patients experience an increased mortality rate driven by two distinct clinical end points: histological transformation and early progression after immunochemotherapy. The nature of tumor clonal dynamics leading to these clinical end points is poorly understood, and previously determined genetic alterations do not explain the majority of transformed cases or accurately predict early progressive disease...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27899636/the-monarch-initiative-an-integrative-data-and-analytic-platform-connecting-phenotypes-to-genotypes-across-species
#13
Christopher J Mungall, Julie A McMurry, Sebastian Köhler, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J P Gourdine, Julius O B Jacobsen, Dan Keith, Bryan Laraway, Suzanna E Lewis, Jeremy NguyenXuan, Kent Shefchek, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, Melissa A Haendel
The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899602/the-human-phenotype-ontology-in-2017
#14
Sebastian Köhler, Nicole A Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Ségolène Aymé, Gareth Baynam, Susan M Bello, Cornelius F Boerkoel, Kym M Boycott, Michael Brudno, Orion J Buske, Patrick F Chinnery, Valentina Cipriani, Laureen E Connell, Hugh J S Dawkins, Laura E DeMare, Andrew D Devereau, Bert B A de Vries, Helen V Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna A Jähn, Roger James, Roland Krause, Stanley J F Laulederkind, Hanns Lochmüller, Gholson J Lyon, Soichi Ogishima, Annie Olry, Willem H Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H Scott, Michael Segal, Panagiotis I Sergouniotis, Richard Sever, Cynthia L Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W M Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O B Jacobsen, Tudor Groza, Damian Smedley, Christopher J Mungall, Melissa Haendel, Peter N Robinson
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27851968/analysis-of-normal-human-mammary-epigenomes-reveals-cell-specific-active-enhancer-states-and-associated-transcription-factor-networks
#15
Davide Pellacani, Misha Bilenky, Nagarajan Kannan, Alireza Heravi-Moussavi, David J H F Knapp, Sitanshu Gakkhar, Michelle Moksa, Annaick Carles, Richard Moore, Andrew J Mungall, Marco A Marra, Steven J M Jones, Samuel Aparicio, Martin Hirst, Connie J Eaves
The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27824051/genomic-analyses-identify-recurrent-mef2d-fusions-in-acute-lymphoblastic-leukaemia
#16
Zhaohui Gu, Michelle Churchman, Kathryn Roberts, Yongjin Li, Yu Liu, Richard C Harvey, Kelly McCastlain, Shalini C Reshmi, Debbie Payne-Turner, Ilaria Iacobucci, Ying Shao, I-Ming Chen, Marcus Valentine, Deqing Pei, Karen L Mungall, Andrew J Mungall, Yussanne Ma, Richard Moore, Marco Marra, Eileen Stonerock, Julie M Gastier-Foster, Meenakshi Devidas, Yunfeng Dai, Brent Wood, Michael Borowitz, Eric E Larsen, Kelly Maloney, Leonard A Mattano, Anne Angiolillo, Wanda L Salzer, Michael J Burke, Francesca Gianni, Orietta Spinelli, Jerald P Radich, Mark D Minden, Anthony V Moorman, Bella Patel, Adele K Fielding, Jacob M Rowe, Selina M Luger, Ravi Bhatia, Ibrahim Aldoss, Stephen J Forman, Jessica Kohlschmidt, Krzysztof Mrózek, Guido Marcucci, Clara D Bloomfield, Wendy Stock, Steven Kornblau, Hagop M Kantarjian, Marina Konopleva, Elisabeth Paietta, Cheryl L Willman, Mignon L Loh, Stephen P Hunger, Charles G Mullighan
Chromosomal rearrangements are initiating events in acute lymphoblastic leukaemia (ALL). Here using RNA sequencing of 560 ALL cases, we identify rearrangements between MEF2D (myocyte enhancer factor 2D) and five genes (BCL9, CSF1R, DAZAP1, HNRNPUL1 and SS18) in 22 B progenitor ALL (B-ALL) cases with a distinct gene expression profile, the most common of which is MEF2D-BCL9. Examination of an extended cohort of 1,164 B-ALL cases identified 30 cases with MEF2D rearrangements, which include an additional fusion partner, FOXJ2; thus, MEF2D-rearranged cases comprise 5...
November 8, 2016: Nature Communications
https://www.readbyqxmd.com/read/27794045/update-of-the-fantom-web-resource-high-resolution-transcriptome-of-diverse-cell-types-in-mammals
#17
Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A Medvedeva, Andreas Lennartsson, Finn Drabløs, Jordan A Ramilowski, Owen Rackham, Julian Gough, Robin Andersson, Albin Sandelin, Hans Ienasescu, Hiromasa Ono, Hidemasa Bono, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Takeya Kasukawa, Hideya Kawaji
Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27785453/distributed-cognition-and-process-management-enabling-individualized-translational-research-the-nih-undiagnosed-diseases-program-experience
#18
Amanda E Links, David Draper, Elizabeth Lee, Jessica Guzman, Zaheer Valivullah, Valerie Maduro, Vlad Lebedev, Maxim Didenko, Garrick Tomlin, Michael Brudno, Marta Girdea, Sergiu Dumitriu, Melissa A Haendel, Christopher J Mungall, Damian Smedley, Harry Hochheiser, Andrew M Arnold, Bert Coessens, Steven Verhoeven, William Bone, David Adams, Cornelius F Boerkoel, William A Gahl, Murat Sincan
The National Institutes of Health Undiagnosed Diseases Program (NIH UDP) applies translational research systematically to diagnose patients with undiagnosed diseases. The challenge is to implement an information system enabling scalable translational research. The authors hypothesized that similar complex problems are resolvable through process management and the distributed cognition of communities. The team, therefore, built the NIH UDP integrated collaboration system (UDPICS) to form virtual collaborative multidisciplinary research networks or communities...
2016: Frontiers in Medicine
https://www.readbyqxmd.com/read/27733503/ontobee-a-linked-ontology-data-server-to-support-ontology-term-dereferencing-linkage-query-and-integration
#19
Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27702824/significance-of-tp53-mutation-in-wilms-tumors-with-diffuse-anaplasia-a-report-from-the-children-s-oncology-group
#20
Ariadne H A G Ooms, Samantha Gadd, Daniela S Gerhard, Malcolm A Smith, Jaime M Guidry Auvil, Daoud Meerzaman, Qing-Rong Chen, Chih Hao Hsu, Chunhua Yan, Cu Nguyen, Ying Hu, Yussanne Ma, Zusheng Zong, Andrew J Mungall, Richard A Moore, Marco A Marra, Vicki Huff, Jeffrey S Dome, Yueh-Yun Chi, Jing Tian, James I Geller, Charles G Mullighan, Jing Ma, David A Wheeler, Oliver A Hampton, Amy L Walz, Marry M van den Heuvel-Eibrink, Ronald R de Krijger, Nicole Ross, Julie M Gastier-Foster, Elizabeth J Perlman
PURPOSE: To investigate the role and significance of TP53 mutation in diffusely anaplastic Wilms tumors (DAWTs). EXPERIMENTAL DESIGN: All DAWTs registered on National Wilms Tumor Study-5 (n = 118) with available samples were analyzed for TP53 mutations and copy loss. Integrative genomic analysis was performed on 39 selected DAWTs. RESULTS: Following analysis of a single random sample, 57 DAWTs (48%) demonstrated TP53 mutations, 13 (11%) copy loss without mutation, and 48 (41%) lacked both [defined as TP53-wild-type (wt)]...
November 15, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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