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Application of non-negative matrix factorization in oncology: one approach for establishing precision medicine

Ryuji Hamamoto, Ken Takasawa, Hidenori Machino, Kazuma Kobayashi, Satoshi Takahashi, Amina Bolatkan, Norio Shinkai, Akira Sakai, Rina Aoyama, Masayoshi Yamada, Ken Asada, Masaaki Komatsu (+3 others)
2022 Briefings in Bioinformatics  
In this review, the importance of NMF in the field of medicine, with a focus on the field of oncology, is described by explaining the mathematical science of NMF and the characteristics of the algorithm  ...  A meta-analysis integrating multiple data is necessary when analyzing large-scale medical data; as indicated in this review, NMF is useful for the meta-analysis.  ...  Machine learning has a long history; it is believed that the concept was created by Arthur Samuel in 1959 and came to be used as an academic term [3] .  ... 
doi:10.1093/bib/bbac246 pmid:35788277 pmcid:PMC9294421 fatcat:l5jpplwrnbbohmfk74vex6h5bm

Meta-gene markers predict meningioma recurrence with high accuracy

Zsolt Zador, Alexander P. Landry, Benjamin Haibe-Kains, Michael D. Cusimano
2020 Scientific Reports  
We therefore sought to apply systems-biology approaches to transcriptomic data to better predict meningioma recurrence.  ...  In our study, we demonstrate the potential utility of a meta-gene based systems biology approach in meningioma prognostication.  ...  Thirty of the top genes in validation cohort 1 must be removed before the updated module metagene yields an AUC less than 90% of the full model (sparse model 1), and thirteen in validation cohort 2 (sparse  ... 
doi:10.1038/s41598-020-74482-2 pmid:33093491 fatcat:veiq5gqhlbgf5k3d3xxbxtfcne

Evaluation of Semi-Automatic Metadata Generation Tools: A Survey of the Current State of the Art

Jung-ran Park, Andrew Brenza
2015 Information Technology and Libraries  
To address such needs, this study examines the range of semi--automatic metadata generation tools (N = 39) while providing an analysis of their techniques, features, and functions.  ...  One promising approach to managing the ever--increasing amount of information is with semi-automatic metadata generation tools. Semi--automatic metadata generation tools Jung--ran Park  ...  The remainder of the article provides an overview of the primary techniques developed for the semi--automatic generation of metadata and a review of the open--source metadata generation tools that employ  ... 
doi:10.6017/ital.v34i3.5889 fatcat:ee6cptjz2vh4vc3er32zksjgji

Big Data Analytics and Organizational Performance: A Meta-Analysis Study

Mihai BOGDAN, Babeș-Bolyai University Cluj-Napoca, Romania, Anca BORZA, Babeș-Bolyai University Cluj-Napoca, Romania
2019 Management and Economics Review  
The purpose of this study is to run a meta-analysis review on the empirical articles that tackle big data analytics and organizational performance topics.  ...  Based on this standard, we included 37 articles in our meta-analysis. The findings confirm that big data analytics play an important role in organizational performance.  ...  R package meta was used with the metagen function.  ... 
doi:10.24818/mer/2019.12-06 fatcat:kxqqxnabb5fypfbkfjonnjouky

Mentoring programs to affect delinquency and associated outcomes of youth at risk: A comprehensive meta-analytic review

Patrick H. Tolan, David B. Henry, Michael S. Schoeny, Peter Lovegrove, Emily Nichols
2013 Journal of Experimental Criminology  
Objectives To conduct a meta-analytic review of selective and indicated mentoring interventions for effects for youth at risk on delinquency and key associated outcomes (aggression, drug use, academic  ...  This report is based on a Campbell Collaboration systematic review.  ...  Three authors have conducted prior meta-analyses on mentoring or related topics prior to our review: (1) DuBois et al. (2002) on mentoring in general; (2) Lipsey and Wilson (1998) on delinquency interventions  ... 
doi:10.1007/s11292-013-9181-4 pmid:25386111 pmcid:PMC4224303 fatcat:peefzcfqp5fudj7w3vwkm7rhmu

Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System

Victor M. Markowitz, I-Min A. Chen, Ken Chu, Amrita Pati, Natalia N. Ivanova, Nikos C. Kyrpides
2015 Trends in Microbiology  
the complexity of maintaining such a system in an academic 24 setting with limited budgets and computing and data management infrastructure. 25 Rationale for developing IMG 26 U.S.  ...  In addition IMG provided tools for reviewing the quality of annotations of 38 the JGI genomes, thus serving as an extension of, and a feedback mechanism for, JGI's microbial 39 genome annotation pipeline  ...  Finding an effective long term funding mechanism 508 for such systems, including appropriate monitoring of their costs and quality remains an open The value of a (meta)genome comparative analysis system  ... 
doi:10.1016/j.tim.2015.07.012 pmid:26439299 fatcat:lle62btblrbehdepp2x7wntyee

Derivation and Application of Molecular Signatures to Prostate Cancer: Opportunities and Challenges

Dimitrios Doultsinos, Ian G. Mills
2021 Cancers  
In this review, we present an overview of these signatures, the strategies for their derivation, and future perspectives on their continued development and evolution.  ...  Thus, in this review, we focus on the generation and utility of transcriptional signatures in PCa.  ...  A summary of the activity signatures generated in PCa oncology, both commercially and in academic medical research, can be found in Table 1 . Table 1 . Signatures involving TF biology in PCa.  ... 
doi:10.3390/cancers13030495 pmid:33525365 fatcat:22kaa7dnq5dd5czyjp72j5dlr4

Epigenetic Reprogramming Mediated by Maternal Diet Rich in Omega-3 Fatty Acids Protects From Breast Cancer Development in F1 Offspring

Ata Abbas, Theodore Witte, William L. Patterson, Johannes F. Fahrmann, Kai Guo, Junguk Hur, W. Elaine Hardman, Philippe T. Georgel
2021 Frontiers in Cell and Developmental Biology  
We earlier reported that in transgenic mice prone to develop breast cancer (BCa), a diet supplemented with canola oil, rich in omega-3-rich FA (as opposed to an omega-6-rich diet containing corn oil),  ...  To investigate the underlying mechanisms of the cancer protective effect of canola oil in the F1 generation, we designed and performed the present study with the same diets using BALB/c mice to remove  ...  Fruit and vegetables and cancer risk: a review of southern European studies. Br. J. Nutr. 113(Suppl. 2), S102–S110. Vanamala, J. (2017). Food systems approach to cancer prevention. Crit. Rev.  ... 
doi:10.3389/fcell.2021.682593 pmid:34179012 pmcid:PMC8222782 fatcat:qxxjznha6ncyjpi7mndzcpvr6m

The Human Blood Transcriptome in a Large Population Cohort and Its Relation to Aging and Health

Maria Schmidt, Lydia Hopp, Arsen Arakelyan, Holger Kirsten, Christoph Engel, Kerstin Wirkner, Knut Krohn, Ralph Burkhardt, Joachim Thiery, Markus Loeffler, Henry Loeffler-Wirth, Hans Binder
2020 Frontiers in Big Data  
The blood transcriptome is expected to provide a detailed picture of an organism's physiological state with potential outcomes for applications in medical diagnostics and molecular and epidemiological  ...  We find a striking overlap of signatures shared by multiple diseases, aging, and obesity driven by an underlying common pattern, which was associated with the immune response and the increase of inflammatory  ...  Phenotype-to-metagene correlation maps were generated by correlating each of the phenotype parameter-profiles over all participants with each of the metagene expression profiles.  ... 
doi:10.3389/fdata.2020.548873 pmid:33693414 pmcid:PMC7931910 fatcat:lv4bsrwzdbfedgrd5tjwtjoojq

Environmental risk factors for non-Hodgkin's lymphoma: umbrella review and comparison of meta-analyses of summary and individual participant data

Xiaoting Shi, Haoran Zhuo, Yuxuan Du, Kate Nyhan, John Ioannidis, Joshua D Wallach
2022 BMJ Medicine  
of summary level data and meta-analyses of individual participant data.DesignUmbrella review and comparison of meta-analyses of summary and individual participant level data.Data sourcesMedline, Embase  ...  umbrella review suggests evidence of many meta-analyses of summary level data reporting weak associations between environmental risk factors and non-Hodgkin's lymphoma.  ...  population Autoimmune diseases Rheumatoid arthritis Patients v general population Primary Sjogren's Patients v general syndrome population Systemic lupus erythe-Patients v general matosus population Coeliac  ... 
doi:10.1136/bmjmed-2022-000184 fatcat:222vpzutnfhglgih6bus2mbjuq

US studies may overestimate effect sizes in softer research

D. Fanelli, J. P. A. Ioannidis
2013 Proceedings of the National Academy of Sciences of the United States of America  
These problems are hypothesized to be worsened by lack of consensus on theories and methods, by selective publication processes, and by career systems too heavily oriented toward productivity, such as  ...  Behavioral studies have lower methodological consensus and higher noise, making US researchers potentially more likely to express an underlying propensity to report strong and significant findings. publish  ...  Following the suggestion of one reviewer, we also examined how centering weights by meta-analysis affected our results.  ... 
doi:10.1073/pnas.1302997110 pmid:23980165 pmcid:PMC3773789 fatcat:vgxnslvvx5hslhm76pu2u5chry

Equivalent Transformations of Heterogeneous Meta-Programs

Vytautas Štuikys, Robertas Damaševičius
2013 Informatica  
We consider a generalization of heterogeneous meta-programs by (1) introducing an extra level of abstraction within the meta-program structure, and (2) meta-program transformations.  ...  into meta-meta-programs and vice versa; (c) introduction of metrics to evaluate complexity of meta-specifications.  ...  Authors would like to thank anonymous reviewers for their comments that enabled us to revise the paper anew and to improve it substantially.  ... 
doi:10.15388/informatica.2013.398 fatcat:7glofhf4k5csjgmzeuxxjcuzym

The combined use of steroids and immune checkpoint inhibitors in brain metastasis patients: a systematic review and meta-analysis

Charissa A C Jessurun, Alexander F C Hulsbergen, Anouk E de Wit, Ishaan A Tewarie, Tom J Snijders, Joost Verhoeff, John Phillips, David A Reardon, Rania A Mekary, Marike L D Broekman
2021 Neuro-Oncology  
Hence, the aim of this study was to perform a systematic literature review and meta-analysis on the association between steroid use and overall survival (OS) in BM patients receiving ICI.  ...  Likewise, steroids have been an integral component of symptomatic management of BM patients.  ...  Meta-analysis was conducted using the metagen function of the meta package in R. 23 Unless specified otherwise, a p-value of less than 5% was considered significant.  ... 
doi:10.1093/neuonc/noab046 pmid:33631792 pmcid:PMC8328028 fatcat:7ophr43wpvgmxdddpo5e7b6ljq

International Society for Nutritional Psychiatry Research Practice Guidelines for Omega-3 Fatty Acids in the Treatment of Major Depressive Disorder

Ta-Wei Guu, David Mischoulon, Jerome Sarris, Joseph Hibbeln, Robert K. McNamara, Kei Hamazaki, Marlene P. Freeman, Michael Maes, Yutaka J. Matsuoka, R.H. Belmaker, Felice Jacka, Carmine Pariante (+3 others)
2019 Psychotherapy and Psychosomatics  
The subcommittee of the International Society for Nutritional Psychiatry Research organized an expert panel and conducted a literature review and a Delphi process to develop a consensus-based practice  ...  The guideline focuses on 5 thematic areas: general concepts, acute treatment strategy, depression recurrence monitoring and prevention, use in special populations, and potential safety issues.  ...  She is supported by an NHMRC Career Development Fellowship (2; #1108125).  ... 
doi:10.1159/000502652 pmid:31480057 fatcat:4m64wbz5xrekllpsys2fqyhvee

Total Fructose Intake and Risk of Hypertension: A Systematic Review and Meta-Analysis of Prospective Cohorts

Viranda H. Jayalath, John L. Sievenpiper, Russell J. de Souza, Vanessa Ha, Arash Mirrahimi, Ingrid D. Santaren, Sonia Blanco Mejia, Marco Di Buono, Alexandra L. Jenkins, Lawrence A. Leiter, Thomas M. S. Wolever, Joseph Beyene (+2 others)
2014 Journal of the American College of Nutrition  
To quantify the association between fructose-containing sugar (high-fructose corn syrup, sucrose, and fructose) intake and incident hypertension, a systematic review and meta-analysis of prospective cohort  ...  Two independent reviewers reviewed and extracted relevant data.  ...  cells, endothelial dysfunction, and the renin-angiotensin system [9] .  ... 
doi:10.1080/07315724.2014.916237 pmid:25144126 pmcid:PMC4261182 fatcat:powkf2lyqrh2lmdebmfugiqmx4
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