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https://www.readbyqxmd.com/read/28335044/semi-automated-de-identification-of-german-content-sensitive-reports-for-big-data-analytics
#1
Hannes Seuss, Peter Dankerl, Matthias Ihle, Andrea Grandjean, Rebecca Hammon, Nicola Kaestle, Peter A Fasching, Christian Maier, Jan Christoph, Martin Sedlmayr, Alexander Cavallaro, Matthias Hammon
Purpose Projects involving collaborations between different institutions require data security via selective de-identification of words or phrases. A semi-automated de-identification tool was developed and evaluated on different types of medical reports natively and after adapting the algorithm to the text structure. Materials and Methods A semi-automated de-identification tool was developed and evaluated for its sensitivity and specificity in detecting sensitive content in written reports. Data from 4671 pathology reports (4105 + 566 in two different formats), 2804 medical reports, 1008 operation reports, and 6223 radiology reports of 1167 patients suffering from breast cancer were de-identified...
March 23, 2017: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
https://www.readbyqxmd.com/read/28326610/dose-and-temporal-evaluation-of-ethylene-oxide-induced-mutagenicity-in-the-lungs-of-male-big-blue-mice-following-inhalation-exposure-to-carcinogenic-concentrations
#2
Mugimane G Manjanatha, Sharon D Shelton, Ying Chen, Barbara L Parsons, Meagan B Myers, Karen L McKim, B Bhaskar Gollapudi, Nigel P Moore, Lynne T Haber, Bruce Allen, Martha M Moore
Ethylene oxide (EO) is a direct acting alkylating agent; in vitro and in vivo studies indicate that it is both a mutagen and a carcinogen. However, it remains unclear whether the mode of action (MOA) for cancer for EO is a mutagenic MOA, specifically via point mutation. To investigate the MOA for EO-induced mouse lung tumors, male Big Blue (BB) B6C3F1 mice (10/group) were exposed to EO by inhalation, 6 hr/day, 5 days/week for 4 (0, 10, 50, 100, or 200 ppm EO), 8, or 12 weeks (0, 100, or 200 ppm EO). Lung DNA samples were analyzed for cII mutant frequency (MF) at 4, 8 and 12 weeks of exposure; the mutation spectrum was analyzed for mutants from control and 200 ppm EO treatments...
March 22, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28316892/from-big-data-to-diagnosis-and-prognosis-gene-expression-signatures-in-liver-hepatocellular-carcinoma
#3
Hong Yang, Xin Zhang, Xiao-Yong Cai, Dong-Yue Wen, Zhi-Hua Ye, Liang Liang, Lu Zhang, Han-Lin Wang, Gang Chen, Zhen-Bo Feng
BACKGROUND: Liver hepatocellular carcinoma accounts for the overwhelming majority of primary liver cancers and its belated diagnosis and poor prognosis call for novel biomarkers to be discovered, which, in the era of big data, innovative bioinformatics and computational techniques can prove to be highly helpful in. METHODS: Big data aggregated from The Cancer Genome Atlas and Natural Language Processing were integrated to generate differentially expressed genes...
2017: PeerJ
https://www.readbyqxmd.com/read/28287094/enlightening-discriminative-network-functional-modules-behind-principal-component-analysis-separation-in-differential-omic-science-studies
#4
Sara Ciucci, Yan Ge, Claudio Durán, Alessandra Palladini, Víctor Jiménez-Jiménez, Luisa María Martínez-Sánchez, Yuting Wang, Susanne Sales, Andrej Shevchenko, Steven W Poser, Maik Herbig, Oliver Otto, Andreas Androutsellis-Theotokis, Jochen Guck, Mathias J Gerl, Carlo Vittorio Cannistraci
Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28281147/molecular-tumor-boards-ethical-issues-in-the-new-era-of-data-medicine
#5
Henri-Corto Stoeklé, Marie-France Mamzer-Bruneel, Charles-Henry Frouart, Christophe Le Tourneau, Pierre Laurent-Puig, Guillaume Vogt, Christian Hervé
The practice and development of modern medicine requires large amounts of data, particularly in the domain of cancer. The future of personalized medicine lies neither with "genomic medicine" nor with "precision medicine", but with "data medicine" (DM) (big data, data mining). The establishment of this DM has required far-reaching changes, to establish four essential elements connecting patients and doctors: biobanks, databases, bioinformatic platforms and genomic platforms. The "transformation" of scientific research areas, such as genetics, bioinformatics and biostatistics, into clinical specialties has generated a new vision of care...
March 9, 2017: Science and Engineering Ethics
https://www.readbyqxmd.com/read/28279424/cardio-oncology-the-role-of-big-data
#6
REVIEW
Anant Mandawat, Andrew E Williams, Sanjeev A Francis
Despite its challenges, a "big data" approach offers a unique opportunity within the field of cardio-oncology. A pharmacovigilant approach using large data sets can help characterize cardiovascular toxicities of the rapidly expanding armamentarium of targeted therapies. Creating a broad coalition of data sharing can provide insights into the incidence of cardiotoxicity and stimulate research into the underlying mechanisms. Population health necessitates the use of big data and can help inform public health interventions to prevent both cancer and cardiovascular disease...
April 2017: Heart Failure Clinics
https://www.readbyqxmd.com/read/28273479/systems-biology-of-metabolism-a-driver-for-developing-personalized-and-precision-medicine
#7
REVIEW
Jens Nielsen
Systems biology uses mathematical models to analyze large datasets and simulate system behavior. It enables integrative analysis of different types of data and can thereby provide new insight into complex biological systems. Here will be discussed the challenges of using systems medicine for advancing the development of personalized and precision medicine to treat metabolic diseases like insulin resistance, obesity, NAFLD, NASH, and cancer. It will be illustrated how the concept of genome-scale metabolic models can be used for integrative analysis of big data with the objective of identifying novel biomarkers that are foundational for personalized and precision medicine...
March 7, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28265786/precision-medicine-driven-by-cancer-systems-biology
#8
Fabian V Filipp
Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research community has identified distinct subtypes involving chronic sun-induced damage and the mitogen-activated protein kinase driver pathway. In addition, despite low mutation burden, non-genomic mitogen-activated protein kinase melanoma drivers are found in membrane receptors, metabolism, or epigenetic signaling with the ability to bypass central mitogen-activated protein kinase molecules and activating a similar program of mitogenic effectors...
March 7, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28255369/prostate-cancer-between-prognosis-and-adequate-proper-therapy
#9
REVIEW
T Grozescu, F Popa
Knowing the indolent, non-invasive nature of most types of prostate cancer, as well as the simple fact that the disease seems more likely to be associated with age rather than with other factors (50% of men at the age of 50 and 80% at the age of 80 have it [1], with or without presenting any symptom), the big challenge of this clinical entity was to determine severity indicators (so far insufficient) to guide the physician towards an adequate attitude in the clinical setting. The risk of over-diagnosing and over-treating many prostate cancer cases (indicated by all the major European and American studies) is real and poses many question marks...
January 2017: Journal of Medicine and Life
https://www.readbyqxmd.com/read/28226351/-significance-and-contemplation-of-clinical-diagnosis-and-therapy-on-the-renewal-of-the-eighth-edition-of-gastric-cancer-tnm-staging-system
#10
Hongqing Xi, Kecheng Zhang, Bo Wei, Lin Chen
TNM staging is essential for clinical decision-making and prognostic prediction for patients with gastric cancer. The 7th TNM staging manual was formulated in 2009 and implemented in 2010. However, it was published that there were some deficiencies of the 7th edition of gastric cancer TNM staging system in clinical application process, and this old staging system could not meet the clinical needs. With the cooperation and promotion of the American Joint Committee on Cancer (AJCC), the International Union for Cancer Control (UICC) and the International Gastric Cancer Association (IGCA), and through the accumulation and analysis of gastric cancer big data, the 8th TNM staging system was published at the end of 2016...
February 25, 2017: Zhonghua Wei Chang Wai Ke za Zhi, Chinese Journal of Gastrointestinal Surgery
https://www.readbyqxmd.com/read/28215665/11-years-follow-up-of-trastuzumab-after-adjuvant-chemotherapy-in-her2-positive-early-breast-cancer-final-analysis-of-the-herceptin-adjuvant-hera-trial
#11
David Cameron, Martine J Piccart-Gebhart, Richard D Gelber, Marion Procter, Aron Goldhirsch, Evandro de Azambuja, Gilberto Castro, Michael Untch, Ian Smith, Luca Gianni, Jose Baselga, Nedal Al-Sakaff, Sabine Lauer, Eleanor McFadden, Brian Leyland-Jones, Richard Bell, Mitch Dowsett, Christian Jackisch
BACKGROUND: Clinical trials have shown that trastuzumab, a recombinant monoclonal antibody against HER2 receptor, significantly improves overall survival and disease-free survival in women with HER2-positive early breast cancer, but long-term follow-up data are needed. We report the results of comparing observation with two durations of trastuzumab treatment at a median follow-up of 11 years, for patients enrolled in the HERA (HERceptin Adjuvant) trial. METHODS: HERA (BIG 1-01) is an international, multicentre, open-label, phase 3 randomised trial of 5102 women with HER2-positive early breast cancer, who were enrolled from hospitals in 39 countries between Dec 7, 2001, and June 20, 2005...
February 16, 2017: Lancet
https://www.readbyqxmd.com/read/28187294/comprehensible-knowledge-model-creation-for-cancer-treatment-decision-making
#12
Muhammad Afzal, Maqbool Hussain, Wajahat Ali Khan, Taqdir Ali, Sungyoung Lee, Eui-Nam Huh, Hafiz Farooq Ahmad, Arif Jamshed, Hassan Iqbal, Muhammad Irfan, Manzar Abbas Hydari
BACKGROUND: A wealth of clinical data exists in clinical documents in the form of electronic health records (EHRs). This data can be used for developing knowledge-based recommendation systems that can assist clinicians in clinical decision making and education. One of the big hurdles in developing such systems is the lack of automated mechanisms for knowledge acquisition to enable and educate clinicians in informed decision making. MATERIALS AND METHODS: An automated knowledge acquisition methodology with a comprehensible knowledge model for cancer treatment (CKM-CT) is proposed...
March 1, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28163155/next-generation-sequencing-big-data-meets-high-performance-computing
#13
REVIEW
Bertil Schmidt, Andreas Hildebrandt
The progress of next-generation sequencing has a major impact on medical and genomic research. This high-throughput technology can now produce billions of short DNA or RNA fragments in excess of a few terabytes of data in a single run. This leads to massive datasets used by a wide range of applications including personalized cancer treatment and precision medicine. In addition to the hugely increased throughput, the cost of using high-throughput technologies has been dramatically decreasing. A low sequencing cost of around US$1000 per genome has now rendered large population-scale projects feasible...
February 2, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28162205/-calm-thinking-for-precision-medicine-of-breast-cancer-in-the-boom
#14
Z F Jiang, F R Xu
In the past two years, researchers have been exploring the precision medicine. Thanks to the development of sequence industry and clinical study, the big data about the precision medicine have been more and more sufficient. However, how to deal with the precision data is still a question for clinicians. We focus on the hot issues that disturb clinicians most, wanting to help them to make suitable decisions between the traditional and precision medicine of breast cancer. We believe the precision medicine is on the way...
February 1, 2017: Zhonghua Wai Ke za Zhi [Chinese Journal of Surgery]
https://www.readbyqxmd.com/read/28154510/multiple-group-testing-procedures-for-analysis-of-high-dimensional-genomic-data
#15
Hyoseok Ko, Kipoong Kim, Hokeun Sun
In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28148207/clinical-cancer-advances-2017-annual-report-on-progress-against-cancer-from-the-american-society-of-clinical-oncology
#16
Harold J Burstein, Lada Krilov, Jeanny B Aragon-Ching, Nancy N Baxter, E Gabriela Chiorean, Warren Allen Chow, John Frederick De Groot, Steven Michael Devine, Steven G DuBois, Wafik S El-Deiry, Andrew S Epstein, John Heymach, Joshua Adam Jones, Deborah K Mayer, Rebecca A Miksad, Nathan A Pennell, Michael S Sabel, Richard L Schilsky, Lynn Mara Schuchter, Nadine Tung, Karen Marie Winkfield, Lori J Wirth, Don S Dizon
A MESSAGE FROM ASCO'S PRESIDENT I am pleased to present Clinical Cancer Advances 2017, which highlights the most promising advances in patient-oriented cancer research over the past year. The report gives us an opportunity to reflect on what an exciting time it is for cancer research and how swiftly our understanding of cancer has improved. One year ago, the White House announced the national Cancer Moonshot program to accelerate progress against cancer. This shared vision of progress has reinvigorated the research community, identified new areas of scientific collaboration, and raised our ambitions regarding what may be possible beyond the progress we have already made...
February 1, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28118106/qualitative-study-of-oncologists-views-on-the-cancerlinq-rapid-learning-system
#17
Rachel M Mayo, Julie F Summey, Joel E Williams, Rebecca A Spence, Shally Kim, Reshma Jagsi
INTRODUCTION: ASCO is actively developing CancerLinQ (CLQ), a rapid learning system for oncology care. The purpose of this study was to explore providers' opinions and concerns related to implementation of CLQ, including ethical issues. METHODS: Twenty key informant oncologists were recruited for individual in-depth interviews through ASCO contacts, purposively selected to represent a wide variety of cancer specialties as well as different levels of familiarity with CLQ (familiar v unfamiliar)...
March 2017: Journal of Oncology Practice
https://www.readbyqxmd.com/read/28113782/cancer-subtype-discovery-based-on-integrative-model-of-multigenomic-data
#18
Shu-Guang Ge, Junfeng Xia, Wen Sha, Chun-Hou Zheng
One major goal of large-scale cancer omics study is to understand molecular mechanisms of cancer and find new biomedical targets. To deal with the high-dimensional multidimensional cancer omics data (DNA methylation, mRNA expression, etc.), which can be used to discover new insight on identifying cancer subtypes, clustering methods are usually used to find an effective low-dimensional subspace of the original data and then cluster cancer samples in the reduced subspace. However, due to data-type diversity and big data volume, few methods can integrate these data and map them into an effective low-dimensional subspace...
October 26, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28113169/the-case-for-big-data-new-york-city-s-kalvi-human-project-aims-to-use-big-data-in-resolving-big-health-questions
#19
Leslie Mertz
Cigarette smoking is tied to lung cancer, but people still smoke. Why do people start smoking in the first place? That is one of the many complex, interdisciplinary questions behind the Kavli HUMAN Project (http://kavlihumanproject.org), a massive data-collection endeavor with the goal of learning how everything-from biology to behavior and environment-affects the human condition.
September 2016: IEEE Pulse
https://www.readbyqxmd.com/read/28111421/combined-approaches-using-adverse-outcome-pathways-and-big-data-to-find-potential-diseases-associated-with-humidifier-disinfectant
#20
Jong-Han Leem, Kyu Hyuck Chung
According to previous survey, about two million of people were expected to suffer from toxic effects due to humidifier disinfectant (HD), regardless of healing or not. Extremely small group are recognized as HDs' victims. Up to now, previous research tried to focus on interstitial fibrosis on terminal bronchiole because it is specific finding, compared with other diseases. To figure out overall effects from HDs, we recommend adverse outcome pathways (AOPs) as new approach. Reactive oxygen species (ROS) generation, decreased T-cell and pro-inflammatory cytokine release from macrophage could be key events between the exposure to HDs and diseases...
2016: Environmental Health and Toxicology
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