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https://www.readbyqxmd.com/read/29040639/the-medical-science-dmz-a-network-design-pattern-for-data-intensive-medical-science
#1
Sean Peisert, Eli Dart, William Barnett, Edward Balas, James Cuff, Robert L Grossman, Ari Berman, Anurag Shankar, Brian Tierney
Objective: We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods: High-end networking, packet-filter firewalls, network intrusion-detection systems. Results: We describe a "Medical Science DMZ" concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs...
October 6, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28990311/comprehensive-data-of-3-820-patients-newly-diagnosed-with-colorectal-liver-metastasis-between-2005-and-2007-report-of-a-nationwide-survey-in-japan
#2
Katsunori Sakamoto, Goro Honda, Toru Beppu, Kenjiro Kotake, Masakazu Yamamoto, Keiichi Takahashi, Itaru Endo, Kiyoshi Hasegawa, Michio Itabashi, Yojiro Hashiguchi, Yoshihito Kotera, Shin Kobayashi, Tatsuro Yamaguchi, Satoshi Morita, Masaru Miyazaki, Kenichi Sugihara
To collect big data for further research to improve treatment outcomes in patients with colorectal liver metastasis (CRLM), the Joint Committee for Nationwide Survey on Colorectal Liver Metastasis was established by the Japanese Society for Cancer of the Colon and Rectum and the Japanese Society of Hepato-Biliary-Pancreatic Surgery. The joint committee initiated data collection since 2014. The data of 4,237 patients newly diagnosed with CRLM between 2005 and 2007 were registered from 134 departments of 127 institutions (64%) among 209 departments (from 201 institutions) that agreed to participate in this study...
October 9, 2017: Journal of Hepato-biliary-pancreatic Sciences
https://www.readbyqxmd.com/read/28984189/the-international-conference-on-intelligent-biology-and-medicine-icibm-2016-from-big-data-to-big-analytical-tools
#3
EDITORIAL
Zhandong Liu, W Jim Zheng, Genevera I Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao
The 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held on December 8-10, 2016 in Houston, Texas, USA. ICIBM included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics on 3D genomics structural analysis, next generation sequencing (NGS) analysis, computational drug discovery, medical informatics, cancer genomics, and systems biology. Here, we present a summary of the nine research articles selected from ICIBM 2016 program for publishing in BMC Bioinformatics...
October 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28983483/a-comprehensive-infrastructure-for-big-data-in-cancer-research-accelerating-cancer-research-and-precision-medicine
#4
Izumi V Hinkson, Tanja M Davidsen, Juli D Klemm, Anthony R Kerlavage, Warren A Kibbe
Advancements in next-generation sequencing and other -omics technologies are accelerating the detailed molecular characterization of individual patient tumors, and driving the evolution of precision medicine. Cancer is no longer considered a single disease, but rather, a diverse array of diseases wherein each patient has a unique collection of germline variants and somatic mutations. Molecular profiling of patient-derived samples has led to a data explosion that could help us understand the contributions of environment and germline to risk, therapeutic response, and outcome...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28975931/patient-reported-outcomes-in-cancer-care-hearing-the-patient-voice-at-greater-volume
#5
REVIEW
Thomas W LeBlanc, Amy P Abernethy
Recording of patient-reported outcomes (PROs) enables direct measurement of the experiences of patients with cancer. In the past decade, the use of PROs has become a prominent topic in health-care innovation; this trend highlights the role of the patient experience as a key measure of health-care quality. Historically, PROs were used solely in the context of research studies, but a growing body of literature supports the feasibility of electronic collection of PROs, yielding reliable data that are sometimes of better quality than clinician-reported data...
October 4, 2017: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/28974484/effects-of-the-ambient-fine-particulate-matter-on-public-awareness-of-lung-cancer-risk-in-china-evidence-from-the-internet-based-big-data-platform
#6
Hongxi Yang, Shu Li, Li Sun, Xinyu Zhang, Jie Hou, Yaogang Wang
BACKGROUND: In October 2013, the International Agency for Research on Cancer classified the particulate matter from outdoor air pollution as a group 1 carcinogen and declared that particulate matter can cause lung cancer. Fine particular matter (PM2.5) pollution is becoming a serious public health concern in urban areas of China. It is essential to emphasize the importance of the public's awareness and knowledge of modifiable risk factors of lung cancer for prevention. OBJECTIVE: The objective of our study was to explore the public's awareness of the association of PM2...
October 3, 2017: JMIR Public Health and Surveillance
https://www.readbyqxmd.com/read/28969540/recent-advances-in-the-development-of-pharmaceutical-agents-for-metabolic-disorders-a-computational-perspective
#7
Sridhara Janardhan, Varvara Konova, Alexey Lagunin, Venkateswara Rao, Narahari Sastry, Vladimir Poroikov
BACKGROUND: Metabolic disorders comprise a set of different disorders varying from epidemic diseases such as diabetes mellitus to inborn metabolic orphan diseases such as phenylketonuria. Despite considerable evidence showing the importance of the computational methods in discovery and development of new pharmaceuticals, there are no systematic reviews outlining how they are utilized in the field of metabolic disorders. This review aims to discuss the necessity of the development of web-based tools and databases by integration of available information for solving Big Data problems in network pharmacology of metabolic disorders...
October 2, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28968302/a-conversation-about-hormone-therapy-is-there-an-appropriate-dose-route-and-duration-of-use
#8
(no author information available yet)
The North American Menopause Society (NAMS) held the 3rd Utian Translational Symposium on October 4, 2016, in Orlando, Florida, to answer questions about the benefits and risks of hormone therapy (HT) for postmenopausal women. This report is a record of the proceedings of that symposium.The maxim about HT for the past 15 years since the publication of the initial results of the Women's Health Initiative (WHI) has been to prescribe the "lowest dose for the shortest period of time." With new clinical trials, observational data, and further analysis of the WHI and the cumulative 13 years' follow-up, it was time to hold a conversation about the state of the evidence and recommendations for HT dose, route, and duration of use...
October 2, 2017: Menopause: the Journal of the North American Menopause Society
https://www.readbyqxmd.com/read/28954976/precision-cancer-medicine-and-super-computing-system
#9
Toshifumi Wakai
Precision Cancer Medicine: Tumors are classified into several molecular subtypes by Genomic Sequencing. Comprehensive targeted-gene panel provides more therapeutic options. CANCERPLEX-JP version 4.0 includes 435 actionable genes, which clinical approaches are available. Utilizing the gene panel platform, we assessed the genes and pathways most frequently altered in Japanese and US cases (Genome Med 2016;8:136). We demonstrate concordance of CANCERPLEX-JP with whole-exome sequencing from the TCGA in identifying hypermutated samples and microsatellite instability in multiple cancer types, such as colorectal and gastric cancer...
2017: Keio Journal of Medicine
https://www.readbyqxmd.com/read/28925997/precision-annotation-of-digital-samples-in-ncbi-s-gene-expression-omnibus
#10
Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D Azad, Mohamad O Hadied, Shuaib Raza, Benjamin Abhishek Rayikanti, Bin Chen, Hyojung Paik, Dvir Aran, Jordan Spatz, Daniel Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A Musen, Atul J Butte
The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. We introduce the Search Tag Analyze Resource for GEO as a web application (http://STARGEO.org) to curate better annotations of sample phenotypes uniformly across different studies, and to use these sample annotations to define robust genomic signatures of disease pathology by meta-analysis...
September 19, 2017: Scientific Data
https://www.readbyqxmd.com/read/28918048/mir-133a-promotes-trail-resistance-in-glioblastoma-via-suppressing-death-receptor-5-and-activating-nf-%C3%AE%C2%BAb-signaling
#11
Shan-Shan Wang, Lu Feng, Bao-Guang Hu, Ying-Fei Lu, Wei-Mao Wang, Wei Guo, Chun-Wai Suen, Bao-Hua Jiao, Jian-Xin Pang, Wei-Ming Fu, Jin-Fang Zhang
Recombinant tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), as a novel cancer therapeutic, is being tested in phase II and III clinical trials; however, TRAIL resistance remains a big obstacle preventing its clinical application. Considering that TRAIL-induced apoptosis through death receptors DR4 and DR5, their activation may be an alternative pathway to suppress TRAIL resistance. In this study, a negative correlation between DR5 expression and TRAIL resistance was observed, and miR-133a was predicted to be the most promising candidate to suppress DR5 expression...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28886003/functional-precision-cancer-medicine-moving-beyond-pure-genomics
#12
Anthony Letai
The essential job of precision medicine is to match the right drugs to the right patients. In cancer, precision medicine has been nearly synonymous with genomics. However, sobering recent studies have generally shown that most patients with cancer who receive genomic testing do not benefit from a genomic precision medicine strategy. Although some call the entire project of precision cancer medicine into question, I suggest instead that the tools employed must be broadened. Instead of relying exclusively on big data measurements of initial conditions, we should also acquire highly actionable functional information by perturbing-for example, with cancer therapies-viable primary tumor cells from patients with cancer...
September 8, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28877694/assembling-and-validating-data-from-multiple-sources-to-study-care-for-veterans-with-bladder-cancer
#13
Florian R Schroeck, Brenda Sirovich, John D Seigne, Douglas J Robertson, Philip P Goodney
BACKGROUND: Despite the high prevalence of bladder cancer, research on optimal bladder cancer care is limited. One way to advance observational research on care is to use linked data from multiple sources. Such big data research can provide real-world details of care and outcomes across a large number of patients. We assembled and validated such data including (1) administrative data from the Department of Veterans Affairs (VA), (2) Medicare claims, (3) data abstracted by tumor registrars, (4) data abstracted via chart review from the national electronic health record, and (5) full text pathology reports...
September 6, 2017: BMC Urology
https://www.readbyqxmd.com/read/28873265/dyadic-effects-of-coping-strategies-time-perspectives-and-personality-on-the-quality-of-life-of-cancer-patients-and-their-caregivers
#14
Zeinab Hamidou, Pascal Auquier, Tanguy Leroy, Fabrice Barlesi, Sébastien Salas, Olivier Chinot, Karine Baumstarck
OBJECTIVE: Researchers are interested in studying whether the quality of life (QoL) of cancer patients and caregivers is influenced by internal psycho-behavioral processes (temporality and coping strategies) and the personality traits that they or their relatives experience. We examined these associations in a sample of patient-caregiver dyads using the actor-partner interdependence model (APIM). METHODS: This cross-sectional study involved 156 cancer patient-caregiver dyads...
September 5, 2017: Psycho-oncology
https://www.readbyqxmd.com/read/28840365/radiology-and-enterprise-medical-imaging-extensions-remix
#15
Barbaros S Erdal, Luciano M Prevedello, Songyue Qian, Mutlu Demirer, Kevin Little, John Ryu, Thomas O'Donnell, Richard D White
Radiology and Enterprise Medical Imaging Extensions (REMIX) is a platform originally designed to both support the medical imaging-driven clinical and clinical research operational needs of Department of Radiology of The Ohio State University Wexner Medical Center. REMIX accommodates the storage and handling of "big imaging data," as needed for large multi-disciplinary cancer-focused programs. The evolving REMIX platform contains an array of integrated tools/software packages for the following: (1) server and storage management; (2) image reconstruction; (3) digital pathology; (4) de-identification; (5) business intelligence; (6) texture analysis; and (7) artificial intelligence...
August 24, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/28837592/development-and-validation-of-a-set-of-six-adaptable-prognosis-prediction-sap-models-based-on-time-series-real-world-big-data-analysis-for-patients-with-cancer-receiving-chemotherapy-a-multicenter-case-crossover-study
#16
Yu Uneno, Kei Taneishi, Masashi Kanai, Kazuya Okamoto, Yosuke Yamamoto, Akira Yoshioka, Shuji Hiramoto, Akira Nozaki, Yoshitaka Nishikawa, Daisuke Yamaguchi, Teruko Tomono, Masahiko Nakatsui, Mika Baba, Tatsuya Morita, Shigemi Matsumoto, Tomohiro Kuroda, Yasushi Okuno, Manabu Muto
BACKGROUND: We aimed to develop an adaptable prognosis prediction model that could be applied at any time point during the treatment course for patients with cancer receiving chemotherapy, by applying time-series real-world big data. METHODS: Between April 2004 and September 2014, 4,997 patients with cancer who had received systemic chemotherapy were registered in a prospective cohort database at the Kyoto University Hospital. Of these, 2,693 patients with a death record were eligible for inclusion and divided into training (n = 1,341) and test (n = 1,352) cohorts...
2017: PloS One
https://www.readbyqxmd.com/read/28836909/random-forest
#17
Steven J Rigatti
For the task of analyzing survival data to derive risk factors associated with mortality, physicians, researchers, and biostatisticians have typically relied on certain types of regression techniques, most notably the Cox model. With the advent of more widely distributed computing power, methods which require more complex mathematics have become increasingly common. Particularly in this era of "big data" and machine learning, survival analysis has become methodologically broader. This paper aims to explore one technique known as Random Forest...
2017: Journal of Insurance Medicine
https://www.readbyqxmd.com/read/28782717/in-silico-approaches-for-unveiling-novel-glycobiomarkers-in-cancer
#18
Rita Azevedo, André M N Silva, Celso A Reis, Lúcio Lara Santos, José Alexandre Ferreira
Glycosylation is one of the most common and dynamic post-translational modification of cell surface and secreted proteins. Cancer cells display unique glycosylation patterns that decisively contribute to drive oncogenic behavior, including disease progression and dissemination. Moreover, alterations in glycosylation are often responsible for the creation of protein signatures holding significant biomarker value and potential for targeted therapeutics. Accordingly, many analytical protocols have been outlined for the identification of abnormally glycosylated proteins by mass spectrometry...
August 4, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28774262/parallel-multiple-instance-learning-for-extremely-large-histopathology-image-analysis
#19
Yan Xu, Yeshu Li, Zhengyang Shen, Ziwei Wu, Teng Gao, Yubo Fan, Maode Lai, Eric I-Chao Chang
BACKGROUND: Histopathology images are critical for medical diagnosis, e.g., cancer and its treatment. A standard histopathology slice can be easily scanned at a high resolution of, say, 200,000×200,000 pixels. These high resolution images can make most existing imaging processing tools infeasible or less effective when operated on a single machine with limited memory, disk space and computing power. RESULTS: In this paper, we propose an algorithm tackling this new emerging "big data" problem utilizing parallel computing on High-Performance-Computing (HPC) clusters...
August 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28767418/cancer-specific-evaluation-system-canes-a-high-accuracy-platform-for-preclinical-single-multi-biomarker-discovery
#20
Min-Seok Kwon, Seungyoon Nam, Sungyoung Lee, Young Zoo Ahn, Hae Ryung Chang, Yon Hui Kim, Taesung Park
The recent creation of enormous, cancer-related "Big Data" public depositories represents a powerful means for understanding tumorigenesis. However, a consistently accurate system for clinically evaluating single/multi-biomarkers remains lacking, and it has been asserted that oft-failed clinical advancement of biomarkers occurs within the very early stages of biomarker assessment. To address these challenges, we developed a clinically testable, web-based tool, CANcer-specific single/multi-biomarker Evaluation System (CANES), to evaluate biomarker effectiveness, across 2,134 whole transcriptome datasets, from 94,147 biological samples (from 18 tumor types)...
July 15, 2017: Oncotarget
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