iCOD : an integrated clinical omics database based on the systems-pathology view of disease

<p>Abstract</p> <p>Background</p> <p>Variety of information relating between genome and the pathological findings in disease will yield a wealth of clues to discover new function, the role of genes and pathways, and future medicine. In addition to molecular information such as gene expression and genome copy number, detailed clinical information is essential for such systematic omics analysis.</p> <p>Results</p> <p>In order to provide a basic platform to realize a future medicine based on the integration of molecular and clinico-pathological information of disease, we have developed an integrated clinical omics database (iCOD) in which comprehensive disease information of the patients is collected, including not only molecular omics data such as CGH (Comparative Genomic Hybridization) and gene expression profiles but also comprehensive clinical information such as clinical manifestations, medical images (CT, X-ray, ultrasounds, etc), laboratory tests, drug histories, pathological findings and even life-style/environmental information. The iCOD is developed to combine the molecular and clinico-pathological information of the patients to provide the holistic understanding of the disease. Furthermore, we developed several kinds of integrated view maps of disease in the iCOD, which summarize the comprehensive patient data to provide the information for the interrelation between the molecular omics data and clinico-pathological findings as well as estimation for the disease pathways, such as three layer-linked disease map, disease pathway map, and pathome-genome map.</p> <p>Conclusions</p> <p>With these utilities, our iCOD aims to contribute to provide the omics basis of the disease as well as to promote the pathway-directed disease view. The iCOD database is available online, containing 140 patient cases of hepatocellular carcinoma, with raw data of each case as supplemental data set to download. The iCOD and supplemental data can be accessed at</p> <p><url>http://omics.tmd.ac.jp/icod_pub_eng</url></p

Portable Electrochemical Gas Sensing System with a Paper-Based Enzyme Electrode

An unconventional portable electrochemical gas sensor composed of a smartphone, a finger-sized sensing chip and a single use paper-based enzyme electrode was proposed to detect a particular target gaseous inclusion for self-breath-analysis with ease. This attempt allowed us to monitor our physical status immediately and continuously regardless of a time, place or person due to the improved convenience, immediacy, and affordability. The custom CMOS chip with the capability of performing an amperometric determination when the power voltage supplied from the earphone jack of a smartphone was designed as an analytical device. A disposable enzyme electrode was prepared simply from a chromatography paper and a commercial carbon pencil instead of the conventional indisposable material and complex manufacturing process. The quantification of ethanol in gaseous samples was demonstrated in range from 50 to 500ppm (V/V) in accord with concentrations in exhaled breath. The response current increased linearly with increasing vapor ethanol concentration

Portable Electrochemical Sensing System Attached to Smartphones and Its Incorporation with Paper-based Electrochemical Glucose Sensor

This paper described the development of a small and low cost biosensor consisting of a smartphone-based electrochemical biosensor device and a paper-based biosensor. The device harvested power from the smartphone and transferred data through audio jack. We designed CMOS circuits including a power supply circuit, a potentiostat, and a ΔΣ modulator. The fabrication of a paper-based biosensor was simple: the three electrodes were directly drawn on chromatography paper using a carbon pencil. The paper-based biosensor was low cost, disposable, portable and friendly to the environment. The sensing system was designed to perform the chronoamperometry measurement, and the glucose concentration in a liquid specimen was detected. Results showed that the sensing system was capable of measuring the glucose concentration as precisely as expensive equipments

Practical Electrochemical Anodic Oxidation of Polycyclic Lactams for Late Stage Functionalization

Electrochemistry provides a powerful tool for the late-stage functionalization of complex lactams. A two-stage protocol for converting lactams, many of which can be prepared through the intramolecular Schmidt reaction of keto azides, is presented. In the first step, anodic oxidation in MeOH using a repurposed power source provides a convenient route to lactams bearing a methoxy group adjacent to nitrogen. Treatment of these intermediates with a Lewis acid in dichloromethane permits the regeneration of a reactive acyliminium ion that is then reacted with a range of nucleophilic species

Detection of Radical Species after Plateau Carbon-Ion Irradiation to Lipid Molecules

Carbon-ion (C-ion) beams are known to exhibit a sharp maximum of the energy deposition, called as a Bragg peak, at a certain penetration depth. Thus, the cancer cells are precisely killed by adjusting the Bragg peak to a tumor. However, the dose in the plateau region of the C-ion beams before the Bragg peak is not necessarily zero. Thus, the quantitative evaluation of changes in the redox state induced by the plateau C-ion beams is considerable importance to eliminate the adverse effects of radiation therapy on normal tissues adjacent to the tumor. We have recently demonstrated that isopropyl myristate (IPM), one of lipid molecules, is more susceptible to the plateau C-ion beams than to X-rays using 2,2-diphenyl-1-picrylhydrazyl radical used as a redox probe. In this study, the effect of the plateau C-ion beams on lipid molecules was further investigated by 2,2,6-trimethyl-4-(4-nitrobenzo[1,2,5]oxadiazol-7-ylamino)-6-pentylpiperidine-1-oxyl (NBD-Pen), a highly selective fluorescence probe for lipid radicals with high sensitivity. NBD-Pen reacts with the lipid radicals generated by the oxidation of lipid molecules to form highly fluorescent radical adducts. IPM solutions of NBD-Pen (5.0 µM) were irradiated by the plateau C-ion beams (290 MeV, 13 keV/µm) using the Heavy Ion Medical Accelerator in Chiba (HIMAC) at room temperature. An increase in fluorescence intensity at 509 nm was observed for the IPM solutions of NBD-Pen after the C-ion irradiation (5, 10, 15, 20, and 30 Gy) on a Shimadzu RF-5300PC spectrofluorophotometer. This indicates that radical species were generated by the C-ion irradiation to IPM. The fluorescence intensity increased with an increase in the radiation dose and reached its maximum value around at 10 Gy. The effect of the plateau C-ion beams on the lipid oxidation will be discussed as compared to that of X-rays based on the results obtained in this study.16th International Congress of Radiation Research (ICRR 2019