ICTBioMed NCIP Science Gateway: A Hub for Collaborative Cancer Research

<div><div><i><br></i></div><div><i>Cancer is a leading cause of morbidity and mortality worldwide according to the World Health Organization and it imposes a big challenge for the researchers and the scientific community. Complex problems like cancer cannot be solved by a single research institute by using traditional methods. The fight against cancer requires the collaborative efforts of multidisciplinary institutes and research labs across the countries. The collaborative efforts should be augmented with the support of high-performance computing and databases by providing a common platform for integrated research. The National Cancer Informatics Program (NCIP) launched by National Institutes of Health (NIH) supports biomedical informatics in cancer research. NCIP offers among other resources the NCIP Hub, a science gateway for helping to accelerate innovation in the cancer research community. NCIP Hub is based on the science gateway framework HUBzero® and allows for creation of projects sharing data and running data analysis with different tools such as 3D Slicer, an open source software platform for medical image informatics, image processing, and three-dimensional visualization.</i></div><div><i>The ICTBioMed (International Consortium for Technology in Biomedicine) consortium applies the NCIP Hub to combine efforts of a variety of knowledge and expertise benefiting the cancer research. ICTBioMed is a consortium of domain researchers, experts in high-performance computing centers and organizations concerned with applications in health informatics. Members include OHSL (Open Health Systems Laboratory), USA; C-DAC (Centre for Development of Advanced Computing), Pune, India; PSNC (Poznan Supercomputing and Networking Center), Poznan, Poland; the University of Notre Dame Center for Research Computing, Notre Dame, USA; Chalmers University Life Sciences Supercomputing Networking Center, Gothenburg, Sweden and Internet2, USA. Additionally, experts from Arizona State University's Computational Sciences and Complex Adaptive Systems Initiative; Duke Comprehensive Cancer Center and Tata Memorial Center in India are also involved. The ICTBioMed team is working with the HUBzero® team of Purdue University for implementing a Docker [9] execution host model, which integrates into the HUBzero® platform. ICTBioMed has created Docker containers with pre-configured workflows used by cancer researchers. Example data sets are included in the Docker container for the proof of concept and the prototype for testing these Docker containers is underway.</i></div><div><i>The enhancement will provide a seamless approach for execution of cancer-related workflows and will be available to all projects in the NCIP Hub. The science gateway opens new avenues for future collaborations across the countries to solve common problems and gives stronger opportunity to fight cancer. </i></div></div

Olfactory response and locomotion are unaffected by ethanol.

<p>(<b>A–C</b>) Response indices are shown for larvae when placed in the middle of an agar dish with ethyl acetate on one side and liquid paraffin on the other. The number of larvae in each odor zone was counted after 3 minutes. <b>A</b>. The Olfactory response shows a mild reduction with 30% ethanol treatment but not with 20% ethanol treatment. <b>B</b>. Larvae had been previously submerged for 20 minutes in either pure water or 20% EtOH. No significant difference was seen. <b>C</b>. Automated tracking. Left: Response index over a three-minute period when larvae are being tracked. Larvae had been previously submerged for 20 minutes in either pure water or 20% EtOH. <b>D</b>. Average speed in the absence of a stimulus is shown for larvae during the three minute tracking period. 20% EtOH did not cause a significant reduction in either locomotion speed or olfaction.</p

Effects of ethanol are temporary.

<p>Behavioral recovery of learning ability after ethanol exposure was tested by dividing both the ethanol-exposed and water-exposed groups into two subgroups, one conditioned immediately after treatment and one conditioned three hours later. No significant difference was observed in the conditioning scores of alcohol and water treated groups at the end of three hours in contrast to the immediately-conditioned group (p = 0.8, n = 5).</p

Perdurance of internal ethanol.

<p><b>A</b>. Example standard curve for ethanol gas chromatography. All of the measurements noted in this document fall within the linear range of the gas chromatograph standard curve. <b>B</b>. Chromatographs of ethanol from larvae. Standard responses for known concentrations of ethanol (4.25 mM, 2.13 mM, 1.06 mM, 0.53 mM, and 0.26 mM) diluted in toluene as well as pure toluene are shown. Representative traces from larvae treated for 20 minutes with 20% ethanol (EtOH larvae 1 and 2) or water (control larvae) are also shown. <b>C</b>. The amount of ethanol absorbed by larvae depended on the amount of ethanol in the treatment solution. <b>D</b>. The brief heat shocks (41°C and 35°C) that were used in the conditioning experiments did not reduce internal ethanol below that measured in sham-treated larvae. Animals were treated for 20 minutes with 20% ethanol (Loading Dose) and then taken through the heat shock protocol at 35°C or 41°C as used in conditioning experiments. The loading dose is the same data shown in the panel C 20% bar graph and is repeated for comparison purposes. Sham-treated animals were taken through same protocol except that they did not receive the heat shocks but instead were moved to room temperature (24°C) plates.</p

Experimental design.

<p><b>A</b>. Schematic of the flow of the experiment. <b>B</b>. Schematic of the ethanol/water treatment protocol.</p

Ethanol treatment affects olfactory learning when the heat shock unconditioned stimulus is below the temperature optima.

<p><b>A</b>. Either heat alone or odor alone presentations resulted in the same response index (RI = #Larvae in odor zone/#Larvae total) as sham-treated larvae (p>0.05 for any comparison). <b>B</b>. Response indices for untrained (control) and trained larvae are shown for animals that either received water or 20% EtOH. All larvae were trained to associate the odor with a 41°C heat-shock. The response indices were similar for water-treated and ethanol-treated groups when comparisons were made for similar conditions such as the untrained group or the trained group. <b>C</b>. Learning indices (LI = (RI_control−RI_conditioned)/RI_control) calculated from the data in Panel B. <b>D</b>. Response indices for untrained (control) and trained larvae are shown for animals that either received water or 20% EtOH. All larvae were trained to associate the odor with a 35°C heat-shock. The conditioned response indices are significantly different in the ethanol treated groups (n = 32; p = 0.044). <b>E</b>. Learning indices calculated from the data in Panel D. Ethanol induced a significant reduction in learning.</p