Integrating shotgun proteomics and mRNA expression data to improve protein identification

Motivation: Tandem mass spectrometry (MS/MS) offers fast and reliable characterization of complex protein mixtures, but suffers from low sensitivity in protein identification. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other information available, e.g. the probability of a protein's presence is likely to correlate with its mRNA concentration

Mary Tudor

Abstract not availabl

Science Operations Planning and Implementation for the OSIRIS-REx Mission, Part 1: Process

The Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer (OSIRIS-REx) spacecraft arrived at the near-Earth asteroid (101955) Bennu in December 2018 and executed a science observation campaign to comprehensively characterize the asteroid. Proximity operations at Bennu included orbital phases and flyby phases with various viewing geometries and altitudes. The complexity of the mission plan, integrated instrument operations, and the challenges of spacecraft navigation in the microgravity environment required an intricate planning and implementation process that included participation and coordination among all mission elements. The Science Planning Team (SPT) and the Implementation Team (IpT) at the University of Arizona planned and implemented all science and most optical navigation observations. Prior to the formal planning process, science requirements were mapped to mission phases and observation geometry constraints. During development of the mission phases, the navigation team produced a spacecraft trajectory, and the SPT developed the pointing and attitude profile to meet the specified constraints. In the strategic planning process, which began three months prior to execution, the SPT conducted sensitivity analysis of the observation designs against a set of perturbed trajectories delivered by the navigation team to ensure that they were robust to navigational uncertainties. Planning of the specific observations to occur within each phase was divided into units of weeks, and the plans for each week were developed and implemented on a rolling eight-week tactical planning and implementation cycle, ending with execution and data downlink. This cycle included a standardized schedule of activities and gateways to ensure that every observation plan underwent a full suite of analysis, verification, and approval in the allocated timeframe. Checklists guided the SPT and IpT through the build and verification process to confirm plan safety and fidelity. The SPT led the first four weeks of the tactical process, with participation from the IpT and other stakeholders. During the first two weeks, the SPT gathered information from stakeholders, conducted preliminary planning to confirm the science observations were feasible and obeyed spacecraft constraints, and determined how to integrate instrument commanding with the spacecraft pointing profile. The SPT started the final observation design and planning six weeks prior to execution. Once complete, plan walkthroughs were conducted with stakeholders, which culminated in a go/no-go decision to proceed with implementation at the four-week point. In the last four weeks of the tactical planning and implementation process, the IpT led the final processing of science plans with participation from stakeholders. The IpT compiled the plans, performed comprehensive safety checks against established spacecraft and instrument flight rules, and generated flight products and artifacts. After IpT delivered the flight products, the spacecraft team integrated them with the spacecraft sequencing, performed ground testing, and produced an integrated report. IpT reviewed the report, verifying instrument health and safety and confirming nominal plan execution in the ground simulation. The final flight products were uplinked to the spacecraft a few days prior to the execution week. During execution, the IpT and other stakeholders monitored instrument performance and viewed science and navigation data. Resulting science data products were used for operational decisions and science investigations.Immediate accessThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Utility of nuclear stress imaging for detecting coronary artery bypass graft disease

<p>Abstract</p> <p>Background</p> <p>The value of Single Photon Emission Computed Tomography stress myocardial perfusion imaging (SPECT-MPI) for detecting graft disease after coronary artery bypass surgery (CABG) has not been studied prospectively in an unselected cohort.</p> <p>Methods</p> <p>Radial Artery Versus Saphenous Vein Graft Study is a Veterans Affairs Cooperative Study to determine graft patency rates after CABG surgery. Seventy-nine participants agreed to SPECT-MPI within 24 hours of their coronary angiogram, one-year after CABG. The choice of the stress protocol was made at the discretion of the nuclear radiologist and was either a symptom-limited exercise test (n = 68) or an adenosine infusion (n = 11). The SPECT-MPI results were interpreted independent of the angiographic results and estimates of sensitivity, specificity and accuracy were based on the prediction of a graft stenosis of ≥70% on coronary angiogram.</p> <p>Results</p> <p>A significant stenosis was present in 38 (48%) of 79 patients and 56 (22%) of 251 grafts. In those stress tests with an optimal exercise heart rate response (>80% maximum predicted heart rate) (n = 26) sensitivity, specificity and accuracy of SPECT-MPI for predicting the graft stenosis was 77%, 69% and 73% respectively. With adenosine (n = 11) it was 75%, 57% and 64%, respectively. Among participants with a suboptimal exercise heart rate response, the sensitivity of SPECT-MPI for predicting a graft stenosis was <50%. The accuracy of SPECT-MPI for detecting graft disease did not vary significantly with ischemic territory.</p> <p>Conclusions</p> <p>Under optimal stress conditions, SPECT-MPI has a good sensitivity and accuracy for detecting graft disease in an unselected patient population 1 year post-CABG.</p