Bioinformatic identification of proteins with tissue-specific expression for biomarker discovery

<p>Abstract</p> <p>Background</p> <p>There is an important need for the identification of novel serological biomarkers for the early detection of cancer. Current biomarkers suffer from a lack of tissue specificity, rendering them vulnerable to non-disease-specific increases. The present study details a strategy to rapidly identify tissue-specific proteins using bioinformatics.</p> <p>Methods</p> <p>Previous studies have focused on either gene or protein expression databases for the identification of candidates. We developed a strategy that mines six publicly available gene and protein databases for tissue-specific proteins, selects proteins likely to enter the circulation, and integrates proteomic datasets enriched for the cancer secretome to prioritize candidates for further verification and validation studies.</p> <p>Results</p> <p>Using colon, lung, pancreatic and prostate cancer as case examples, we identified 48 candidate tissue-specific biomarkers, of which 14 have been previously studied as biomarkers of cancer or benign disease. Twenty-six candidate biomarkers for these four cancer types are proposed.</p> <p>Conclusions</p> <p>We present a novel strategy using bioinformatics to identify tissue-specific proteins that are potential cancer serum biomarkers. Investigation of the 26 candidates in disease states of the organs is warranted.</p

Supply Considerations for Scaling Up Clean Cooking Fuels for Household Energy in Low- and Middle-Income Countries

Promoting access to clean household cooking energy is an important subject for policy making in low‐ and middle‐income countries, in light of urgent and global efforts to achieve universal energy access by 2030 (Sustainable Development Goal 7). In 2014, the World Health Organization issued “Guidelines for Indoor Air Quality: Household Fuel Combustion”, which recommended a shift to cleaner fuels rather than promotion of technologies that more efficiently combust solid fuels. This study fills an important gap in the literature on transitions to household use of clean cooking energy by reviewing supply chain considerations for clean fuel options in low‐ and middle‐income countries. For the purpose of this study, we consider electricity, liquefied petroleum gas (LPG), alcohol fuels, biogas, and compressed biomass pellets burned in high performing gasifier stoves to be clean fuel options. Each of the clean fuels reviewed in this study, as well as the supply of electricity, presents both constraints and opportunities for enhanced production, supply, delivery, and long‐term sustainability and scalability in resource‐poor settings. These options are reviewed and discussed together with policy and regulatory considerations to help in making these fuel and energy choices available and affordable. Our hope is that researchers, government officials and policy makers, and development agencies and investors will be aided by our comparative analysis of these clean household energy choices.Key PointsDesigning effective energy policies that support and accelerate transitions to clean cooking fuels is a top global priorityCountries depend on a portfolio of fuels for cooking and should plan an optimal mix of clean fuels, both in the medium and long‐termRisk and sustainability of cookfuel supply chains depend on multiple factors that ultimately influence long‐term viability and scalePeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153562/1/gh2133.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153562/2/gh2133_am.pd

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources

As more digital resources are produced by the research community, it is becoming increasingly important to harmonize and organize them for synergistic utilization. The findable, accessible, interoperable, and reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge. The FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual and automated FAIR assessments. FAIR assessments are visualized as an insignia that can be embedded within digital-resources-hosting websites. Using FAIRshake, a variety of biomedical digital resources were manually and automatically evaluated for their level of FAIRness