Tumor removal completeness during surgery depends on the surgeon's ability to differentiate tumor from normal tissue using subjective criteria that are not easily quantifiable. One study describes the use of activatable cell-penetrating peptides (ACPPS) that fluorescently labels tumor cells to aid in the precision of tumor identification. The table below shows the fluorescence after two hours for tumor and normal tissue for two separate groups of 12 mice. You want to test if the fluorescence after two hours is different between the tumor and normal tissue between the two, independent groups. Fluorescence After 2 Hours Observation 1 2 3 4 5 6 Tumor Normal Tissue 3037 7 3948 3967 3164 3292 2696 3975 5284 2775 4083 2805 1228 2124 2272 2118 1786 3847 2912 3460 3029 3134 4097 8 9 10 11 12 4279 3935 1) Create a boxplot to graphically show what you are testing and describe the data. 2) What assumptions do you have to make about the data to use a two-sample independent t- test? Discuss the assumptions in general and in the context of this question, and then validate the assumptions. Show the qq-plot of the samples along with any discussion. 3) Run the hypothesis test. Specify the steps of the hypothesis test and show the work for the test (by hand or annotated code). Also run the appropriate test in Python. What do you conclude? 4) Construct a 95% confidence interval for the difference between the means for tumor and normal tissue fluorescence. Discuss this finding and how this adds to your understanding of the analysis.

Two genes associated with breast cancer, BRCA1 and BRCA2, were discovered in 1994 and 1995, respectively, and shortly thereafter, were patented by Myriad Genetics, a company based in Utah. Under the patents, testing for mutations in these genes could only be performed by Myriad, at costs from 300 to 3,000. Myriad also patented the process of analyzing the results of such tests, preventing anyone who obtains the sequence of their BRCA genes by other means (which itself would probably be patent infringement) from interpreting the information. The idea that genes can be patented has been a contentious issue from the beginning. Patents are not granted for products of nature, meaning that genes inside the body are not patentable, but biotech companies successfully argued that by removing a gene from the human body, purifying it, and then obtaining its DNA sequence, they created something not found in nature, and which is therefore a patentable invention. The U.S. Patent Office found the argument persuasive, but opponents argue that genes are parts of our bodies and can be identified but not invented. Biotech companies argue that without the protection offered by patents, they would have no incentive for research and development of diagnostic tests. In Europe, patents for BRCA1 and BRCA2 were revoked in 2004 because they did not meet the standards for a patent. After more than a decade of legal disputes, the patents were partially restored in 2008 on a very restricted basis. In the United States, a lawsuit, focused on the patents for the BRCA genes, was filed in May 2009. The suit challenges the basic idea that genes are patentable. In November 2009, the judge ruled that the lawsuit can proceed, and the case is moving forward. In March 2010, a federal court invalidated Myriad Genetics patent on these genes. In August 2011, the U.S. Court of Appeals reversed the lower courts decision and ruled that gene sequences isolated from cells are not a product of nature and are therefore patentable. The case went to the U.S. Supreme Court, which ordered the appeals court to reconsider the case. The Federal Appeals Court did not change its decision, and the case once again, went to the U.S. Supreme Court. A unanimous decision in June 2013 invalidated Myriads patents on the basis that isolating a gene from nature does not make it patentable. This is a landmark decision on gene patenting with widespread ramifications for the biotechnoloogy industry. Will this decision reduce the incentives for companies to invest in new diagnostic tests that would be used by cancer victims or those with serious genetic disorders?

Sterile normal saline is used in most surgical procedures as an irrigation solution. During certain surgical procedures, such as those for malignancy, the surgeon may request that sterile water be used for irrigation instead of saline following excision of the cancerous mass. Why is normal saline usually used in healthy tissues?

A few recent cancer detection studies have used trained dogs to detect lung cancer in urine samples. What is the hypothesis behind this study? Why are dogs a better choice of detectors in this study than humans?