R Markdown: Integrating A Reproducible Analysis Tool into Introductory Statistics

Nolan and Temple Lang argue that “the ability to express statistical computations is an es- sential skill.” A key related capacity is the ability to conduct and present data analysis in a way that another person can understand and replicate. The copy-and-paste workflow that is an artifact of antiquated user-interface design makes reproducibility of statistical analysis more difficult, especially as data become increasingly complex and statistical methods become increasingly sophisticated. R Markdown is a new technology that makes creating fully-reproducible statistical analysis simple and painless. It provides a solution suitable not only for cutting edge research, but also for use in an introductory statistics course. We present experiential and statistical evidence that R Markdown can be used effectively in introductory statistics courses, and discuss its role in the rapidly-changing world of statistical computation.

Rapid complete response of metastatic melanoma in a patient undergoing ipilimumab immunotherapy in the setting of active ulcerative colitis.

While blockade of the cytotoxic T-lymphocyte antigen-4 (CTLA-4) T cell regulatory receptor has become a commonly utilized strategy in the management of advanced melanoma, many questions remain regarding the use of this agent in patient populations with autoimmune disease. We present a case involving the treatment of a patient with stage IV melanoma and ulcerative colitis (UC) with anti-CTLA-4 antibody immunotherapy. Upon initial treatment, the patient developed grade III colitis requiring tumor necrosis factor-alpha (TNF-α) blocking antibody therapy, however re-treatment with anti-CTLA-4 antibody following a total colectomy resulted in a rapid complete response accompanied by the development of a tracheobronchitis, a previously described extra-intestinal manifestation of UC. This case contributes to the evolving literature on the use of checkpoint inhibitors in patients also suffering from autoimmune disease, supports future clinical trials investigating the use of these agents in patients with autoimmune diseases, and suggests that an understanding of the specific molecular pathways involved in a patient's autoimmune pathology may provide insight into the development of more effective novel combinatorial immunotherapeutic strategies.

Efects of mineral suspension and dissolution on strength and compressibility of soft carbonate rocks

© 2014 Elsevier B.V.Calcarenites are highly porous soft rocks formed of mainly carbonate grains bonded together by calcite bridges. The above characteristics make them prone to water-induced weathering, frequently featuring large caverns and inland natural underground cavities. This study is aimed to determine the main physical processes at the base of the short- and long-term weakening experienced by these rocks when interacting with water. We present the results of microscale experimental investigations performed on calcarenites from four different sites in Southern Italy. SEM, thin sections, X-ray CT observations and related analyses are used for both the interpretation-definition of the structure changes, and the identification-quantification of the degradation mechanisms. Two distinct types of bonding have been identified within the rock: temporary bonding (TB) and persistent bonding (PB). The diverse mechanisms linked to these two types of bonding explain both the observed fast decrease in rock strength when water fills the pores (short-term effect of water), identified with a short-term debonding (STD), and a long-term weakening of the material, when the latter is persistently kept in water-saturated conditions (long-term effect of water), identified with a long-term debonding (LTD). To highlight the micro-hydro-chemo-mechanical processes of formation and annihilation of the TB bonds and their role in the evolution of the mechanical strength of the material, mechanical tests on samples prepared by drying partially saturated calcarenite powder, or a mix of glass ballotini and calcarenite powder were conducted. The long-term debonding processes have also been investigated, using acid solutions in order to accelerate the reaction rates. This paper attempts to identify and quantify differences between the two types of bonds and the relative micro-scale debonding processes leading to the macro-scale material weakening mechanisms.