Comparison of Bayesian and frequentist group-sequential clinical trial designs

Background: There is a growing interest in the use of Bayesian adaptive designs in late-phase clinical trials. This includes the use of stopping rules based on Bayesian analyses in which the frequentist type I error rate is controlled as in frequentist group-sequential designs. Methods: This paper presents a practical comparison of Bayesian and frequentist group-sequential tests. Focussing on the setting in which data can be summarised by normally distributed test statistics, we evaluate and compare boundary values and operating characteristics. Results: Although Bayesian and frequentist group-sequential approaches are based on fundamentally different paradigms, in a single arm trial or two-arm comparative trial with a prior distribution specified for the treatment difference, Bayesian and frequentist group-sequential tests can have identical stopping rules if particular critical values with which the posterior probability is compared or particular spending function values are chosen. If the Bayesian critical values at different looks are restricted to be equal, O’Brien and Fleming’s design corresponds to a Bayesian design with an exceptionally informative negative prior, Pocock’s design to a Bayesian design with a non-informative prior and frequentist designs with a linear alpha spending function are very similar to Bayesian designs with slightly informative priors. This contrasts with the setting of a comparative trial with independent prior distributions specified for treatment effects in different groups. In this case Bayesian and frequentist group-sequential tests cannot have the same stopping rule as the Bayesian stopping rule depends on the observed means in the two groups and not just on their difference. In this setting the Bayesian test can only be guaranteed to control the type I error for a specified range of values of the control group treatment effect. Conclusions: Comparison of frequentist and Bayesian designs can encourage careful thought about design parameters and help to ensure appropriate design choices are made

Freire re-viewed

The work of Paulo Freire is associated with themes of oppression and liberation, and his critical pedagogy is visionary in its attempts to bring about social transformation. Freire has created a theory of education that embeds these issues within social relations that center around both ideological and material domination. In this review essay, Sue Jackson explores three books: Freire’s final work Pedagogy of Indignation; Cesar Augusto Rossatto’s Engaging Paulo Freire’s Pedagogy of Possibility, which attempts to engage Freire’s pedagogy of possibility; and C.A. Bowers and Frederique Apffel-Marglin’s edited collection Re-thinking Freire, which asks readers to reconsider Freire’s work in light of globalization and environmental crises. Jackson questions the extent to which Freire’s pedagogical approaches are useful to educators as well as to “the oppressed,” and whether challenges to re-think Freire can lead to new kinds of critical pedagogies

Using a new design rules practice and science talk development to enhance conceptual understanding, scientific reasoning, and transfer in Learning by Design classrooms

Thesis (M.S.Ed.)--University of Kansas, Teaching and Leadership, 2003

Now may be heard a discouraging word : the impact of climate fluctuation on Texas ranching in the 1880s

This thesis deals with the negative interrelationship between climate fluctuation and cattle ranching during the 1880s. The focus is on three large ranches that were used as case studies on the Texas Panhandle. These ranches were selected because of their size, longevity, and the number of primary documents that were available at the Panhandle Plains Museum and Archive in Canyon, Texas. The temporal focus is from 1880 to 1890. The primary documents that have been examined are letters from ranchers to the Capitol Syndicates that owned the ranch and the financial documents of each ranch. Scientific journals that examined grassland ecology, animal ecology, and climate were used in conjunction with the primary documents. The combination of these sources led to a nuanced reinterpretation of a cattle disaster from the 1880s. The disaster was a massive loss of stock through a series of extremely cold winters and a drought that lasted several years. In the wake of this disaster, through the use of technology, these ranches were able to recover and increase their stock numbers beyond what they were prior to the years dominated by stock losses and low cattle prices

Don't mind the gap: Bridging network-wide objectives and device-level configurations

We reflect on the historical context that lead to Propane, a high-level language and compiler to help network operators bridge the gap between network-wide routing objectives and low-level configurations of devices that run complex, distributed protocols. We also highlight the primary contributions that Propane made to the networking literature and describe ongoing challenges. We conclude with an important lesson learned from the experience

Analysis of the cyclostratigraphy at the Devonian-Carboniferous boundary in south-central Oklahoma

An outcrop in La Serre, France, was officially ratified by the ICS in 1989, and the IUGS in 1990, as the location of the Global Boundary Stratotype Section and Point (GSSP) for the Famennian–Tournaisian, and subsequently the Devonian–Carboniferous (D–C) boundary. GSSPs, like this one, are official outcrops that provide physical representations of geologic time boundaries, essentially geological standards that define geologic time, providing a vital framework to model a variety of interpretations of geological phenomena from paleoclimate to paleontological. It has been acknowledged that the GSSP in La Serre, France is in need of revision due to fossil reworking and general outcrop quality. The D–C boundary has also traditionally been a challenging boundary to place with precision because of problems associated with Siphonodella sulcata, whose first occurrence is the current definition of the boundary. With the aim of improving D–C boundary correlation, especially in the central United States, outcrops from the Woodford Shale in south-central Oklahoma and a New Albany Shale core from Johnson County, Indiana have been analyzed for cyclostratigraphy through measurement of mass-dependant, low-field magnetic susceptibility (χ), and also gamma radiation (GR). Gamma Ray Spectroscopy (GRS; field based) measurements were used for general correlation, along with previous conodont biostratigraphic work. Combined use of χ and GR measurements for 40K allows for a deeper layer of stratigraphic comparison. With the combined statistical techniques of the periodogram, multi-taper method (MTM), and wavelet analysis, a detailed timescale was pieced together for both the Oklahoma outcrops and Indiana core by comparing the periodic elements of the cyclostratigraphic signal represented by these geophysical proxies. Future work studying faunal assemblages can be compared with the cyclostratigraphic framework provided here to allow greater precision in interpretation

Initial Plant Growth in Sand Mine Spoil Amended with Peat Moss and Fertilizer Under Greenhouse Conditions: Potential Species for Use in Reclamation

The Great Lakes Basin exhibits the largest collection of freshwater sand dunes in the world. Sand dunes are ecologically important and support a unique assemblage of flora and fauna. Sand dunes are also economically valuable. However, when sand dunes are mined, soil quality is drastically reduced. Therefore, soil quality improvements followed by revegetation maybe necessary for successful reclamation. This study evaluates the germination and initial growth of 2 legume species, sundial lupine (Lupinus perennis) and Illinois bundleflower (Desmanthus illinoensis), and 2 warm-season grass species, Indian grass (Sorghastrum nutans) and little bluestem (Schizachyrium scoparium), in the presence of 2 soil amendments (inorganic fertilizer and sphagnum peat moss) added to spoil from a local sand mine. We sowed species in pots and propagated them under greenhouse conditions. Results indicate that sundial lupine and Illinois bundleflower exhibited the greatest germination and growth among species. Peat moss had the greatest overall impact on germination and growth while the addition of fertilizer positively affected initial growth. Based on these results, sundial lupine is recognized as a primary candidate for sand mine reclamation, while Illinois bundleflower is also recommended as an appropriate species for revegetation efforts. We recommend using soil amendments that are functionally equivalent to peat in increasing soil water holding capacity. We further suggest that fertilization may be accomplished by including legumes in plant species mixes used for revegetation. Results presented here may help to identify appropriate species and soil amendments for the reclamation of former sand mines or restoration of freshwater sand dunes

Consequences of Cisplatin Binding on Nucleosome Structure and Dynamics

The effects of cisplatin binding to DNA were explored at the nucleosome level to incorporate key features of the eukaryotic nuclear environment. An X-ray crystal structure of a site-specifically platinated nucleosome carrying a 1,3-cis-{Pt(NH[subscript 3])[subscript 2]}[superscript 2+]-d(GpTpG) intrastrand cross-link reveals the details of how this adduct dictates the rotational positioning of DNA in the nucleosome. Results from in vitro nucleosome mobility assays indicate that a single platinum adduct interferes with ATP-independent sliding of DNA around the octamer core. Data from in vitro transcription experiments suggest that RNA polymerases can successfully navigate along cisplatin-damaged DNA templates that contain nucleosomes, but stall when the transcription elongation complex physically contacts a platinum cross-link located on the template strand. These results provide information about the effects of cisplatin binding to nuclear DNA and enhance our understanding of the mechanism of transcription inhibition by platinum anticancer compounds.National Cancer Institute (U.S.) (Grant CA034992)David H. Koch Cancer Research FundNational Center for Research Resources (U.S.) (Award RR-15301)United States. Dept. of Energy. Office of Basic Energy Sciences (DE-AC02-06CH11357

Structure of duplex DNA containing the cisplatin 1,2-{Pt(NH3)2}2+-d(GpG) crosslink at 1.77 Å resolution

We report the 1.77-Å resolution X-ray crystal structure of a dodecamer DNA duplex with the sequence 5′-CCTCTGGTCTCC-3′ that has been modified to contain a single engineered 1,2-cis-{Pt(NH3)2}2+-d(GpG) cross-link, the major DNA adduct of cisplatin. These data represent a significant improvement in resolution over the previously published 2.6-Å structure. The ammine ligands in this structure are clearly resolved, leading to improved visualization of the cross-link geometry with respect to both the platinum center and to the nucleobases, which adopt a higher energy conformation. Also better resolved are the deoxyribose sugar puckers, which allow us to re-examine the global structure of platinum-modified DNA. Another new feature of this model is the location of four octahedral [Mg(H2O)6]2+ ions associated with bases in the DNA major groove and the identification of 124 ordered water molecules that participate in hydrogen-bonding interactions with either the nucleic acid or the diammineplatinum(II) moiety.National Cancer Institute (U.S.) (grant CA034992)David H. Koch Institute for Integrative Cancer Research at MIT (Koch Fund Fellowship