A simulation study using the hybrid statistic and the meta-analysis t-test for data with matched and unmatched subjects in the interim analysis of clinical trials

An interim analysis is usually applied in later phase II or phase III trials to find convincing evidence of a significant treatment difference that may lead to trial termination at an earlier point than planned at the beginning. This can result in the saving of patient resources and shortening of drug development and approval time. In addition, ethics and economics are also the reasons to stop a trial earlier. In clinical trials of eyes, ears, knees, arms, kidneys, lungs, and other clustered treatments, data may include distribution-free random variables with matched and unmatched subjects in one study. It is important to properly include both subjects in the interim and the final analyses so that the maximum efficiency of statistical and clinical inferences can be obtained at different stages of the trials. So far, no publication has applied a statistical method for distribution-free data with matched and unmatched subjects in the interim analysis of clinical trials. In this simulation study, the hybrid statistic was used to estimate the empirical powers and the empirical type I errors among the simulated datasets with different sample sizes, different effect sizes, different correlation coefficients for matched pairs, and different data distributions, respectively, in the interim and final analysis with 4 different group sequential methods. Empirical powers and empirical type I errors were also compared to those estimated by using the meta-analysis t-test among the same simulated datasets. Results from this simulation study show that, compared to the meta-analysis t-test commonly used for data with normally distributed observations, the hybrid statistic has a greater power for data observed from normally, log-normally, and multinomially distributed random variables with matched and unmatched subjects and with outliers. Powers rose with the increase in sample size, effect size, and correlation coefficient for the matched pairs. In addition, lower type I errors were observed estimated by using the hybrid statistic, which indicates that this test is also conservative for data with outliers in the interim analysis of clinical trials.^

Changing Tides and Changing Focus: Mapping the Challenges and Successes of One State's Implementation Of the Adoption and Safe Families Act of 1997

In 1997, the Adoption and Safe Families Act shifted from the preservation of families to an emphasis on safety, permanency, and well-being through expediting the termination of parental rights, establishing exceptions to the reasonable efforts clause of preserving the family, and fiscal incentives for finalizing adoptions. The current project assessed the role of a full service array in achieving the outcomes set forth in ASF A. Concept mapping was utilized to elicit information from participants (both urban and rural) regarding the identified research question. Participants recognized family preservation versus safety, community connections, mandates versus reality, and worker recruitment and retention as critical components for meeting ASFA goals. Perceived importance and level of success in implementing these services was also highlighted. Recommendations supported through the data are also provided.

Optimal, minimax, and Bayesian two-stage designs in two-dose phase II clinical trials

Background: For most cytotoxic and biologic anti-cancer agents, the response rate of the drug is commonly assumed to be non-decreasing with an increasing dose. However, an increasing dose does not always result in an appreciable increase in the response rate. This may especially be true at high doses for a biologic agent. Therefore, in a phase II trial the investigators may be interested in testing the anti-tumor activity of a drug at more than one (often two) doses, instead of only at the maximum tolerated dose (MTD). This way, when the lower dose appears equally effective, this dose can be recommended for further confirmatory testing in a phase III trial under potential long-term toxicity and cost considerations. A common approach to designing such a phase II trial has been to use an independent (e.g., Simon's two-stage) design at each dose ignoring the prior knowledge about the ordering of the response probabilities at the different doses. However, failure to account for this ordering constraint in estimating the response probabilities may result in an inefficient design. In this dissertation, we developed extensions of Simon's optimal and minimax two-stage designs, including both frequentist and Bayesian methods, for two doses that assume ordered response rates between doses. ^ Methods: Optimal and minimax two-stage designs are proposed for phase II clinical trials in settings where the true response rates at two dose levels are ordered. We borrow strength between doses using isotonic regression and control the joint and/or marginal error probabilities. Bayesian two-stage designs are also proposed under a stochastic ordering constraint. ^ Results: Compared to Simon's designs, when controlling the power and type I error at the same levels, the proposed frequentist and Bayesian designs reduce the maximum and expected sample sizes. Most of the proposed designs also increase the probability of early termination when the true response rates are poor. ^ Conclusion: Proposed frequentist and Bayesian designs are superior to Simon's designs in terms of operating characteristics (expected sample size and probability of early termination, when the response rates are poor) Thus, the proposed designs lead to more cost-efficient and ethical trials, and may consequently improve and expedite the drug discovery process. The proposed designs may be extended to designs of multiple group trials and drug combination trials.^

Metabolism and actions of 2 -chloro-2$\sp\prime$-fluoro-arabinosyladenine

2-Chloro-9-(2-deoxy-2-fluoro-$\beta $-D-arabinofuranosyl)adenine(Cl-F-ara-A) is a new deoxyadenosine analogue which is resistant to phosphorolytic cleavage and deamination, and exhibits therapeutic activity for both leukemia and solid tumors in experimental systems. To characterize its mechanism of cytotoxicity, the present study investigated the cellular pharmacology and the biochemical and molecular mechanisms of action of Cl-F-ara-A, from entrance of the drug into the cell, chemical changes to active metabolites, targeting on different cellular enzymes, to final programmed cell death response to the drug treatment.^ Cl-F-ara-A exhibited potent inhibitory action on DNA synthesis in a concentration-dependent and irreversible manner. The mono-, di-, and triphosphates of Cl-F-ara-A accumulated in cells, and their elimination was non-linear with a prolonged terminal phase, which resulted in prolonged dNTP depression. Ribonucleotide reductase activity was inversely correlated with the cellular Cl-F-ara-ATP level, and the inhibition of the reductase was saturated at higher cellular Cl-F-ara-ATP concentrations. The sustained inhibition of ribonucleotide reductase and the consequent depletion of deoxynucleotide triphosphate pools result in a cellular Cl-F-ara-ATP to dATP ratio which favors analogue incorporation into DNA.^ Incubation of CCRF-CEM cells with Cl-F-ara-A resulted in the incorporation of Cl-F-ara-AMP into DNA. A much lesser amount was associated with RNA, suggesting that Cl-F-ara-A is a more DNA-directed compound. The site of Cl-F-ara-AMP in DNA was related to the ratio of the cellular concentrations of the analogue triphosphate and the natural substrate dATP. Clonogenicity assays showed a strong inverse correlation between cell survival and Cl-F-ara-AMP incorporation into DNA, suggesting that the incorporation of Cl-F-ara-A monophosphate into DNA is critical for the cytotoxicity of Cl-F-ara-A.^ Cl-F-ara-ATP competed with dATP for incorporation into the A-site of the extending DNA strand catalyzed by both DNA polymerase $\alpha$ and $\varepsilon$. The incorporation of Cl-F-ara-AMP into DNA resulted in termination of DNA strand elongation, with the most pronounced effect being observed at Cl-F-ara-ATP:dATP ratio $>$1. The presence of Cl-F-ara-AMP at the 3$\sp\prime$-terminus of DNA also resulted in an increased incidence of nucleotide misincorporation in the following nucleotide position. The DNA termination and the nucleotide misincorporation induced by the incorporation of Cl-F-ara-AMP into DNA may contribute to the cytotoxicity of Cl-F-ara-A. ^

Stability and potential application of spliced nuclear pre -mRNA introns

A major portion of this thesis work was dedicated to study the nature and significance of spliced introns. The initial work was focused on studying the IVS1$\sb{\rm C\beta 1}$ intron from a T-cell receptor (TCR)-$\beta$ gene. Compared to an intron lariat control from adenovirus pre-mRNA that was spliced in vitro, IVS1$\sb{\rm C\beta 1}$ was debranched less efficiently by HeLa S100 extracts, although IVS1$\sb{\rm C\beta 1}$ also used the consensus branchpoint in vivo. Subcellular-fractionation analysis showed that most IVS1$\sb{\rm C\beta 1}$ lariats cofractionated with pre-mRNA in the nucleus, consistent with the possibility that intron degradation releases splicing factors which will be available for further rounds of splicing. The half-life of IVS1$\sb{\rm C\beta 1}$ from the endogenous TCR-$\beta$ gene was measured using the general transcription inhibitor actinomycin D to be about $\sim$15 min, which was similar to that of unstable mRNAs such as c-myc mRNA.^ The general transcription inhibitor DRB was also used for intron stability analysis. Unexpectedly, DRB decreased intron and pre-mRNA levels only initially, it later increased the levels of intron-containing RNAs. Inhibition of transcription initiation appeared to be the major early effect (the reduction phase); whereas enhanced premature transcription termination was dominant later (the induction phase).^ Having established the procedures for studying in vivo spliced introns, this approach was applied to study the mechanism of nonsense-mediated downregulation (NMD), a phenomena in which premature termination codons (PTCs) decrease the levels of mRNAs. In this study, the novel intron-oriented approach was applied to study the mechanism of NMD. The levels of spliced introns immediately upstream and downstream of a PTC-bearing exon in a TCR-$\beta$ gene were identified and analyzed along with their pre-mRNA. Although PTC reduced the mRNA levels by 4 to 9 fold, the steady-state levels of spliced introns and the pre-mRNA-to-intron ratios were not significantly altered, indicating that the PTC did not significantly inhibit TCR-$\beta$ RNA splicing. Consistent with this conclusion, the half-lives of the PTC$\sp+$ and PTC$\sp-$ pre-mRNA were similar. The protein synthesis inhibitor cyclohexmide (CHX) upregulated the levels of the PTC$\sp+$ mRNA over 10 fold without affecting the levels of the spliced introns, suggesting that the reversal effect of CHX was through stabilization, not production. These results indicated that inhibition of splicing could not be the major mechanism for the NMD pathway of the TCR-$\beta$ gene, instead, suggesting that mRNA destabilization may be more important. (Abstract shortened by UMI.) ^

A role for p53 in sensing DNA damage and triggering apoptotic responses to anticancer agents

The p53 tumor suppressor protein plays a major role in cellular responses to anticancer agents that target DNA. DNA damage triggers the accumulation of p53, resulting in the transactivation of genes, which induce cell cycle arrest to allow for repair of the damaged DNA, or signal apoptosis. The exact role that p53 plays in sensing DNA damage and the functional consequences remain to be investigated. The main goal of this project was to determine if p53 is directly involved in sensing DNA damage induced by anticancer agents and in mediating down-stream cellular responses. This was tested in two experimental models of DNA damage: (1) DNA strand termination caused by anticancer nucleoside analogs and (2) oxidative DNA damage induced by reactive oxygen species (ROS). Mobility shift assays demonstrated that p53 and DNA-PK/Ku form a complex that binds DNA containing the anticancer nucleoside analog gemcitabine monophosphate in vitro. Binding of the p53-DNA-PK/Ku complex to the analog-containing DNA inhibited DNA strand elongation. Furthermore, treatment of cells with gemcitabine resulted in the induction of apoptosis, which was associated with the accumulation of p53 protein, its phosphorylation, and nuclear localization, suggesting the activation of p53 to trigger apoptosis following gemcitabine induced DNA strand termination. The role of p53 as a DNA damage sensor was further demonstrated in response to oxidative DNA damage. Protein pull-down assays demonstrated that p53 complexes with OGG1 and APE, and binds DNA containing the oxidized DNA base 8-oxoG. Importantly, p53 enhances the activities of APE and OGG1 in excising the 8-oxoG residue as shown by functional assays in vitro. This correlated with the more rapid removal of 8-oxoG from DNA in intact cells with wild-type p53 exposed to exogenous ROS stress. Interestingly, persistent exposure to ROS resulted in the accelerated onset of apoptosis in cells with wild-type p53 when compared to isogenic cells lacking p53. Apoptosis in p53+/+ cells was associated with accumulation and phosphorylation of p53 and its nuclear localization. Taken together, these results indicate that p53 plays a key role in sensing DNA damage induced by anticancer nucleoside analogs and ROS, and in triggering down-stream apoptotic responses. This study provides new mechanistic insights into the functions of p53 in cellular responses to anticancer agents. ^

Plio-Pleistocene diatom biostratigraphy from ODP Leg 177, Atlantic sector of the Southern Ocean

Seven sites were drilled during Ocean Drilling Program Leg 177 in the Atlantic sector of the Southern Ocean (SO) on a transect over the Antarctic Circumpolar Current from the Subantarctic to the Antarctic Zone. At four sites sediments were recovered with a Pliocene/Pleistocene sediment package of up to 580 m allowing the refinement of previous diatom zonation concepts. Samples were analyzed on stratigraphic distribution and abundance of diatom species. A refined diatom biozonation tied to the geomagnetic polarity record is proposed. For the middle and late Pleistocene two zonations applicable to the northern and southern area of the SO were constructed, considering different latitudinal distributions of biostratigraphic diatom marker species. The southern zonation for the Pleistocene relies on the occurrence of species of the genus Rouxia, R. leventerae and R. constricta n. sp. as well as on a revised last occurrence datum (LOD) of Actinocyclus ingens (0.38 Ma, late marine isotope stage (MIS) 11). The use of these new stratigraphic marker species refines the temporal resolution for biostratigraphic age assignment to up to 0.1 Myr. In particular the LOD of R. leventerae as an indicator for the MIS 6/5 boundary (Termination II) will improve future dating of carbonate-free Antarctic sediments. These new data were obtained from sediments of Sites 1093 and 1094 (Antarctic Zone). The northern zonation for the middle and late Pleistocene time interval is based on the Pleistocene abundance pattern of Hemidiscus karstenii which was already proposed by previous investigations (e.g. Gersonde and Barcena, 1998). One new species (R. constricta) and two new combinations (Fragilariopsis clementia, Fragilariopsis reinholdii) are proposed in this study.

Monthly Tahiti coral Sr/Ca and oxygen isotope data from IODP Hole 310-M0024A

The early last glacial termination was characterized by intense North Atlantic cooling and weak overturning circulation. This interval between ~18,000 and 14,600 years ago, known as Heinrich Stadial 1, was accompanied by a disruption of global climate and has been suggested as a key factor for the termination. However, the response of interannual climate variability in the tropical Pacific (El Niño-Southern Oscillation) to Heinrich Stadial 1 is poorly understood. Here we use Sr/Ca in a fossil Tahiti coral to reconstruct tropical South Pacific sea surface temperature around 15,000 years ago at monthly resolution. Unlike today, interannual South Pacific sea surface temperature variability at typical El Niño-Southern Oscillation periods was pronounced at Tahiti. Our results indicate that the El Niño-Southern Oscillation was active during Heinrich Stadial 1, consistent with climate model simulations of enhanced El Niño-Southern Oscillation variability at that time. Furthermore, a greater El Niño-Southern Oscillation influence in the South Pacific during Heinrich Stadial 1 is suggested, resulting from a southward expansion or shift of El Niño-Southern Oscillation sea surface temperature anomalies.

Planktonic foraminifera of the Mediterranean Sea

A high-resolution biochronology is presented for the Late Quaternary of the central Mediterranean. In the Late Pleistocene-Holocene successions three assemblage zones are distinguished on the basis of frequency patterns of planktic foraminifera. The age of these zones is determined by Accelerator Mass Spectrometry (AMS)14C dating. The zonal boundaries are dated at 12,700 yr B.P. (the end of Termination Ia) and 9600 yr B.P. (the start of Termination Ib), respectively. The AMS dates show that major changes in the planktic and benthic realms occurred synchronously over wide areas, although records of individual species may show important regional differences. In the studied areas, resedimentation processes revealed by anomalous successions of14C dates, play a far more important role than indicated by the sedimentological and micropaleontological data. Possibly these processes contribute to the very high accumulation rates in the glacial Zone III. Although the AMS technique has increased the accuracy of14C-measurements, admixture of older carbonate may still lead to substantial age differences between areas with different sedimentary regimes.

Geological investigations on sediment core MD07-3128

Glacial millennial-scale paleoceanographic changes in the Southeast Pacific and the adjacent Southern Ocean are poorly known due to the scarcity of well-dated and high resolution sediment records. Here we present new surface water records from sediment core MD07-3128 recovered at 53°S off the Pacific entrance of the Strait of Magellan. The alkenone-derived sea surface temperature (SST) record reveals a very strong warming of ca. 8°C over the last Termination and substantial millennial-scale variability in the glacial section largely consistent with our planktonic foraminifera oxygen isotope (d18O) record of Neogloboquadrina pachyderma (sin.). The timing and structure of the Termination and some of the millennial-scale SST fluctuations are very similar to those observed in the well-dated SST record from ODP Site 1233 (41°S) and the temperature record from Drowning Maud Land Antarctic ice core supporting the hemispheric-wide Antarctic timing of SST changes. However, differences in our new SST record are also found including a long-term warming trend over Marine Isotope Stage (MIS) 3 followed by a cooling toward the Last Glacial Maximum (LGM). We suggest that these differences reflect regional cooling related to the proximal location of the southern Patagonian Ice Sheet and related meltwater supply at least during the LGM consistent with the fact that no longer SST cooling trend is observed in ODP Site 1233 or any SST Chilean record. This proximal ice sheet location is documented by generally higher contents of ice rafted debris (IRD) and tetra-unsaturated alkenones, and a slight trend toward lighter planktonic d18O during late MIS 3 and MIS 2.