Bayesian Adaptive Designs for Early Phase Clinical Trials

My dissertation focuses mainly on Bayesian adaptive designs for phase I and phase II clinical trials. It includes three specific topics: (1) proposing a novel two-dimensional dose-finding algorithm for biological agents, (2) developing Bayesian adaptive screening designs to provide more efficient and ethical clinical trials, and (3) incorporating missing late-onset responses to make an early stopping decision. Treating patients with novel biological agents is becoming a leading trend in oncology. Unlike cytotoxic agents, for which toxicity and efficacy monotonically increase with dose, biological agents may exhibit non-monotonic patterns in their dose-response relationships. Using a trial with two biological agents as an example, we propose a phase I/II trial design to identify the biologically optimal dose combination (BODC), which is defined as the dose combination of the two agents with the highest efficacy and tolerable toxicity. A change-point model is used to reflect the fact that the dose-toxicity surface of the combinational agents may plateau at higher dose levels, and a flexible logistic model is proposed to accommodate the possible non-monotonic pattern for the dose-efficacy relationship. During the trial, we continuously update the posterior estimates of toxicity and efficacy and assign patients to the most appropriate dose combination. We propose a novel dose-finding algorithm to encourage sufficient exploration of untried dose combinations in the two-dimensional space. Extensive simulation studies show that the proposed design has desirable operating characteristics in identifying the BODC under various patterns of dose-toxicity and dose-efficacy relationships. Trials of combination therapies for the treatment of cancer are playing an increasingly important role in the battle against this disease. To more efficiently handle the large number of combination therapies that must be tested, we propose a novel Bayesian phase II adaptive screening design to simultaneously select among possible treatment combinations involving multiple agents. Our design is based on formulating the selection procedure as a Bayesian hypothesis testing problem in which the superiority of each treatment combination is equated to a single hypothesis. During the trial conduct, we use the current values of the posterior probabilities of all hypotheses to adaptively allocate patients to treatment combinations. Simulation studies show that the proposed design substantially outperforms the conventional multi-arm balanced factorial trial design. The proposed design yields a significantly higher probability for selecting the best treatment while at the same time allocating substantially more patients to efficacious treatments. The proposed design is most appropriate for the trials combining multiple agents and screening out the efficacious combination to be further investigated. The proposed Bayesian adaptive phase II screening design substantially outperformed the conventional complete factorial design. Our design allocates more patients to better treatments while at the same time providing higher power to identify the best treatment at the end of the trial. Phase II trial studies usually are single-arm trials which are conducted to test the efficacy of experimental agents and decide whether agents are promising to be sent to phase III trials. Interim monitoring is employed to stop the trial early for futility to avoid assigning unacceptable number of patients to inferior treatments. We propose a Bayesian single-arm phase II design with continuous monitoring for estimating the response rate of the experimental drug. To address the issue of late-onset responses, we use a piece-wise exponential model to estimate the hazard function of time to response data and handle the missing responses using the multiple imputation approach. We evaluate the operating characteristics of the proposed method through extensive simulation studies. We show that the proposed method reduces the total length of the trial duration and yields desirable operating characteristics for different physician-specified lower bounds of response rate with different true response rates.

Interferon-gamma release assays for latent tuberculosis infection in child and young adult candidates or recipients of tumor necrosis factor inhibitor therapy

Background. Inhibition of tumor necrosis factor (TNF) is associated with progression of latent tuberculosis infection (LTBI) to active disease. LTBI screening prior to starting TNF inhibitor therapy is recommended. Blood tests, collectively known as interferon-gamma release assays (IGRAs), offer a means other than the tuberculin skin test (TST) of screening for LTBI. However, in the setting of immune compromise, anergy may limit the clinical utility of IGRAs. ^ Methods. A cross-sectional study was conducted in children and young adults ≤ 21 years of age who were cared for at Texas Children's Hospital in Houston, TX, during 2011 and who were candidates for, or were receiving, tumor necrosis factor (TNF)-inhibitor therapy. All subjects answered a risk factor questionnaire and were tested for LTBI by two commercially available IGRAs (QuantiFERON-Gold In-Tube assay and the T-SPOT.TB assay), along with the TST. T-cell phenotypes were evaluated through flow cytometry, both at baseline and after antigen stimulation. ^ Results. Twenty-eight subjects were enrolled. All were TST negative and none were IGRA positive. Results were negative for the 27 subjects who were tested with QuantiFERON-Gold In-Tube. However, 26% of subjects demonstrated anergy in the T-SPOT.T. Patients with T-SPOT. TB anergy had lower quantitative IFN-γ responses to mitogen in the QFT assay—the mean IFN-γ level to mitogen in patients without T-SPOT.TB anergy was 9.84 IU/ml compared to 6.91 IU/ml in patients with T-SPOT.TB anergy (P = 0.046). Age and use of TNF inhibitors, corticosteroids, or methotrexate use were not significantly associated with T-SPOT.TB anergy. Antigen stimulation revealed depressed expression of intracellular IFN-γ in subjects with T-SPOT. TB anergy. ^ Conclusions. The frequency of anergy in this population is higher than would be expected from studies in adults. There appears to be inappropriate IFN-γ responses to antigen in subjects with T-SPOT. TB anergy. This immune defect was detected by the T-SPOT. TB assay but not by the QuantiFERON-Gold In-Tube assay. Further data are needed to clarify the utility of IGRAs in this population.^

Bayesian adaptive designs in early phase clinical trials

There are two practical challenges in the phase I clinical trial conduct: lack of transparency to physicians, and the late onset toxicity. In my dissertation, Bayesian approaches are used to address these two problems in clinical trial designs. The proposed simple optimal designs cast the dose finding problem as a decision making process for dose escalation and deescalation. The proposed designs minimize the incorrect decision error rate to find the maximum tolerated dose (MTD). For the late onset toxicity problem, a Bayesian adaptive dose-finding design for drug combination is proposed. The dose-toxicity relationship is modeled using the Finney model. The unobserved delayed toxicity outcomes are treated as missing data and Bayesian data augment is employed to handle the resulting missing data. Extensive simulation studies have been conducted to examine the operating characteristics of the proposed designs and demonstrated the designs' good performances in various practical scenarios.^

Let their voices be heard: Understanding the barriers to seeking early prenatal care for low-income non-Hispanic Black women

Background: Receipt of early prenatal care, care during the first three months of pregnancy, is the standard in the United States. Sixty percent of non-Hispanic Black women who had a live birth in the Sunnyside community of Houston did not obtain early prenatal care in 2009. ^ This study's aims were to: 1) Describe the barriers to obtaining early prenatal care in non-Hispanic Black women who live in the Sunnyside community of Houston; and, 2) Describe the actions that could encourage non-Hispanic Black women who live in the Sunnyside Community to obtain early prenatal care. The goal was to provide information to organizations that promote early prenatal care use in non-Hispanic Black women in Harris County that may aid in developing interventions. ^ Methods: The Participatory Learning for Action rapid assessment qualitative method was used in a group setting to answer the research questions on behalf of women in the community. Women who participated in the group sessions also participated in an in-depth interview. Key informants who work in the community with pregnant women, or promote the use of prenatal care services, were also interviewed. An inductive analysis of the data was conducted to identify common themes that address the study's aims. ^ Results: Aim 1: Group participants identified fear of the reaction from family and/or the baby's daddy and shame, not having insurance or money, and lack of knowledge of the pregnancy and resources as the top three barriers to early prenatal care for women in the community. Aim 2: Group participants stated that to help women to overcome these barriers, communication, awareness and support; help, resources and services; and information and early education are needed. Participant in-depth interviewees echoed the themes of fear of the reaction from family and/or the baby's daddy and not knowing of the pregnancy. Key informants mentioned these themes as well, though not at the same priority level. Participants and key informants also mentioned similar themes for helping women to overcome barriers to early prenatal care. ^ Conclusion: A comprehensive approach is needed to improve early prenatal care use in the Sunnyside community. Education efforts must include all members of the community, young and old, to promote support for pregnant women. Community members must be a part of the process for developing education campaigns. Engaging the community builds a relationship with organizations that serve the community, which may promote use of the organizations' services, and build trust with the community. All efforts must be ongoing so that women and men of all ages in the community understand the importance of prenatal care and support women obtaining care early in the pregnancy.^

Retrospective assesment of the levonorgestrel intrauterine device to treat complex atypical hyperplasia and early endometrioid endometrial cancer

Objective: The primary objective of this project was to describe the efficacy of the Levonorgestrel Intrauterine Device (LIUD) for treatment of Complex Endometrial Cancer (CAH) and Grade 1 Endometrial Cancer (G1EEC) in terms of rate of Complete Response (CR) and Partial Response (PR) after 6 months of therapy. Finally, we assessed if any clinical or pathologic features were associated with response to the LIUD. ^ Methods: This study was a retrospective case series designed to report the response rate of patients with CAH or G1EEC treated with LIUD therapy. In addition, this study has a laboratory component to assess molecular predictors of response to LIUD therapy. Retrospective data already collected from patients diagnosed with CAH or EEC grade 1 and treated with LIUD therapy at MD Anderson Cancer Center (MDACC) were used for this study. Patients from all ethnic and race groups were included. A Complete Response (CR) was defined in patients diagnosed with CAH if pathologic report at 6 months demonstrated either no evidence of hyperplasia or no atypia in the setting of simple or complex hyperplasia. Partial Response (PR) was recorded if disease downgraded to only CAH from G1EEC. No Response (NR) was recorded if pathologic report demonstrates no change (Stable Disease, SD) or progression to cancer (Progressive Disease, PD). We calculated the proportion of patients with complete response to LIUD therapy with 95% confidence interval. We compared the response rates (CR/PR vs NR) by obesity status (Obese if BMI > 40 kg/m2 vs non-obese if BMI <= 40 kg/m2) as well as other clinical and pathologic factors, such as age, uterine size (median size), and presence of exogenous progesterone effect. ^ Results: There were 39 patients diagnosed with either CAH or G1EEC treated with the LIUD. Of 39 patients, 12 did not have pathological results of biopsy at 6months time period. Of 27 evaluable patients, 17 were diagnosed with CAH and 10 with G1EEC. Overall response rate (RR) was 78% (95% CI = 62-94%) at 6 months, 18 patients had CR (4 in G1EEC; 14 in CAH), 3 patients had PR (3 in G1EEC), 3 had SD (1 in CAH; 2 in G1EEC), 3 had PD (2 in CAH; 1 in G1EEC). After histology stratification, RR at 6 months was 82.35% (14/17; 95%CI = 67.4-97.3%) in CAH and 70% (7/10; 95% CI = 41-98.4%) in G1EEC. ^ There was no difference in response (R) and no response (NR) based on BMI (p=0.56). He observed a trend showing association between age with response (p=0.1). There was no association between uterine size and response to therapy (p=0.17). We recorded strong association between exogenous progesterone effect and response. ^ Conclusion: LIUD therapy for the treatment of CAH and G1EEC may be effective and safe. Presence of exogenous progesterone effect may predict the response to LIUD therapy at earlier time points. There is need of further studies with larger sample size to explore the relationship of response with other clinical and pathologic factors^

Exploring parental factors and their influence on early adolescent sexual health

Black and Hispanic youth experience the largest burden of sexually transmitted infections, teen pregnancy, and childbirth (Hamilton, Martin, & Ventura, 2011). Minority youth are disporportionately more likely to sexually debut at every age and debut before the age of 13 compared to whites (Centers for Disease Control and Prevention, 2011). However, there is little known about pre-coital sexual activity or protective parental factors in early adolscent minority youth. Parental factors such as parent-child communication and parental monitoring influence adolescent sexual behaviors and pre-coital sexual behaviors in early adolescence. Three distinct methods were used in this dissertation. Study one used qualitative methods, semi-structured, in-depth, individual interviews, to explore parent-child communication in African American mother-early adolescent son dyads. Study two used quantitative methods, secondary data analysis of a cross sectional study, to conduct a moderation analysis. For study three, I conducted a systematic review of parent-based adolescent sexual health interventions. Study one found that mothers feel comfortable talking about sex with adolescents, provide a two-prong sexual health message, and want their sons to tell their when they are thinking of having sex. Study found that parental monitoring moderates the relation between parent-child communication and pre-coital sexual behaviors. Study three found that interventions use a variety of theory, methods, and strategies and that no parent-based programs target faith-based organizations, mother-son or father-daughter dyads, or parents of LGBTQ youth. Adolescent sexual health interventions should consider addressing youth-to-parent disclosure of sexual activity or intentions to debut, addressing both parent-child sexual health communication and parental monitoring, and using a theoretical framework.^

The SasS -SasR two-component signal transduction system required for early Myxococcus xanthus multicellular *development

Initiation of Myxococcus xanthus multicellular development requires both nutrient limitation and high cell density. The extracellular signal, A signal, which consists of a set of amino acids at specific concentrations, serves as a cell density signal in M. xanthus early development. A reporter gene, designated 4521, that requires both starvation and A signal for developmental expression was used to identify mutations in the signal transduction pathways. A group of point mutations located in the chromosomal sasB locus that bypasses both requirements was previously isolated. One of these point mutations, sasB7, was mapped to the sasS gene, which is predicted to encode a transmembrane histidine protein kinase required for normal development. SasS is a positive regulator of 4521 and a candidate A signal sensor. This dissertation continues the characterization of the sasB locus, focusing on the sasR gene and the functional relationship of SasS and SasR. ^ The sasR gene is located 2.2-kb downstream of sasS. It is predicted to encode an NtrC-like response regulator, which belongs to the family of sigma54 transcriptional activators. SasR is a positive regulator of 4521 gene and is required for normal development. The sasR mutant displays phenotypes similar to that of sasS mutant. Both SasS and SasR are required for the A-signal-dependent 4521 expression. Genetic epistasis analysis indicates that SasR functions downstream of SasS. Biochemical studies show that SasS has autokinase activity, and phosphorylated SasS is able to transfer its phosphate to SasR. We propose that SasS and SasR form a two-component signal transduction system in the A signal transduction pathway. ^ To search for the genes regulated by SasS and SasR, expression patterns of a group of developmental genes were compared in wild-type and sasS null mutant backgrounds. SasS and SasR were found to positively regulate sasN and 4521. The sasN gene was previously identified as a negative regulator of 4521, located at about 170-bp downstream of sasR. It is required for normal fruiting body development. Based on the above data, a regulatory network consisting of sasS, sasR, sasN, and 4521 is hypothesized, and the interactions of the components in this network can now be further studied. ^

Late Pliocene and Early Pleistocene dinoflagellate cysts and sea surface temperture reconstruction for several IODP and DSDP sites in the North Atlantic

In an attempt to document the palaeoecological affinities of individual extant and extinct dinoflagellate cysts, Late Pliocene and Early Pleistocene dinoflagellate cyst assemblages have been compared with geochemical data from the same samples. Mg/Ca ratios of Globigerina bulloides were measured to estimate the spring-summer sea-surface temperatures from four North Atlantic IODP/DSDP sites. Currently, our Pliocene-Pleistocene database contains 204 dinoflagellate cyst samples calibrated to geochemical data. This palaeo-database is compared with modern North Atlantic and global datasets. The focus lies in the quantitative relationship between Mg/Ca-based (i.e. spring-summer) sea-surface temperature (SSTMg/Ca) and dinoflagellate cyst distributions. In general, extant species are shown to have comparable spring-summer SST ranges in the past and today, demonstrating that our new approach is valid for inferring spring-summer SST ranges for extinct species. For example, Habibacysta tectata represents SSTMg/Ca values between 10° and 15°C when it exceeds 30% of the assemblage, and Invertocysta lacrymosa exceeds 15% when SSTMg/Ca values are between 18.6° and 23.5°C. However, comparing Pliocene and Pleistocene SSTMg/Ca values with present day summer values for the extant Impagidinium pallidum suggests a greater tolerance of higher temperatures in the past. This species occupies more than 5% of the assemblage at SSTMg/Ca values of 11.6-17.9°C in the Pliocene and Pleistocene, whereas present day summer SSTs are around -1.7 to 6.9°C. This observation questions the value of Impagidinium pallidum as reliable indicator of cold waters in older deposits, and may explain its bipolar distribution.

Isotope measurements from late Paleocene - early Eocene of 5 cores from Atlantic and Pacific Ocean

High-resolution stable carbon isotope records for upper Paleocene - lower Eocene sections at Ocean Drilling Program Sites 1051 and 690 and Deep Sea Drilling Project Sites 550 and 577 show numerous rapid (40 - 60 kyr duration) negative excursions of up to 1 per mill. We demonstrate that these transient decreases are the expected result of nonlinear insolation forcing of the carbon cycle in the context of a long carbon residence time. The transients occur at maxima in Earth's orbital eccentricity, which result in high-amplitude variations in insolation due to forcing by climatic precession. The construction of accurate orbital chronologies for geologic sections older than ~ 35 Ma relies on identifying a high-fidelity recorder of variations in Earth's orbital eccentricity. We use the carbon isotope records as such a recorder, establishing a robust orbitally tuned chronology for latest Paleocene-earliest Eocene events. Moreover, the transient decreases provide a means of precise correlation among the four sites that is independent of magnetostratigraphic and biostratigraphic data at the <10^5-year scale. While the eccentricity-controlled transient decreases bear some resemblance to the much larger-amplitude carbon isotope excursion (CIE) that marks the Paleocene/Eocene boundary, the latter event is found to occur near a minimum in the ~400-kyr eccentricity cycle. Thus the CIE occurred during a time of minimal variability in insolation, the dominant mechanism for forcing climate change on 104-year scales. We argue that this is inconsistent with mechanisms that rely on a threshold climate event to trigger the Paleocene/Eocene thermal maximum since any threshold would more likely be crossed during a period of high-amplitude climate variations.

Integrated Data Sets of the EU FP5 Research Project ORFOIS: Origin and fate of biogenic particle fluxes in the ocean and their interactions with atmospheric CO2 concentrations as well as the marine sediment

For a reliable simulation of the time and space dependent CO2 redistribution between ocean and atmosphere an appropriate time dependent simulation of particle dynamics processes is essential but has not been carried out so far. The major difficulties were the lack of suitable modules for particle dynamics and early diagenesis (in order to close the carbon and nutrient budget) in ocean general circulation models, and the lack of an understanding of biogeochemical processes, such as the partial dissolution of calcareous particles in oversaturated water. The main target of ORFOIS was to fill in this gap in our knowledge and prediction capability infrastructure. This goal has been achieved step by step. At first comprehensive data bases (already existing data) of observations of relevance for the three major types of biogenic particles, organic carbon (POC), calcium carbonate (CaCO3), and biogenic silica (BSi or opal), as well as for refractory particles of terrestrial origin were collated and made publicly available.

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 and benthic stables Isotopes, age model and carbon analysis of HUD91/039 from the northernmost Baffin Bay

A multiproxy study of palaeoceanographic and climatic changes in northernmost Baffin Bay shows that major environmental changes have occurred since the deglaciation of the area at about 12 500 cal. yr BP. The interpretation is based on sedimentology, benthic and planktonic foraminifera and their isotopic composition, as well as diatom assemblages in the sedimentary records at two core sites, one located in the deeper central part of northernmost Baffin Bay and one in a separate trough closer to the Greenland coast. A revised chronology for the two records is established on the basis of 15 previously published AMS 14C age determinations. A basal diamicton is overlain by laminated, fossil-free sediments. Our data from the early part of the fossiliferous record (12 300 - 11 300 cal. yr BP), which is also initially laminated, indicate extensive seasonal sea-ice cover and brine release. There is indication of a cooling event between 11 300 and 10 900 cal. yr BP, and maximum Atlantic Water influence occurred between 10 900 and 8200 cal. yr BP (no sediment recovery between 8200 and 7300 cal. yr BP). A gradual, but fluctuating, increase in sea-ice cover is seen after 7300 cal. yr BP. Sea-ice diatoms were particularly abundant in the central part of northernmost Baffin Bay, presumably due to the inflow of Polar waters from the Arctic Ocean, and less sea ice occurred at the near-coastal site, which was under continuous influence of the West Greenland Current. Our data from the deep, central part show a fluctuating degree of upwelling after c. 7300 cal. yr BP, culminating between 4000 and 3050 cal. yr BP. There was a gradual increase in the influence of cold bottom waters from the Arctic Ocean after about 3050 cal. yr BP, when agglutinated foraminifera became abundant. A superimposed short-term change in the sea-surface proxies is correlated with the Little Ice Age cooling.

Early and Middle Miocene calcareous nannofossil distribution in the North Atlantic Ocean

Deep Sea Drilling Project Site 563, located on the west flank of the northern Mid-Atlantic Ridge, recovered a long Miocene section from which magnetostratigraphic and isotopic stratigraphy are available. Quantitative analyses of calcareous nannofossil assemblages have been performed in the Lower and Middle Miocene sediments from Site 563. The abundance patterns of the identified species allow us to determine several bioevents for this time interval. The recognized biohorizons, related to the available magnetostratigraphy, provide new data on the biostratigraphic value of many species and on the synchroneity of the events over a wide geographic area. Relations with the oxygen isotope stratigraphy are also reported. Sphenolith distribution is examined in particular detail due to their biostratigraphic importance in the Early Miocene. In particular the recently described species Sphenolithus procerus, Sphenolithus tintinnabulum and Sphenolithus multispinatus can be useful to subdivide the Lower Miocene zones NN2 and NN3. A large variety of Reticulofenestra pseudoumbilicus has been identified within zones NN6 and NN7.

(Table S1) Diatom species richness from the Early Pleistocene to present

The extent to which the spatial distribution of marine planktonic microbes is controlled by local environmental selection or dispersal is poorly understood. Our ability to separate the effects of these two biogeographic controls is limited by the enormous environmental variability both in space and through time. To circumvent this limitation, we analyzed fossil diatom assemblages over the past ~1.5 million years from the world oceans and show that these eukaryotic microbes are not limited by dispersal. The lack of dispersal limitation in marine diatoms suggests that the biodiversity at the microbial level fundamentally differs from that of macroscopic animals and plants for which geographic isolation is a common component of speciation.

Tab. 1: Rb-Sr data on metasediments in the Shackleton Range

Summary: The stratigraphy of the Shackleton Range established by Stephenson (1966) and Clarkson (1972) was revised by results of the German Expedition GEISHA 1987/88. The "Turnpike Bluff Group" does not form a stratigraphic unit. The stratigraphic correlation of its formations is still a matter of discussion. The following four formations are presumed to belong to different units: The Stephenson Bastion Formation and Wyeth Heights Formation are probably of Late Precambrian age. The Late Precambrian Watts Needle Formation, which lies unconformably on the Read Group, is an independant unit which has to be separated from the "Turnpike Bluff Group". The Mount Wegener Formation has been thrusted over the Watts Needle Formation. Early Cambrian fossils (Oldhamia sp., Epiphyton sp., Botomaella (?) sp. and echinoderms) were found in the Mt. Wegener Formation in the Read Mountains. The Middle Cambrian trilobite shales on Mount Provender, which form the Haskard Highlands Formation, are possibly in faulted contact with the basement complex (Pioneers and Stratton Groups). They are overlain by the Blaiklock Glacier Group, for which an Ordovician age is indicated by trilobite tracks and trails, low inclination of the paleomagnetic field and the similarity to the basal units of the Table Mountain Quartzite in South Africa. The Watts Needle Formation represents epicontinental shelf sediments, the Mount Wegener Formation was deposited in a (continental) back-arc environment, and the Blaiklock Glacier Group is a typical molasse sediment of the Ross Orogen.