Adaptive clinical trial design for targeted therapy development

The development of targeted therapy involve many challenges. Our study will address some of the key issues involved in biomarker identification and clinical trial design. In our study, we propose two biomarker selection methods, and then apply them in two different clinical trial designs for targeted therapy development. In particular, we propose a Bayesian two-step lasso procedure for biomarker selection in the proportional hazards model in Chapter 2. In the first step of this strategy, we use the Bayesian group lasso to identify the important marker groups, wherein each group contains the main effect of a single marker and its interactions with treatments. In the second step, we zoom in to select each individual marker and the interactions between markers and treatments in order to identify prognostic or predictive markers using the Bayesian adaptive lasso. In Chapter 3, we propose a Bayesian two-stage adaptive design for targeted therapy development while implementing the variable selection method given in Chapter 2. In Chapter 4, we proposed an alternate frequentist adaptive randomization strategy for situations where a large number of biomarkers need to be incorporated in the study design. We also propose a new adaptive randomization rule, which takes into account the variations associated with the point estimates of survival times. In all of our designs, we seek to identify the key markers that are either prognostic or predictive with respect to treatment. We are going to use extensive simulation to evaluate the operating characteristics of our methods.^

Development of a SPECT -based three-dimensional treatment planner for radionuclide therapy with iodine -131

Accurate calculation of absorbed dose to target tumors and normal tissues in the body is an important requirement for establishing fundamental dose-response relationships for radioimmunotherapy. Two major obstacles have been the difficulty in obtaining an accurate patient-specific 3-D activity map in-vivo and calculating the resulting absorbed dose. This study investigated a methodology for 3-D internal dosimetry, which integrates the 3-D biodistribution of the radionuclide acquired from SPECT with a dose-point kernel convolution technique to provide the 3-D distribution of absorbed dose. Accurate SPECT images were reconstructed with appropriate methods for noise filtering, attenuation correction, and Compton scatter correction. The SPECT images were converted into activity maps using a calibration phantom. The activity map was convolved with an $\sp{131}$I dose-point kernel using a 3-D fast Fourier transform to yield a 3-D distribution of absorbed dose. The 3-D absorbed dose map was then processed to provide the absorbed dose distribution in regions of interest. This methodology can provide heterogeneous distributions of absorbed dose in volumes of any size and shape with nonuniform distributions of activity. Comparison of the activities quantitated by our SPECT methodology to true activities in an Alderson abdominal phantom (with spleen, liver, and spherical tumor) yielded errors of $-$16.3% to 4.4%. Volume quantitation errors ranged from $-$4.0 to 5.9% for volumes greater than 88 ml. The percentage differences of the average absorbed dose rates calculated by this methodology and the MIRD S-values were 9.1% for liver, 13.7% for spleen, and 0.9% for the tumor. Good agreement (percent differences were less than 8%) was found between the absorbed dose due to penetrating radiation calculated from this methodology and TLD measurement. More accurate estimates of the 3-D distribution of absorbed dose can be used as a guide in specifying the minimum activity to be administered to patients to deliver a prescribed absorbed dose to tumor without exceeding the toxicity limits of normal tissues. ^

Molecular and genetic analysis of Myxococcus xanthus early *development

To identify more mutations that can affect the early development of Myxococcus xanthus, the synthetic transposon TnT41 was designed and constructed. By virtue of its special features, it can greatly facilitate the processes of mutation screening/selection, mapping, cloning and DNA sequencing. In addition, it allows for the systematic discovery of genes in regulatory hierarchies using their target promoters. In this study, the minimal regulatory region of the early developmentally regulated gene 4521 was used as a reporter in the TnT41 mutagenesis. Both positive (P) mutations and negative (N) mutations were isolated based on their effects on 4521 expression.^ Four of these mutations, i.e. N1, N2, P52 and P54 were analyzed in detail. Mutations N1 and N2 are insertion mutations in a gene designated sasB. The sasB gene is also identified in this study by genetic and molecular analysis of five UV-generated 4521 suppressor mutations. The sasB gene encodes a protein without meaningful homology in the databases. The sasB gene negatively regulates 4521 expression possibly through the SasS-SasR two component system. A wild-type sasB gene is required for normal M. xanthus fruiting body formation and sporulation.^ Cloning and sequencing analysis of the P52 mutation led to the identification of an operon that encodes the M. xanthus high-affinity branched-chain amino acid transporter system. This liv operon consists of five genes designated livK, livH, livM, livC, and livF, respectively. The Liv proteins are highly similar to their counterparts from other bacteria in both amino acid sequences, functional motifs and predicted secondary structures. This system is required for development since liv null mutations cause abnormality in fruiting body formation and a 100-fold decrease in sporulation efficiency.^ Mutation P54 is a TnT41 insertion in the sscM gene of the ssc chemotaxis system, which has been independently identified by Dr. Shi's lab. The sscM gene encodes a MCP (methyl-accepting chemotaxis protein) homologue. The SscM protein is predicted to contain two transmembrane domains, a signaling domain and at least one putative methylation site. Null mutations of this gene abolish the aggregation of starving cells at a very early stage, though the sporulation levels of the mutant can reach 10% that of wild-type cells. ^

Functions of GCN5 and P /CAF acetyltransferases in mammalian development

Histone acetyltransferases are important chromatin modifiers that function as transcriptional co-activators. The identification of the transcriptional regulator GCN5 as the first nuclear histone acetyltransferase in yeast directly linked chromatin remodeling to transcriptional regulation. Although emerging evidence suggests that acetyltransferases participate in multiple cellular processes, their roles in mammalian development remain undefined. In this study, I have cloned and characterized the mouse homolog of GCN5 and a closely related protein P/CAF that interacts with p300/CBP. In contrast to yeast GCN5, but similar to P/CAF, mouse GCN5 possesses an additional N-terminal domain that confers the ability to acetylate nucleosomal histones. GCN5 and P/CAF exhibit identical substrate specificity and both interact with p300/CBP. Interestingly, expression levels of GCN5 and P/CAF display a complementary pattern in mouse embryos and in adult tissues, suggesting that they have distinct tissue or developmental stage specific roles. To define the in vivo function of GCN5 and P/CAF, I have generated mice that are nullizygous for GCN5 or P/CAF. P/CAF null mice are viable and fertile with no gross morphological defects, indicating that P/CAF is dispensable for development and p300/CBP function in vivo. In contrast, mice lacking GCN5 die between 10.5–11 days of gestation. GCN5 null mice are severely retarded but have anterior ectopic outgrowth. Molecular marker analyses reveal that early mesoderm is formed in GCN5 null mice but further differentiation into distinct mesodermal lineages is perturbed. While presomitic mesoderm and chodamesoderm are missing in GCN5 mutant mice, extraembryonic tissues and lateral mesoderm are unaffected. This is consistent with our finding that GCN5 expression is absent in the heart and extraembryonic tissues but is uniform throughout the rest of the embryo. Remarkably, GCN5 mutant mice exhibit an unusually high incidence of apoptosis in the embryonic ectoderm and mesoderm. Finally, mice doubly null for GCN5 and P/CAF die much earlier than mice harboring the GCN5 mutation alone, suggesting that P/CAF and GCN5 share some overlapping function during embryogenesis. This work is the first study to show that specific acetyltransferase is important for cell survival as well as mesoderm differentiation or maintenance during early mammalian development. ^

Activation of c -Met contributes to growth and metastasis of human colorectal carcinoma

c-Met is the protein tyrosine kinase receptor for hepatocyte growth factor/scatter factor (HGF/SF) and mediates several normal cellular functions including proliferation, survival, and migration. Overexpression of c-Met correlates with progression and metastasis of human colorectal carcinoma (CRC). The goals of this study were to determine if overexpression of c-Met directly contributes to tumorigenicity and liver metastatic potential of colon cancer, and what are the critical pathways regulated by c-Met in this process. The studies used two colon tumor cell lines, KM12SM and KM20, which express high levels of constitutively active c-Met and are highly metastatic in nude mice. To examine the effects of c-Met overexpression, subclones of theses lines with reduced c-Met expression were obtained following transfection with a c-Met specific targeting ribozyme. Reduction of c-Met in KM12SM cells abolished liver metastases when cells were injected intrasplenically in an experimental metastasis assay. However, c-Met downregulation in theses clones was unstable. Three stable KM20 clones with a 25–35% reduction in c-Met protein levels but 60–90% reduction in basal c-Met autophosphorylation and kinase activity were obtained. While HGF increased c-Met kinase activity in the clones with reduced c-Met, the activity was less than that observed in parental or control transfected cells. Correlating with the reduction in c-Met kinase activity, subclones with reduced c-Met expression had significantly reduced in vitro growth rates, soft-agar colony forming abilities, and increased apoptosis. HGF/SF treatment did not affect anchorage-dependent growth or soft-agar colony forming abilities. Further, c-Met downregulation significantly impaired the ability of HGF/SF to induce migration. To examine the effects of reduced c-Met on tumor formation, parental and c-Met reduced KM20 cells were grown subcutaneously and intrahepatically in nude mice. c-Met downregulation delayed, but did not abolish growth at the subcutaneous site. When these cells were injected intrahepatically, both tumor incidences and size were significantly reduced. To further understand the molecular basis of c-Met in promoting tumor growth, the activation of several signaling intermediates that have been implicated in c-Met mediated growth, survival and migration were compared between KM20 parental cells and subclones with reduced c-Met expression levels. The expression and activity (as determined by phosphorylation) of AKT and Erk1/2 were unaltered. In contrast, Src kinase activity, as measured by immune complex kinase assay, was reduced 2–5 fold following c-Met downregulation. As Src has been implicated in growth, survival and migration, Src activation in c-Met overexpressing lines is likely contributing to the tumorigenic and metastatic capabilities of colon tumor cell lines that overexpress c-Met. Collectively, these results suggest that c-Met overexpression plays a causal role in the development of CRC liver metastases, and that c-Src and c-Met inhibitors may be of potential therapeutic benefit for late-stage colon cancer. ^

Compilation of scientific results of the OASIS project

Seamounts are of great interest to science, industry and conservation because of their potential role as 'stirring rods' of the oceans, their enhanced productivity, their high local biodiversity, and the growing exploitation of their natural resources. This is accompanied by rising concern about the threats to seamount ecosystems, e.g. through over-fishing and the impact of trawling. OASIS described the functioning characteristics of seamount ecosystems. OASIS' integrated hydrographic, biogeochemical and biological information. Based on two case studies. The scientific results, condensed in conceptual and mass balanced ecosystem models, were applied to outline a model management plan as well as site-specific management plans for the seamounts investigated. OASIS addressed five main objectives: Objective 1: To identify and describe the physical forcing mechanisms effecting seamount systems Objective 2: To assess the origin, quality and dynamics of particulate organic material within the water column and surface sediment at seamounts. Objective 3: To describe aspects of the biodiversity and the ecology of seamount biota, to assess their dynamics and the maintenance of their production. Objective 4: Modelling the trophic ecology of seamount ecosystems. Objective 5: Application of scientific knowledge to practical conservation.

Sea surface temperatures during Marine Isotope Stage (MIS) 11

The Marine Isotope Stage (MIS) 11 (424-374 ka) was characterized by a protracted deglaciation and an unusually long climatic optimum. It remains unclear to what degree the climate development during this interglacial reflects the unusually weak orbital forcing or greenhouse gas trends. Previously, arguments about the duration and timing of the MIS11 climatic optimum and about the pace of the deglacial warming were based on a small number of key records, which appear to show regional differences. In order to obtain a global signal of climate evolution during MIS11, we compiled a database of 78 sea surface temperature (SST) records from 57 sites spanning MIS11, aligned these individually on the basis of benthic (N = 28) or planktonic (N = 31) stable oxygen isotope curves to a common time frame and subjected 48 of them to an empirical orthogonal function (EOF) analysis. The analysis revealed a high commonality among all records, with the principal SST trend explaining almost 49% of the variability. This trend indicates that on the global scale, the surface ocean underwent rapid deglacial warming during Termination V, in pace with carbon dioxide rise, followed by a broad SST optimum centered at ~410 kyr. The second EOF, which explained ~18% of the variability, revealed the existence of a different SST trend, characterized by a delayed onset of the temperature optimum during MIS11 at ~398 kyr, followed by a prolonged warm period lasting beyond 380 kyr. This trend is most consistently manifested in the mid-latitude North Atlantic and Mediterranean Sea and is here attributed to the strength of the Atlantic meridional overturning circulation. A sensitivity analysis indicates that these results are robust to record selection and to age-model uncertainties of up to 3-6 kyr, but more sensitive to SST seasonal attribution and SST uncertainties >1 °C. In order to validate the CCSM3 (Community Climate System Model, version 3) predictive potential, the annual and seasonal SST anomalies recorded in a total of 74 proxy records were compared with runs for three time slices representing orbital configuration extremes during the peak interglacial of MIS11. The modeled SST anomalies are characterized by a significantly lower variance compared to the reconstructions. Nevertheless, significant correlations between proxy and model data are found in comparisons on the seasonal basis, indicating that the model captures part of the long-term variability induced by astronomical forcing, which appears to have left a detectable signature in SST trends.

Project development for older adults : Orientation's contribution

This paper systematizes the work developed during the first year of the initiation scholarship for the research project entitled 'Orientation within the new Active Aging Model: educational, work-related, personal and social choices (1)'. This project articulates the Active Aging Model and the Theoretical Operative Model in Orientation, in order to learn how new projects are developed by older adults who used to be part of the formal system of labor and by those who were out of it, and to design programmatic proposals for educational, work-related, personal and social Orientation choices for such population. The sample is made up by seventy people between 64 and 74 years of age, residing in La Plata. The first conclusions evidence the importance that older adults place on project development at this stage of their life cycle, giving special importance to educational, personal and social projects; as well as on the identification of economic factors, health state, family needs for care and social support, among other things, as conditioning the fulfillment of such projects. The differences found in terms of the labor system they used to belong to can be especially observed in the type of project developed.

The development of professor's professional knowledge in Psychology

This work belongs to the Project "Teaching and learning Psychology: a study of the educational practice in professors and beginners". It is part of an investigation program developed in the context of the subject "Didactic and Practical Planning of Psychology teaching" in which we have been working since 1998. This subject is also considered as the final stage of the formative itinerary for Psychology s professors. The reached results show the incidence that the beliefs and professors' representations have in the teaching processes. By getting into the studies centered in the educational knowledge we guide the inquiry around the development of the professor's professional knowledge and particularly the development of their formation. Our proposal contemplates a formation device which incorporates the observation, reflection, evaluation and self-evaluation of the practice in order to facilitate the reconstruction, significance and re-significance of the teaching and learning processes by giving relevance to the development of the teacher professional knowledge. The analysis of teaching practices process reveals that the mediations that cross the knowledge in the being taught instances are constituted in reflections axes. This involves the future professor's relationship with the knowledge and their projection in the construction of the professional identity.

Project development for older adults : Orientation's contribution

This paper systematizes the work developed during the first year of the initiation scholarship for the research project entitled 'Orientation within the new Active Aging Model: educational, work-related, personal and social choices (1)'. This project articulates the Active Aging Model and the Theoretical Operative Model in Orientation, in order to learn how new projects are developed by older adults who used to be part of the formal system of labor and by those who were out of it, and to design programmatic proposals for educational, work-related, personal and social Orientation choices for such population. The sample is made up by seventy people between 64 and 74 years of age, residing in La Plata. The first conclusions evidence the importance that older adults place on project development at this stage of their life cycle, giving special importance to educational, personal and social projects; as well as on the identification of economic factors, health state, family needs for care and social support, among other things, as conditioning the fulfillment of such projects. The differences found in terms of the labor system they used to belong to can be especially observed in the type of project developed.

The development of professor's professional knowledge in Psychology

This work belongs to the Project "Teaching and learning Psychology: a study of the educational practice in professors and beginners". It is part of an investigation program developed in the context of the subject "Didactic and Practical Planning of Psychology teaching" in which we have been working since 1998. This subject is also considered as the final stage of the formative itinerary for Psychology s professors. The reached results show the incidence that the beliefs and professors' representations have in the teaching processes. By getting into the studies centered in the educational knowledge we guide the inquiry around the development of the professor's professional knowledge and particularly the development of their formation. Our proposal contemplates a formation device which incorporates the observation, reflection, evaluation and self-evaluation of the practice in order to facilitate the reconstruction, significance and re-significance of the teaching and learning processes by giving relevance to the development of the teacher professional knowledge. The analysis of teaching practices process reveals that the mediations that cross the knowledge in the being taught instances are constituted in reflections axes. This involves the future professor's relationship with the knowledge and their projection in the construction of the professional identity.

Project development for older adults : Orientation's contribution

This paper systematizes the work developed during the first year of the initiation scholarship for the research project entitled 'Orientation within the new Active Aging Model: educational, work-related, personal and social choices (1)'. This project articulates the Active Aging Model and the Theoretical Operative Model in Orientation, in order to learn how new projects are developed by older adults who used to be part of the formal system of labor and by those who were out of it, and to design programmatic proposals for educational, work-related, personal and social Orientation choices for such population. The sample is made up by seventy people between 64 and 74 years of age, residing in La Plata. The first conclusions evidence the importance that older adults place on project development at this stage of their life cycle, giving special importance to educational, personal and social projects; as well as on the identification of economic factors, health state, family needs for care and social support, among other things, as conditioning the fulfillment of such projects. The differences found in terms of the labor system they used to belong to can be especially observed in the type of project developed.

The development of professor's professional knowledge in Psychology

This work belongs to the Project "Teaching and learning Psychology: a study of the educational practice in professors and beginners". It is part of an investigation program developed in the context of the subject "Didactic and Practical Planning of Psychology teaching" in which we have been working since 1998. This subject is also considered as the final stage of the formative itinerary for Psychology s professors. The reached results show the incidence that the beliefs and professors' representations have in the teaching processes. By getting into the studies centered in the educational knowledge we guide the inquiry around the development of the professor's professional knowledge and particularly the development of their formation. Our proposal contemplates a formation device which incorporates the observation, reflection, evaluation and self-evaluation of the practice in order to facilitate the reconstruction, significance and re-significance of the teaching and learning processes by giving relevance to the development of the teacher professional knowledge. The analysis of teaching practices process reveals that the mediations that cross the knowledge in the being taught instances are constituted in reflections axes. This involves the future professor's relationship with the knowledge and their projection in the construction of the professional identity.

Liver proteome profiling of juvenile Chinese sturgeon (Acipenser sinensis) using GeLC-MS/MS approach

Chinese sturgeon (Acipenser sinensis), mainly distributed in the Yangtze River, has been listed as a grade I protected animal in China because of a dramatic decline in population owing to loss of natural habitat for reproduction and interference by human activities. Understanding the proteome profile of Chinese sturgeon liver would provide an invaluable resource for protecting and increasing the stocks of this species. In this study, we have analyzed proteome profiles of juvenile Chinese sturgeon liver using a one-dimensional gel electrophoresis coupled to LC-MS/MS approach. A total of 1059 proteins and 2084 peptides were identified. The liver proteome was found to be associated with diverse biological processes, cellular components and molecular functions. The proteome profile identified a variety of significant pathways including carbohydrate metabolism, fatty acid metabolism and amino acid metabolism pathways. It also established a network for protein biosynthesis, folding and catabolic processes. The proteome profile established in this study can be used for understanding the development of Chinese sturgeon and studying the molecular mechanisms of action under environmental or chemical stress, providing very useful omics information that can be applied to preserve this species.

Geochemistry of tropical Atlantic sediments of Marine Isotope Stage 4

Antarctic Intermediate Water (AAIW) and Subantarctic Mode Water (SAMW) are the main conduits for the supply of dissolved silicon (silicic acid) from the deep Southern Ocean (SO) to the low-latitude surface ocean and therefore have an important control on low-latitude diatom productivity. Enhanced supply of silicic acid by AAIW (and SAMW) during glacial periods may have enabled tropical diatoms to outcompete carbonate-producing phytoplankton, decreasing the relative export of inorganic to organic carbon to the deep ocean and lowering atmospheric pCO2. This mechanism is known as the "silicic acid leakage hypothesis" (SALH). Here we present records of neodymium and silicon isotopes from the western tropical Atlantic that provide the first direct evidence of increased silicic acid leakage from the Southern Ocean to the tropical Atlantic within AAIW during glacial Marine Isotope Stage 4 (~60-70 ka). This leakage was approximately coeval with enhanced diatom export in the NW Atlantic and across the eastern equatorial Atlantic and provides support for the SALH as a contributor to CO2 drawdown during full glacial development.