Barriers to cross-border research projects: A prelude to improving professional collaborations between the United States and Mexico

Study objective. This was a secondary data analysis of a study designed and executed in two phases in order to investigate several questions: Why aren't more investigators conducting successful cross-border research on human health issues? What are the barriers to conducting this research? What interventions might facilitate cross-border research? ^ Methods. Key informant interviews and focus groups were used in Phase One, and structured questionnaires in Phase Two. A multi-question survey was created based on the findings of focus groups and distributed to a wider circle of researchers and academics for completion. The data was entered and analyzed using SPSS software. ^ Setting. El Paso, TX located on the U.S-Mexico Border. ^ Participants. Individuals from local academic institutions and the State Department of Health. ^ Results. From the transcribed data of the focus groups, eight major themes emerged: Political Barriers, Language/Cultural Barriers, Differing Goals, Geographic Issues, Legal Barriers, Technology/Material Issues, Financial Barriers, and Trust Issues. Using these themes, the questionnaire was created. ^ The response rate for the questionnaires was 47%. The largest obstacles revealed by this study were identifying a funding source for the project (47% agreeing or strongly agreeing), difficulties paying a foreign counterpart (33% agreeing or strongly agreeing) and administrative changes in Mexico (31% agreeing or strongly agreeing). ^ Conclusions. Many U.S. investigators interested in cross-border research have been discouraged in their efforts by varying barriers. The majority of respondents in the survey felt financial issues and changes in Mexican governments were the most significant obstacles. While some of these barriers can be overcome simply by collaboration among motivated groups, other barriers may be more difficult to remove. Although more evaluation of this research question is warranted, the information obtained through this study is sufficient to support creation of a Cross-Border Research Resource Manual to be used by individuals interested in conducting research with Mexico. ^

Molecular consequences of the loss of 3'→5' exonuclease activity of DNA polymerases delta and epsilon

The DNA replication polymerases δ and ϵ have an inherent proofreading mechanism in the form of a 3'→5' exonuclease. Upon recognition of errant deoxynucleotide incorporation into DNA, the nascent primer terminus is partitioned to the exonuclease active site where the incorrectly paired nucleotide is excised before resumption of polymerization. The goal of this project was to identify the cellular and molecular consequences of an exonuclease deficiency. The proofreading capability of model system MEFs with EXOII mutations was abolished without altering polymerase function.^ It was hypothesized that 3'→5' exonucleases of polymerases δ and ϵ are critical for prevention of replication stress and important for sensitization to nucleoside analogs. To test this hypothesis, two aims were formulated: Determine the effect of the exonuclease active site mutation on replication related molecular signaling and identify the molecular consequences of an exonuclease deficiency when replication is challenged with nucleoside analogs.^ Via cell cycle studies it was determined that larger populations of exonuclease deficient cells are in the S-phase. There was an increase in levels of replication proteins, cell population growth and DNA synthesis capacity without alteration in cell cycle progression. These findings led to studies of proteins involved in checkpoint activation and DNA damage sensing. Finally, collective modifications at the level of DNA replication likely affect the strand integrity of DNA at the chromosomal level.^ Gemcitabine, a DNA directed nucleoside analog is a substrate of polymerases δ and ϵ and exploits replication to become incorporated into DNA. Though accumulation of gemcitabine triphosphate was similar in all cell types, incorporation into DNA and rates of DNA synthesis were increased in exonuclease defective cells and were not consistent with clonogenic survival. This led to molecular signaling investigations which demonstrated an increase in S-phase cells and activation of a DNA damage response upon gemcitabine treatment.^ Collectively, these data indicate that the loss of exonuclease results in a replication stress response that is likely required to employ other repair mechanisms to remove unexcised mismatches introduced into DNA during replication. When challenged with nucleoside analogs, this ongoing stress response coupled with repair serves as a resistance mechanism to cell death.^

Epidemiologic and methodological issues in serial measurements of blood pressure: The blood pressure study in Mexican children

The Blood Pressure Study in Mexican Children (BPSMC) is a short term longitudinal study of serial blood pressure collected in three observation periods by standardized examinations of 233 female children, 10 to 12 years of age, enrolled in public and private primary schools in Tlalpan, Mexico. Study objectives were: (1) to describe from baseline information the distribution and relationship of blood pressure to age and selected anthropometric factors, as well as to compare the BPSMC results with other blood pressure studies, (2) to examine the sources and amount of variation present in serial blood pressure of 123 children, and (3) to evaluate observer performance by means of intra- and inter-observer variability.^ Stepwise regression results from baseline revealed that of all anthropometric factors and age, weight was the best predictor for blood pressure.^ The results of serial blood pressure measurements show that, besides the known sources of blood pressure variability (subject, day, reading), the physiologic event of menarche has an important bearing upon the variability and characterization of blood pressure in young girls. The assessment of the effects of blood pressure variability and reliability upon the design and analysis of epidemiologic studies, became apparent among post-menarcheal girls; where blood pressure measurements taken from them have low reliability. Research is needed to propose alternatives for assessing blood pressure during puberty.^ Finally, observer performance of blood pressure and anthropometry were evaluated. Anthropometric measurements had reliabilities in excess of R = 0.96. Acceptable reliabilities (R = 0.88 to 0.95) were obtained for systolic and diastolic (phase 4 and 5) blood pressures. The BPSMC showed a 50 percent decrease in measurement error from the first to the third observation periods. ^

Bayesian adaptive designs for drug combinations in early phase clinical trials

Treating patients with combined agents is a growing trend in cancer clinical trials. Evaluating the synergism of multiple drugs is often the primary motivation for such drug-combination studies. Focusing on the drug combination study in the early phase clinical trials, our research is composed of three parts: (1) We conduct a comprehensive comparison of four dose-finding designs in the two-dimensional toxicity probability space and propose using the Bayesian model averaging method to overcome the arbitrariness of the model specification and enhance the robustness of the design; (2) Motivated by a recent drug-combination trial at MD Anderson Cancer Center with a continuous-dose standard of care agent and a discrete-dose investigational agent, we propose a two-stage Bayesian adaptive dose-finding design based on an extended continual reassessment method; (3) By combining phase I and phase II clinical trials, we propose an extension of a single agent dose-finding design. We model the time-to-event toxicity and efficacy to direct dose finding in two-dimensional drug-combination studies. We conduct extensive simulation studies to examine the operating characteristics of the aforementioned designs and demonstrate the designs' good performances in various practical scenarios.^

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.

Geochemistry of Fe-Mn crusts in sediments of the Central Indian Ridge

Layered Fe-Mn crusts from the off-axis region of the first segment of the Central Indian Ridge north of the Rodrigues Triple Junction were studied geochemically and mineralogically. Vernadite (delta-MnO2) is the main mineral oxide phase. 230Thxs and Co concentrations suggest high growth rates of up to 29 mm/Myr and a maximum age of the basal crust layer of 1 Ma. Whereas most of the major and minor elements show concentrations which are typical of hydrogenetic formation, Co, Pb, Ni and Ti concentrations are strikingly lower. Concentrations and distribution of the strictly trivalent rare-earths and yttrium (REY) are typical of hydrogenetic ferromanganese oxide precipitates, but in marked contrast, the crusts are characterized by negative CeSN (shale normalized) anomalies and (Ce/Pr)SN ratios less than unity. Profiles through the crusts reveal only minor variations of the REY distribution and (Ce/Pr)SN ratios range from 0.45 to 0.68 (compared to ratios of up to 2 for typical hydrogenetic crusts from the Central Indian Basin). The apparent bulk partition coefficients between the crusts and seawater suggest that for the strictly trivalent REY the adsorption-desorption equilibrium has been reached. Positive Ce anomalies in the partition coefficient patterns reveal preferential uptake of Ce, but to a lesser extent than in normal hydrogenetic crusts. A new parameter (excess Ce, Cexs) to quantify the degree of decoupling of Ce from REY(III) is established on the basis of partition coefficients. Cexs/Cebulk ratios suggest that the CIR crusts formed by precipitation of Fe-Mn oxides from a hydrothermal plume and that in hydrothermal plumes and normal seawater the enrichment of Ce results from the same oxidative sorption process. The growth rates, calculated with 230Thxs data as well as with the Co formula, are inversely related to Cexs.

Gotland Deep (Baltic Sea) independent age model based on Palaeomagnetic Secular Variation (PSV) and lead (Pb) deposition profiles

Dating of sediment cores from the Baltic Sea has proven to be difficult due to uncertainties surrounding the 14C reservoir age and a scarcity of macrofossils suitable for dating. Here we present the results of multiple dating methods carried out on cores in the Gotland Deep area of the Baltic Sea. Particular emphasis is placed on the Littorina stage (8 ka ago to the present) of the Baltic Sea and possible changes in the 14C reservoir age of our dated samples. Three geochronological methods are used. Firstly, palaeomagnetic secular variations (PSV) are reconstructed, whereby ages are transferred to PSV features through comparison with varved lake sediment based PSV records. Secondly, lead (Pb) content and stable isotope analysis are used to identify past peaks in anthropogenic atmospheric Pb pollution. Lastly, 14C determinations were carried out on benthic foraminifera (Elphidium spec.) samples from the brackish Littorina stage of the Baltic Sea. Determinations carried out on smaller samples (as low as 4 µg C) employed an experimental, state-of-the-art method involving the direct measurement of CO2 from samples by a gas ion source without the need for a graphitisation step - the first time this method has been performed on foraminifera in an applied study. The PSV chronology, based on the uppermost Littorina stage sediments, produced ten age constraints between 6.29 and 1.29 cal ka BP, and the Pb depositional analysis produced two age constraints associated with the Medieval pollution peak. Analysis of PSV data shows that adequate directional data can be derived from both the present Littorina saline phase muds and Baltic Ice Lake stage varved glacial sediments. Ferrimagnetic iron sulphides, most likely authigenic greigite (Fe3S4), present in the intermediate Ancylus Lake freshwater stage sediments acquire a gyroremanent magnetisation during static alternating field (AF) demagnetisation, preventing the identification of a primary natural remanent magnetisation for these sediments. An inferred marine reservoir age offset (deltaR) is calculated by comparing the foraminifera 14C determinations to a PSV & Pb age model. This deltaR is found to trend towards younger values upwards in the core, possibly due to a gradual change in hydrographic conditions brought about by a reduction in marine water exchange from the open sea due to continued isostatic rebound.

Iron and phosphorus speciations in DSDP Leg 92 sediments

We present a detailed study of the co-diagenesis of Fe and P in hydrothermal plume fallout sediments from ~19°S on the southern East Pacific Rise. Three distal sediment cores from 340-1130 km from the ridge crest, collected during DSDP Leg 92, were analysed for solid phase Fe and P associations using sequential chemical extraction techniques. The sediments at all sites are enriched in hydrothermal Fe (oxyhydr)oxides, but during diagenesis a large proportion of the primary ferrihydrite precipitates are transformed to the more stable mineral form of goethite and to a lesser extent to clay minerals, resulting in the release to solution of scavenged P. However, a significant proportion of this P is retained within the sediment, by incorporation into secondary goethite, by precipitation as authigenic apatite, and by readsorption to Fe (oxyhydr)oxides. Molar P/Fe ratios for these sediments are significantly lower than those measured in plume particles from more northern localities along the southern East Pacific Rise, and show a distinct downcore decrease to a depth of ~12 m. Molar P/Fe ratios are then relatively constant to a depth of ~35 m. The Fe and P speciation data indicate that diagenetic modification of the sediments is largely complete by a depth of 2.5 m, and thus depth trends in molar P/Fe ratios can not solely be explained by losses of P from the sediment by diffusion to the overlying water column during early diagenesis. Instead, these sediments are likely recording changes in dissolved P concentrations off the SEPR, possibly as a result of redistribution of nutrients in response to changes in oceanic circulation over the last 10 million years. Furthermore, the relatively low molar P/Fe ratios observed throughout these sediments are not necessarily solely due to losses of scavenged P by diffusion to the overlying water column during diagenesis, but may also reflect post-depositional oxidation of pyrite originating from the volatile-rich vents of the southern East Pacific Rise. This study suggests that the molar P/Fe ratio of oxic Fe-rich sediments may serve as a proxy of relative changes in paleoseawater phosphate concentrations, particularly if Fe sulfide minerals are not an important component during transport and deposition.

Enzyme activity and liver tissue PCB concentrations of chicks of northern fulmars (F. glacialis) and black-legged kittiwakes (R. tridactyla) from Kongsfjorden

Arctic seabirds are exposed to a wide range of halogenated organic contaminants (HOCs). Exposure occurs mainly through food intake, and many pollutants accumulate in lipid-rich tissues. Little is known about how HOCs are biotransformed in arctic seabirds. In this study, we characterized biotransformation enzymes in chicks of northern fulmars (Fulmarus glacialis) and black-legged kittiwakes (Rissa tridactyla) from Kongsfjorden (Svalbard, Norway). Phase I and II enzymes were analyzed at the transcriptional, translational and activity levels. For gene expression patterns, quantitative polymerase chain reactions (qPCR), using gene-sequence primers, were performed. Protein levels were analyzed using immunochemical assays of western blot with commercially available antibodies. Liver samples were analyzed for phase I and II enzyme activities using a variety of substrates including ethoxyresorufin (cytochrome (CYP)1A1/1A2), pentoxyresorufin (CYP2B), methoxyresorufin (CYP1A), benzyloxyresorufin (CYP3A), testosterone (CYP3A/CYP2B), 1-chloro-2,4-nitrobenzene (CDNB) (glutathione S-transferase (GST)) and 4-nitrophenol (uridine diphosphate glucuronyltransferase (UDPGT)). In addition, the hydroxylated (OH-) polychlorinated biphenyls (PCBs) were analyzed in the blood, liver and brain tissue, whereas the methylsulfone (MeSO2-) PCBs were analyzed in liver tissue. Results indicated the presence of phase I (CYP1A4/CYP1A5, CYP2B, and CYP3A) and phase II (GST and UDPGT) enzymes at the activity, protein and/or mRNA level in both species. Northern fulmar chicks had higher enzyme activity than black-legged kittiwake chicks. This in combination with the higher XOH-PCB to parent PCB ratios suggests that northern fulmar chicks have a different biotransformation capacity than black-legged kittiwake chicks.

(Table 1) Polychlorinated biphenyl (PCB) and PCB metabolite concentrations in ringed seals (Phoca hispida) from Svalbard and the Baltic Sea

Polychlorinated biphenyls (PCBs) may induce activity of hepatic enzymes, mainly Phase I monooxygenases and conjugating Phase II enzymes, that catalyze the metabolism of PCBs leading to formation of metabolites and to potential adverse health effects. The present study investigates the concentration and pattern of PCBs, the induction of hepatic phase I and II enzymes, and the formation of hydroxy (OH) and methylsulfonyl (CH3SO2=MeSO2) PCB metabolites in two ringed seal (Phoca hispida) populations, which are contrasted by the degree of contamination exposure, that is, highly contaminated Baltic Sea (n = 31) and less contaminated Svalbard (n = 21). Phase I enzymes were measured as ethoxyresorufin-O-deethylation (EROD), benzyloxyresorufin-O-dealkylation (BROD), methoxyresorufin-O-demethylation (MROD), and pentoxyresorufin-O-dealkylation (PROD) activities, and phase II enzymes were measured as uridine diphosphophate glucuronosyl transferase (UDPGT) and glutathione-S-transferase (GST). Geographical comparison, multivariate, and correlation analysis indicated that sum-PCB had a positive impact on Phase I enzyme and GST activities leading to biotransformation of group III (vicinal ortho-meta-H atoms and <=1 ortho-chlorine (Cl)) and IV PCBs (vicinal meta-para-H atoms and <=2 ortho-Cl). The potential precursors for the main OH-PCBs detected in plasma in the Baltic seals were group III PCBs. MeSO2-PCBs detected in liver were mainly products of group IV PCB metabolism. Both CYP1A- and CYP2B-like enzymes are suggested to be involved in the PCB biotransformation in ringed seals.

Element ratio (Sr/Ca, Ba/Ca, B/Ca, and Mg/Ca) profiles throughout the larval life stage of Mytilus edulis, 2011

Rising anthropogenic CO2 in the surface ocean has raised serious concerns for the ability of calcifying organisms to secrete their shells and skeletons. Previous mollusc carbonate perturbation experiments report deleterious effects at lowered pH (7.8-7.4 pH units), including reduced shell length and thickness and deformed shell morphology. It is not clear whether the reduced shell growth results from a decrease in calcification rate due to lowered aragonite saturation or from an indirect effect on mollusc metabolism. We take a novel approach to discerning between these two processes by examining the impact of lowered pH on the 'vital-effect' associated with element ratios. Reported herein are the first element ratio (Sr/Ca, Ba/Ca, B/Ca, Mg/Ca and Mn/Ca) profiles throughout the larval life stage of Mytilus edulis. Element ratio data for individuals reared in ambient conditions provide new insights into biomineralization during larval development. Sr/Ca ratios are consistent with Sr incorporation in the mineral phase. Mg and Mn are likely hosted in an organic phase. The Ba partition coefficient of early larval shells is one of the highest reported in biogenic aragonite. The reason for the high Ba concentrations is unknown, but may reflect the assimilation of Ba from food and/or Ba concentration in an organic or amorphous carbonate phase. There is no observable difference in the way the studied elements are incorporated into the shells of individuals reared in ambient and lowered pH conditions. The reduced growth rate at lower pH may be a consequence of a disruption to the larval mollusc metabolism.

Upwelling and isolation in oxygen-depleted anticyclonic modewater eddies and implications for nitrate cycling

The physical (temperature, salinity, velocity) and biogeochemical (oxygen, nitrate) structure of an oxygen depleted coherent, baroclinic, anticyclonic mode-water eddy (ACME) is investigated using high-resolution autonomous glider and ship data. A distinct core with a diameter of about 70 km is found in the eddy, extending from about 60 to 200 m depth and. The core is occupied by fresh and cold water with low oxygen and high nitrate concentrations, and bordered by local maxima in buoyancy frequency. Velocity and property gradient sections show vertical layering at the flanks and underneath the eddy characteristic for vertical propagation (to several hundred-meters depth) of near inertial internal waves (NIW) and confirmed by direct current measurements. A narrow region exists at the outer edge of the eddy where NIW can propagate downward. NIW phase speed and mean flow are of similar magnitude and critical layer formation is expected to occur. An asymmetry in the NIW pattern is seen that possible relates to the large-scale Ekman transport interacting with ACME dynamics. NIW/mean flow induced mixing occurs close to the euphotic zone/mixed layer and upward nutrient flux is expected and supported by the observations. Combing high resolution nitrate (NO3-) data with the apparent oxygen utilization (AOU) reveals AOU:NO3- ratios of 16 which are much higher than in the surrounding waters (8.1). A maximum NO3- deficit of 4 to 6 µmol kg-1 is estimated for the low oxygen core. Denitrification would be a possible explanation. This study provides evidence that the recycling of NO3-, extracted from the eddy core and replenished into the core via the particle export, may quantitatively be more important. In this case, the particulate phase is of keys importance in decoupling the nitrogen from the oxygen cycling.