Early identification of symptomatic aortic stenosis using echocardiographic data

Background: Heart failure (CHF) is the most frequent and prognostically severe symptom of aortic stenosis (AS), and the most common indication for surgery. The mainstay of treatment for AS is aortic valve replacement (AVR), and the main indication for an AVR is development of symptomatic disease. ACC/AHA guidelines define severe AS as an aortic valve area (AVA) ≤1cm², but there is little data correlating echocardiogram AVA with the onset of symptomatic CHF. We evaluated the risk of developing CHF with progressively decreasing echocardiographic AVA. We also compared echocardiographic AVA with Jet velocity (V2) and indexed AVA (AVAI) to assess the best predictor of development of symptomatic CHF.^ Methods and Results: This retrospective cohort study evaluated 518 patients with asymptomatic moderate or severe AS from a single community based cardiology practice. A total of 925 echocardiograms were performed over an 11-year period. Each echocardiogram was correlated with concurrent clinical assessments while the investigator was blinded to the echocardiogram severity of AS. The Cox Proportional hazards model was used to analyze the relationship between AVA and the development of CHF. The median age of patients at entry was 76.1 years, with 54% males. A total of 116 patients (21.8%) developed new onset CHF during follow-up. Compared to patients with AVA >1.0cm², patients with lower AVA had an exponentially increasing risk of developing CHF for each 0.2cm² decrement in AVA, becoming statistically significant only at an AVA less than 0.8 cm². Also, compared to V2 and AVAI, AVA added more information to assessing risk for development of CHF (p=0.041). ^ Conclusion: In patients with normal or mildly impaired LVEF, the risk of CHF rises exponentially with decreasing valve area and becomes statistically significant after AVA falls below 0.8cm². AVA is a better predictor of CHF when compared to V2 or AVAI.^

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.

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.^

Onset of long-term cooling of Greenland near the Eocene-Oligocene boundary as revealed by branched tetraether lipids

The Eocene-Oligocene (E-O) boundary interval is considered to be one of the major transitions in Earth's climate, witnessing the first major expansion of the East Antarctic Ice Sheet. However, the extent of the associated climatic cooling, especially for high northern latitude continental landmasses, is poorly constrained. In this study we reconstruct the first mean annual air temperature (MAAT) for the Greenland landmass during the late Eocene and early Oligocene by applying a new proxy based on the distribution of branched tetraether lipids derived from soil bacteria preserved in a marine sediment core from the Greenland Basin. The temperature estimates are compared with a composite continental temperature record based on bio-climatic analysis of pollen assemblages. Both proxies reveal comparable late Eocene MAATs of ~13-15 °C and a gradual long-term cooling of ~3-5 °C starting near the E-O boundary. These data are in agreement with other MAAT reconstructions from northern midlatitude continents and suggest a general cooling of the Northern Hemisphere during the E-O transition.

Chemistry and accumulation rates of Jurassic to early Cretaceous sediments from the central equatorial Pacific

Sedimentation in the central Pacific during the Jurassic and Early Cretaceous was dominated by abundant biogenic silica. A synthesis of the stratigraphy, lithology, petrology, and geochemistry of the radiolarites in Sites 801 and 800 documents the sedimentation processes and trends in the equatorial central Pacific from the Middle Jurassic through the Early Cretaceous. Paleolatitude and paleodepth reconstructions enable comparisons with previous DSDP sites and identification of the general patterns of sedimentation over a wide region of the Pacific. Clayey radiolarites dominated sedimentation on Pacific oceanic crust within tropical paleolatitudes from at least the latest Bathonian through Tithonian. Radiolarian productivity rose to a peak within 5° of the paleoequator, where accumulation rates of biogenic silica exceeded 1000 g/cm**2/m.y. Wavy-bedded radiolarian cherts developed in the upper Tithonian at Site 801 coinciding with the proximity of this site to the paleoequator. Ribbon-bedding of some radiolarian cherts exposed on Pacific margins may have formed from silicification of radiolarite deposited near the equatorial high-productivity zone where radiolarian/clay ratios were high. Silicification processes in sediments extensively mixed by bioturbation or enriched in clay or carbonate generally resulted in discontinuous bands or nodules of porcellanite or chert, e.g., a "knobby" radiolarite. Ribbon-bedded cherts require primary alternations of radiolarian-rich and clay-rich layers as an initial structural template, coupled with abundant biogenic silica in both layers. During diagenesis, migration of silica from clay-rich layers leaves radiolarian "ghosts" or voids, and the precipitation in adjacent radiolarite layers results in silicification of the inter-radiolarian matrix and infilling of radiolarian tests. Alternations of claystone and clay-rich radiolarian grainstone were deposited during the Callovian at Site 801 and during the Berriasian-Valanginian at Site 800, but did not silicify to form bedded chert. Carbonate was not preserved on the Pacific oceanic floor or spreading ridges during the Jurassic, perhaps due to an elevated level of dissolved carbon dioxide. During the Berriasian through Hauterivian, the carbonate compensation depth (CCD) descended to approximately 3500 m, permitting the accumulation of siliceous limestones at near-ridge sites. Carbonate accumulation rates exceeded 1500 g/cm**2/m.y. at sites above the CCD, yet there is no evidence of an equatorial carbonate bulge during the Early Cretaceous. In the Barremian and Aptian, the CCD rose, coincident with the onset of mid-plate volcanic activity. Abundance of Fe and Mn and the associated formation of authigenic Fe-smectite clays was a function of proximity to the spreading ridges, with secondary enrichments occurring during episodes of spreading-center reorganizations. Callovian radiolarite at Site 801 is anomalously depleted in Mn, which resulted either from inhibited precipitation of Mn-oxides by lower pH of interstitial waters induced by high dissolved oceanic CO2 levels or from diagenetic mobilization of Mn. Influx of terrigenous (eolian) clay apparently changed with paleolatitude and geological age. Cyclic variations in productivity of radiolarians and of nannofossils and in the influx of terrigenous clay are attributed to Milankovitch climatic cycles of precession (20,000 yr) and eccentricity (100,000 yr). Diagenetic redistribution of biogenic silica and carbonate enhanced the expression of this cyclic sedimentation. Jurassic and Lower Cretaceous sediments were deposited under oxygenated bottom-water conditions at all depths, accompanied by bioturbation and pervasive oxidation of organic carbon and metals. Despite the more "equable" climate conditions of the Mesozoic, the super-ocean of the Pacific experienced adequate deep-water circulation to prevent stagnation. Efficient nutrient recycling may have been a factor in the abundance of radiolarians in this ocean basin.

Stable isotopes, sedimentology and geochemical analyses of Middle Eocene to early Miocene sediments of ODP Site 177-1090

During Leg 177 of the Ocean Drilling Program (ODP), a well-preserved middle Eocene to lower Miocene sediment record was recovered at Site 1090 on the Agulhas Ridge in the Atlantic sector of the Southern Ocean. This new sediment record shows evidence of a hitherto unknown late Eocene opal pulse. Lithological variations, compositional data, mass-accumulation rates of biogenic and lithogenic sediment constituents, grain-size distributions, geochemistry, and clay mineralogy are used to gain insights into mid-Cenozoic environmental changes and to explore the circumstances of the late Eocene opal pulse in terms of reorganizations in ocean circulation. The base of the section is composed of middle Eocene nannofossil oozes mixed with red clays enriched in authigenic clinoptilolite and smectite, deposited at low sedimentation rates (LE 2 cm/ka). It indicates reduced terrigenous sediment input and moderate biological productivity during this preglacial warm climatic stage. The basal strata are overlain by an extended succession (100 m, 4 cm/ka) of biosiliceous oozes and muds, comprising the upper middle Eocene, the entire late Eocene, and the lowermost early Oligocene. The opal pulse occurred between 37.5 and 33.5 Ma and documents the development of upwelling cells along topographic highs, and the utilization of a marine nutrient- and silica reservoir established during the pre-late Eocene through enhanced submarine hydrothermal activity and the introduction of terrigenous solutions from chemical weathering on adjacent continents. This palaeoceanographic overturn probably was initiated through the onset of increased meridional ocean circulation, caused by the diversion of the Indian equatorial current to the south. The opal pulse was accompanied by increased influxes of terrigenous detritus from southern African sources (illite), mediated by enhanced ocean particle advection in response to modified ocean circulation. The opal pulse ended because of frontal shifts to the south around the Eocene/Oligocene boundary, possibly in response to the opening of the Drake Passage and the incipient establishment of the Antarctic Circumpolar Current. Condensed sediments and a hiatus within the early Oligocene part of the section possibly point to an invigoration of the deep-reaching Antarctic Circumpolar Current. The mid-Oligocene to lower Miocene section on long time scale exhibits less pronounced lithological variations than the older section and points to relatively stable palaeoceanographic conditions after the dramatic changes in the late Eocene to early Oligocene.

The early Eocene global warming events: Implications from ODP Leg 208 Walvis Ridge depth transect

Five sections drilled in multiple holes over a depth transect of more than 2200 m at the Walvis Ridge (SE Atlantic) during Ocean Drilling Program (ODP) Leg 208 resulted in the first complete early Paleogene deep-sea record. Here we present high-resolution stratigraphic records spanning a ~4.3 million yearlong interval of the late Paleocene to early Eocene. This interval includes the Paleocene-Eocene thermal maximum (PETM) as well as the Eocene thermal maximum (ETM) 2 event. A detailed chronology was developed with nondestructive X-ray fluorescence (XRF) core scanning records and shipboard color data. These records were used to refine the shipboard-derived spliced composite depth for each site and with a record from ODP Site 1051 were then used to establish a continuous time series over this interval. Extensive spectral analysis reveals that the early Paleogene sedimentary cyclicity is dominated by precession modulated by the short (100 kyr) and long (405 kyr) eccentricity cycles. Counting of precession-related cycles at multiple sites results in revised estimates for the duration of magnetochrons C24r and C25n. Direct comparison between the amplitude modulation of the precession component derived from XRF data and recent models of Earth's orbital eccentricity suggests that the onset of the PETM and ETM2 are related to a 100-kyr eccentricity maximum. Both events are approximately a quarter of a period offset from a maximum in the 405-kyr eccentricity cycle, with the major difference that the PETM is lagging and ETM2 is leading a 405-kyr eccentricity maximum. Absolute age estimates for the PETM, ETM2, and the magnetochron boundaries that are consistent with recalibrated radiometric ages and recent models of Earth's orbital eccentricity cannot be precisely determined at present because of too large uncertainties in these methods. Nevertheless, we provide two possible tuning options, which demonstrate the potential for the development of a cyclostratigraphic framework based on the stable 405-kyr eccentricity cycle for the entire Paleogene.

Brachiopods in Early Carboniferous

Changes in Mississippian global paleogeography derived from the reconfiguration of the continents, a reversal in ocean currents and global cooling. Although the tectonic and climatic changes are well-documented, their effects on the distribution of brachiopod fauna are poorly documented. Here we present systematic quantitative analyses on global paleobiogeography based on a global brachiopod database from the Mississippian (i.e., Tournaisian, Visean, and Serpukhovian). The dataset consists of 2123 species of 344 brachiopod genera from 1156 localities. Our results reveal that global provincialism was not evident during the Tournaisian and Visean Stages. Two realms, i.e., the Gondwanan and Paleoequatorial Realms, are recognized during the Tournaisian. The Paleoequatorial Realm dominates during the Visean Stage, whereas the Gondwanan Realm is not documented due to the absence of data points. In contrast to the early and middle Mississippian stages, faunal provincialism is greatly enhanced in the Serpukhovian Stage with Paleotethyan and North American realms easily distinguished. This indicates that the Rheic Ocean was closed before the Serpukhovian due to the collision between Gondwana and Laurussia, that disrupted faunal interchange between the Paleotethys and North America. In addition, the paleolatitude-related thermal gradient was enhanced and the Boreal Realm was distinguished from the Paleotethyan Realm during the onset of the Late Palaeozoic Ice Age (LPIA) in the Serpukhovian. The paleolatitude diversity gradient pattern further shows a distinct shift of diversity center from the southern tropic zone in the Tournaisian and Visean to the northern tropic zone in the Serpukhovian.

A maternal diet high in n − 6 polyunsaturated fats alters mammary gland development, puberty onset, and breast cancer risk among female rat offspring

We hypothesized that feeding pregnant rats with a high-fat diet would increase both circulating 17β-estradiol (E2) levels in the dams and the risk of developing carcinogen-induced mammary tumors among their female offspring. Pregnant rats were fed isocaloric diets containing 12% or 16% (low fat) or 43% or 46% (high fat) of calories from corn oil, which primarily contains the n − 6 polyunsaturated fatty acid (PUFA) linoleic acid, throughout pregnancy. The plasma concentrations of E2 were significantly higher in pregnant females fed a high n − 6 PUFA diet. The female offspring of these rats were fed with a laboratory chow from birth onward, and when exposed to 7,12-dimethylbenz(a)anthracene had a significantly higher mammary tumor incidence (60% vs. 30%) and shorter latency for tumor appearance (11.4 ± 0.5 weeks vs. 14.2 ± 0.6 weeks) than the offspring of the low-fat mothers. The high-fat offspring also had puberty onset at a younger age, and their mammary glands contained significantly higher numbers of the epithelial structures that are the targets for malignant transformation. Comparable changes in puberty onset, mammary gland morphology, and tumor incidence were observed in the offspring of rats treated daily with 20 ng of E2 during pregnancy. These data, if extrapolated to humans, may explain the link among diet, early puberty onset, mammary parenchymal patterns, and breast cancer risk, and indicate that an in utero exposure to a diet high in n − 6 PUFA and/or estrogenic stimuli may be critical for affecting breast cancer risk.

Inactivation of the survival motor neuron gene, a candidate gene for human spinal muscular atrophy, leads to massive cell death in early mouse embryos

Proximal spinal muscular atrophy is an autosomal recessive human disease of spinal motor neurons leading to muscular weakness with onset predominantly in infancy and childhood. With an estimated heterozygote frequency of 1/40 it is the most common monogenic disorder lethal to infants; milder forms represent the second most common pediatric neuromuscular disorder. Two candidate genes—survival motor neuron (SMN) and neuronal apoptosis inhibitory protein have been identified on chromosome 5q13 by positional cloning. However, the functional impact of these genes and the mechanism leading to a degeneration of motor neurons remain to be defined. To analyze the role of the SMN gene product in vivo we generated SMN-deficient mice. In contrast to the human genome, which contains two copies, the mouse genome contains only one SMN gene. Mice with homozygous SMN disruption display massive cell death during early embryonic development, indicating that the SMN gene product is necessary for cellular survival and function.

Epigenetic changes at the insulin-like growth factor II/H19 locus in developing kidney is an early event in Wilms tumorigenesis

Relaxation of imprinting at the insulin-like growth factor II (IFG-II)/H19 locus is a major mechanism involved in the onset of sporadic Wilms tumor and several other embryonal tumors. The high prevalence of histologically abnormal foci in kidney adjacent to Wilms tumors suggests that tumor-predisposing genetic/epigenetic lesion might also be found at high frequency in Wilms tumor-bearing kidneys. Focusing on Wilms tumors with relaxation of IFG-II imprinting, we determined the frequency of epigenetic change at the IFG-II/H19 locus in adjacent kidney. In all kidneys adjacent to these Wilms tumors, we detected substantial mosaicism for a population of cells with relaxation of IFG-II imprinting and biallelic H19 methylation, regardless of whether the patient had a tumor-predisposing syndrome or not. The high proportion of epigenetically modified cells among “normal” tissue indicates that the epigenetic error occurred very early in development, before the onset of Wilms tumor. Not only does this suggest that the major Wilms tumor-predisposing event occurs within the first few days of development, but it also suggests that sporadic Wilms tumor may represent one end of a spectrum of overgrowth disorders characterized by mosaic epigenetic change at the IFG-II/H19 locus.

The onset and extent of genomic instability in sporadic colorectal tumor progression

Cancer cell genomes contain alterations beyond known etiologic events, but their total number has been unknown at even the order of magnitude level. By sampling colorectal premalignant polyp and carcinoma cell genomes through use of the technique inter-(simple sequence repeat) PCR, we have found genomic alterations to be considerably more abundant than expected, with the mean number of genomic events per carcinoma cell totaling approximately 11,000. Colonic polyps early in the tumor progression pathway showed similar numbers of events. These results indicate that, as with certain hereditary cancer syndromes, genomic destabilization is an early step in sporadic tumor development. Together these results support the model of genomic instability being a cause rather than an effect of malignancy, facilitating vastly accelerated somatic cell evolution, with the observed orderly steps of the colon cancer progression pathway reflecting the consequences of natural selection.

Early expression of antiinsulin autoantibodies of humans and the NOD mouse: Evidence for early determination of subsequent diabetes

With the development of an insulin autoantibody (IAA) assay performed in 96-well filtration plates, we have evaluated prospectively the development of IAA in NOD mice (from 4 weeks of age) and children (from 7 to 10 months of age) at genetic risk for the development of type 1 diabetes. NOD mice had heterogeneous expression of IAA despite being inbred. IAA reached a peak between 8 and 16 weeks and then declined. IAA expression by NOD mice at 8 weeks of age was strongly associated with early development of diabetes, which occurred at 16–18 weeks of age (NOD mice IAA+ at 8 weeks: 83% (5/6) diabetic by 18 weeks versus 11% (1/9) of IAA negative at 8 weeks; P < .01). In man, IAA was frequently present as early as 9 months of age, the first sampling time. Of five children found to have persistent IAA before 1 year of age, four have progressed to diabetes (all before 3.5 years of age) and the fifth is currently less than age 2. Of the 929 children not expressing persistent IAA before age 1, only one has progressed to diabetes to date (age onset 3), and this child expressed IAA at his second visit (age 1.1). In new onset patients, the highest levels of IAA correlated with an earlier age of diabetes onset. Our data suggest that the program for developing diabetes of NOD mice and humans is relatively “fixed” early in life and, for NOD mice, a high risk of early development of diabetes is often determined by 8 weeks of age. With such early determination of high risk of progression to diabetes, immunologic therapies in humans may need to be tested in children before the development of IAA for maximal efficacy.

Cell cycle-dependent regulation of RNA polymerase I transcription: The nucleolar transcription factor UBF is inactive in mitosis and early G1

Transcription of ribosomal RNA genes by RNA polymerase (pol) I oscillates during the cell cycle, being maximal in S and G2 phase, repressed during mitosis, and gradually recovering during G1 progression. We have shown that transcription initiation factor (TIF)-IB/SL1 is inactivated during mitosis by cdc2/cyclin B-directed phosphorylation of TAFI110. In this study, we have monitored reactivation of transcription after exit from mitosis. We demonstrate that the pol I factor UBF is also inactivated by phosphorylation but recovers with different kinetics than TIF-IB/SL1. Whereas TIF-IB/SL1 activity is rapidly regained on entry into G1, UBF is reactivated later in G1, concomitant with the onset of pol I transcription. Repression of pol I transcription in mitosis and early G1 can be reproduced with either extracts from cells synchronized in M or G1 phase or with purified TIF-IB/SL1 and UBF isolated in the presence of phosphatase inhibitors. The results suggest that two basal transcription factors, e.g., TIF-IB/SL1 and UBF, are inactivated at mitosis and reactivated by dephosphorylation at the exit from mitosis and during G1 progression, respectively.

An ethylene-induced cDNA encoding a lipase expressed at the onset of senescence

A cDNA clone encoding a lipase (lipolytic acyl hydrolase) expressed at the onset of petal senescence has been isolated by screening a cDNA expression library prepared from carnation flowers (Dianthus caryophyllus). The cDNA contains the lipase consensus sequence, ITFAGHSLGA, and encodes a 447-amino acid polypeptide with a calculated molecular mass of 50.2 kDa that appears to be a cytosolic protein. Over-expression of the clone in Escherichia coli yielded a protein of the expected molecular weight that proved capable of deesterifying fatty acids from p-nitrophenylpalmitate, tri-linolein, soybean phospholipid, and Tween in both in vitro and in situ assays of enzyme activity. The abundance of the lipase mRNA increases just as carnation flowers begin to senesce, and expression of the gene is also induced by treatment with ethylene. Southern blot analyses of carnation genomic DNA have indicated that the lipase is a single copy gene. The lipase gene is also expressed in carnation leaves and is up-regulated when the leaves are treated with ethylene. Deesterification of membrane lipids and ensuing loss of membrane structural integrity are well established early events of plant senescence, and the expression pattern of this lipase gene together with the lipolytic activity of its cognate protein indicate that it plays a fundamentally central role in mediating the onset of senescence.