The spatial distribution of water in the inner coma of Comet 9P/Tempel 1: Comparison between models and observations

The near nucleus coma of Comet 9P/Tempel 1 has been simulated with the 3D Direct Simulation Monte Carlo (DSMC) code PDSC++ (Su, C.-C. [2013]. Parallel Direct Simulation Monte Carlo (DSMC) Methods for Modeling Rarefied Gas Dynamics. PhD Thesis, National Chiao Tung University, Taiwan) and the derived column densities have been compared to observations of the water vapour distribution found by using infrared imaging spectrometer on the Deep Impact spacecraft (Feaga, L.M., A’Hearn, M.F., Sunshine, J.M., Groussin, O., Farnham, T.L. [2007]. Icarus 191(2), 134–145. http://dx.doi.org/10.1016/j.icarus.2007.04.038). Modelled total production rates are also compared to various observations made at the time of the Deep Impact encounter. Three different models were tested. For all models, the shape model constructed from the Deep Impact observations by Thomas et al. (Thomas, P.C., Veverka, J., Belton, M.J.S., Hidy, A., A’Hearn, M.F., Farnham, T.L., et al. [2007]. Icarus, 187(1), 4–15. http://dx.doi.org/10.1016/j.icarus.2006.12.013) was used. Outgassing depending only on the cosine of the solar insolation angle on each shape model facet is shown to provide an unsatisfactory model. Models constructed on the basis of active areas suggested by Kossacki and Szutowicz (Kossacki, K., Szutowicz, S. [2008]. Icarus, 195(2), 705–724. http://dx.doi.org/10.1016/j.icarus.2007.12.014) are shown to be superior. The Kossacki and Szutowicz model, however, also shows deficits which we have sought to improve upon. For the best model we investigate the properties of the outflow.

Articulated Statistical Shape Model-Based 2D-3D Reconstruction of a Hip Joint

In this paper, reconstruction of three-dimensional (3D) patient-specific models of a hip joint from two-dimensional (2D) calibrated X-ray images is addressed. Existing 2D-3D reconstruction techniques usually reconstruct a patient-specific model of a single anatomical structure without considering the relationship to its neighboring structures. Thus, when those techniques would be applied to reconstruction of patient-specific models of a hip joint, the reconstructed models may penetrate each other due to narrowness of the hip joint space and hence do not represent a true hip joint of the patient. To address this problem we propose a novel 2D-3D reconstruction framework using an articulated statistical shape model (aSSM). Different from previous work on constructing an aSSM, where the joint posture is modeled as articulation in a training set via statistical analysis, here it is modeled as a parametrized rotation of the femur around the joint center. The exact rotation of the hip joint as well as the patient-specific models of the joint structures, i.e., the proximal femur and the pelvis, are then estimated by optimally fitting the aSSM to a limited number of calibrated X-ray images. Taking models segmented from CT data as the ground truth, we conducted validation experiments on both plastic and cadaveric bones. Qualitatively, the experimental results demonstrated that the proposed 2D-3D reconstruction framework preserved the hip joint structure and no model penetration was found. Quantitatively, average reconstruction errors of 1.9 mm and 1.1 mm were found for the pelvis and the proximal femur, respectively.

Chronology of Lateglacial ice flow reorganization and deglaciation in the Gotthard Pass area, Central Swiss Alps, based on cosmogenic 10Be and in situ 14C

We reconstruct the timing of ice flow reconfiguration and deglaciation of the Central Alpine Gotthard Pass, Switzerland, using cosmogenic 10Be and in situ14C surface exposure dating. Combined with mapping of glacial erosional markers, exposure ages of bedrock surfaces reveal progressive glacier downwasting from the maximum LGM ice volume and a gradual reorganization of the paleoflow pattern with a southward migration of the ice divide. Exposure ages of ∼16–14 ka (snow corrected) give evidence for continuous early Lateglacial ice cover and indicate that the first deglaciation was contemporaneous with the decay of the large Gschnitz glacier system. In agreement with published ages from other Alpine passes, these data support the concept of large transection glaciers that persisted in the high Alps after the breakdown of the LGM ice masses in the foreland and possibly decayed as late as the onset of the Bølling warming. A younger group of ages around ∼12–13 ka records the timing of deglaciation following local glacier readvance during the Egesen stadial. Glacial erosional features and the distribution of exposure ages consistently imply that Egesen glaciers were of comparatively small volume and were following a topographically controlled paleoflow pattern. Dating of a boulder close to the pass elevation gives a minimum age of 11.1 ± 0.4 ka for final deglaciation by the end of the Younger Dryas. In situ14C data are overall in good agreement with the 10Be ages and confirm continuous exposure throughout the Holocene. However, in situ14C demonstrates that partial surface shielding, e.g. by snow, has to be incorporated in the exposure age calculations and the model of deglaciation.

Context Aware e-Learning Objects and their Types from the Perspective of the Object-Oriented Paradigm

The contribution of this article demonstrates how to identify context-aware types of e-Learning objects (eLOs) derived from the subject domains. This perspective is taken from an engineering point of view and is applied during requirements elicitation and analysis relating to present work in constructing an object-oriented (OO), dynamic, and adaptive model to build and deliver packaged e-Learning courses. Consequently, three preliminary subject domains are presented and, as a result, three primitive types of eLOs are posited. These types educed from the subject domains are of structural, conceptual, and granular nature. Structural objects are responsible for the course itself, conceptual objects incorporate adaptive and logical interoperability, while granular objects congregate granular assets. Their differences, interrelationships, and responsibilities are discussed. A major design challenge relates to adaptive behaviour. Future research addresses refinement on the subject domains and adaptive hypermedia systems.

The ecoclimatology of Danum, Sabah, in the context of the world's rainforest regions, with particular reference to dry periods and their impact

Climatic records for Danum for 1985 to 1998, elsewhere in Sabah since 1879, and long monthly rainfall series from other rainforest locations are used to place the climate, and particularly the dry period climatology, of Danum into a world rainforest context. The magnitude frequency and seasonality of dry periods are shown to vary greatly within the world's rainforest zone. The climate of Danum, which is aseasonal but subject, as in 1997 to 1998, to occasional drought, is intermediate between less drought–prone north–western Borneo and the more drought–prone east coast. Changes through time in drought magnitude frequency in Sabah and rainforest locations elsewhere in South–East Asia and in the Neotropics are compared. The 1997 to 1998 ENSO–related drought event in Sabah is placed into a historical context. The effects of drought on tree growth and mortality in the tropics are assessed and a model relating intensity and frequency of drought disturbance to forest structure and composition is discussed.

Calibrating a CGE model with NTBs that Incorporates Standard Models of Modern Trade Theory

We propose a way to incorporate NTBs for the four workhorse models of the modern trade literature in computable general equilibrium models (CGEs). CGE models feature intermediate linkages and thus allow us to study global value chains (GVCs). We show that the Ethier-Krugman monopolistic competition model, the Melitz firm heterogeneity model and the Eaton and Kortum model can be defined as an Armington model with generalized marginal costs, generalized trade costs and a demand externality. As already known in the literature in both the Ethier-Krugman model and the Melitz model generalized marginal costs are a function of the amount of factor input bundles. In the Melitz model generalized marginal costs are also a function of the price of the factor input bundles. Lower factor prices raise the number of firms that can enter the market profitably (extensive margin), reducing generalized marginal costs of a representative firm. For the same reason the Melitz model features a demand externality: in a larger market more firms can enter. We implement the different models in a CGE setting with multiple sectors, intermediate linkages, non-homothetic preferences and detailed data on trade costs. We find the largest welfare effects from trade cost reductions in the Melitz model. We also employ the Melitz model to mimic changes in Non tariff Barriers (NTBs) with a fixed cost-character by analysing the effect of changes in fixed trade costs. While we work here with a model calibrated to the GTAP database, the methods developed can also be applied to CGE models based on the WIOD database.

The Chemical Mechanism of a Brown-Rot Decay Mimtic System and its Application in Paper Recycling Processes

This work is aimed at improving our current knowledge of the non-enzymatic inecl~anisins involved in brown-rot decay, as well as the exploration of potential applications of a brown-rot mimetic model system in paper recycling processes. The study was divided into two parts. The first part focussed on the chemical mechanisms involved in chelation and reduction of iron by a low molecular weight chelator (isolated from the brown-rot fungus Gloeophyllz~m tmbeum) and its model compound 2,3- dihydroxybenzoic acid (2,3-DHBA). Chelation as well as free radical generation mediated by this system were studied by ESR measurement. The results indicate that the effects of the chelator/iron ratio, the pH, and other reaction parameters on hydroxyl radical generation by a Fenton type system could be determined using ESR spin-trapping techniques. The results also support the hypothesis that superoxide radicals are involved in the chelator-mediated Fenton process. In the second part of the study, the effect of a chelator-mediated Fenton system for the improvement of deinking efficiency and the n~odification of fiber and paper properties was studied. For the deinking study, copy paper was laser printed with an identical standard pattern. Then repulping and flotation operations were performed to remove ink particles. Under properly controlled deinking conditions, the chelator mediated treatment (CMT) resulted in a reduction in dirt count over that of conventional deinking procedures with no significant loss of pulp strength. To study the effect of the chelator system treatment on the quality of pulp with different fines content, a fully bleached hardwood kraft pulp was beaten to different freeness levels and treated with the chelator-mediated free radical system. The result shows that virgin fiber and heavily beaten fiber respond differently to the free radical treatment. Unbeaten fibers become more flexible and easier to collapse after free radical treatment, while beaten fibers show a reduction in fines and small materials after mild free radical treatment.

Maternal ingestion of radon-222 in drinking water and the absorbed radiation dose to the embryo

Maternal ingestion of high concentrations of radon-222 (Rn-222) in drinking during pregnancy may pose a significant radiation hazard to the developing embryo. The effects of ionizing radiation to the embryo and fetus have been the subject of research, analyses, and the development of a number of radiation dosimetric models for a variety of radionuclides. Currently, essentially all of the biokinetic and dosimetric models that have been developed by national and international radiation protection agencies and organizations recommend calculating the dose to the mother's uterus as a surrogate for estimating the dose to the embryo. Heretofore, the traditional radiation dosimetry models have neither considered the embryo a distinct and rapidly developing entity, the fact that it is implanted in the endometrial layer of the uterus, nor the physiological interchanges that take place between maternal and embryonic cells following the implantation of the blastocyst in the endometrium. The purpose of this research was to propose a new approach and mathematical model for calculating the absorbed radiation dose to the embryo by utilizing a semiclassical treatment of alpha particle decay and subsequent scattering of energy deposition in uterine and embryonic tissue. The new approach and model were compared and contrasted with the currently recommended biokinetic and dosimetric models for estimating the radiation dose to the embryo. The results obtained in this research demonstrate that the estimated absorbed dose for an embryo implanted in the endometrial layer of the uterus during the fifth week of embryonic development is greater than the estimated absorbed dose for an embryo implanted in the uterine muscle on the last day of the eighth week of gestation. This research provides compelling evidence that the recommended methodologies and dosimetric models of the Nuclear Regulatory Commission and International Commission on Radiological Protection employed for calculating the radiation dose to the embryo from maternal intakes of radionuclides, including maternal ingestion of Rn-222 in drinking water would result in an underestimation of dose. ^

A qualitative assessment of multi-level nutrition strategies for reducing racial and ethnic disparities in diabetes

The purpose of this study is to examine the stages of program realization of the interventions that the Bronx Health REACH program initiated at various levels to improve nutrition as a means for reducing racial and ethnic disparities in diabetes. This study was based on secondary analyses of qualitative data collected through the Bronx Health REACH Nutrition Project, a project conducted under the auspices of the Institute on Urban Family Health, with support from the Centers for Disease Control and Prevention (CDC). Local human subjects' review and approval through the Institute on Urban Family Health was required and obtained in order to conduct the Bronx Health REACH Nutrition Project. ^ The study drew from two theoretical models—Glanz and colleagues' nutrition environments model and Shediac-Rizkallah and Bone's sustainability model. The specific study objectives were two-fold: (1) to categorize each nutrition activity to a specific dimension (i.e. consumer, organizational or community nutrition environment); and (2) to evaluate the stage at which the program has been realized (i.e. development, implementation or sustainability). ^ A case study approach was applied and a constant comparative method was used to analyze the data. Triangulation of data based was also conducted. Qualitative data from this study revealed the following principal findings: (1) communities of color are disproportionately experiencing numerous individual and environmental factors contributing to the disparities in diabetes; (2) multi-level strategies that targeted the individual, organizational and community nutrition environments can appropriately address these contributing factors; (3) the nutrition strategies greatly varied in their ability to appropriately meet criteria for the three program stages; and (4) those nutrition strategies most likely to succeed (a) conveyed consistent and culturally relevant messages, (b) had continued involvement from program staff and partners, (c) were able to adapt over time or setting, (d) had a program champion and a training component, (e) were integrated into partnering organizations, and (f) were perceived to be successful by program staff and partners in their efforts to create individual, organizational and community/policy change. As a result of the criteria-based assessment and qualitative findings, an ecological framework elaborating on Glanz and colleagues model was developed. The qualitative findings and the resulting ecological framework developed from this study will help public health professionals and community leaders to develop and implement sustainable multi-level nutrition strategies for addressing racial and ethnic disparities in diabetes. ^

A path analysis of an after-school health and exercise program for elementary school children in El Paso, Texas

As schools are pressured to perform on academics and standardized examinations, schools are reluctant to dedicate increased time to physical activity. After-school exercise and health programs may provide an opportunity to engage in more physical activity without taking time away from coursework during the day. The current study is a secondary data analysis of data from a randomized trial of a 10-week after-school program (six schools, n = 903) that implemented an exercise component based on the CATCH physical activity component and health modules based on the culturally-tailored Bienestar health education program. Outcome variables included BMI and aerobic capacity, health knowledge and healthy food intentions as assessed through path analysis techniques. Both the baseline model (χ2 (df = 8) = 16.90, p = .031; RMSEA = .035 (90% CI of .010–.058), NNFI = 0.983 and the CFI = 0.995) and the model incorporating intervention participation proved to be a good fit to the data (χ2 (df = 10) = 11.59, p = .314. RMSEA = .013 (90% CI of .010–.039); NNFI = 0.996 and CFI = 0.999). Experimental group participation was not predictive of changes in health knowledge, intentions to eat healthy foods or changes in Body Mass Index, but it was associated with increased aerobic capacity, β = .067, p < .05. School characteristics including SES and Language proficiency proved to be significantly associated with changes in knowledge and physical indicators. Further effects of school level variables on intervention outcomes are recommended so that tailored interventions can be developed aimed at the specific characteristics of each participating school. ^

Information bias and lifetime mortality risks of radiation-induced cancer

Additive and multiplicative models of relative risk were used to measure the effect of cancer misclassification and DS86 random errors on lifetime risk projections in the Life Span Study (LSS) of Hiroshima and Nagasaki atomic bomb survivors. The true number of cancer deaths in each stratum of the cancer mortality cross-classification was estimated using sufficient statistics from the EM algorithm. Average survivor doses in the strata were corrected for DS86 random error ($\sigma$ = 0.45) by use of reduction factors. Poisson regression was used to model the corrected and uncorrected mortality rates with covariates for age at-time-of-bombing, age at-time-of-death and gender. Excess risks were in good agreement with risks in RERF Report 11 (Part 2) and the BEIR-V report. Bias due to DS86 random error typically ranged from $-$15% to $-$30% for both sexes, and all sites and models. The total bias, including diagnostic misclassification, of excess risk of nonleukemia for exposure to 1 Sv from age 18 to 65 under the non-constant relative projection model was $-$37.1% for males and $-$23.3% for females. Total excess risks of leukemia under the relative projection model were biased $-$27.1% for males and $-$43.4% for females. Thus, nonleukemia risks for 1 Sv from ages 18 to 85 (DRREF = 2) increased from 1.91%/Sv to 2.68%/Sv among males and from 3.23%/Sv to 4.02%/Sv among females. Leukemia excess risks increased from 0.87%/Sv to 1.10%/Sv among males and from 0.73%/Sv to 1.04%/Sv among females. Bias was dependent on the gender, site, correction method, exposure profile and projection model considered. Future studies that use LSS data for U.S. nuclear workers may be downwardly biased if lifetime risk projections are not adjusted for random and systematic errors. (Supported by U.S. NRC Grant NRC-04-091-02.) ^

BAYESIAN STATISTICAL METHODS IN GENE-ENVIRONMENT AND GENE-GENE INTERACTION STUDIES

Complex diseases such as cancer result from multiple genetic changes and environmental exposures. Due to the rapid development of genotyping and sequencing technologies, we are now able to more accurately assess causal effects of many genetic and environmental factors. Genome-wide association studies have been able to localize many causal genetic variants predisposing to certain diseases. However, these studies only explain a small portion of variations in the heritability of diseases. More advanced statistical models are urgently needed to identify and characterize some additional genetic and environmental factors and their interactions, which will enable us to better understand the causes of complex diseases. In the past decade, thanks to the increasing computational capabilities and novel statistical developments, Bayesian methods have been widely applied in the genetics/genomics researches and demonstrating superiority over some regular approaches in certain research areas. Gene-environment and gene-gene interaction studies are among the areas where Bayesian methods may fully exert its functionalities and advantages. This dissertation focuses on developing new Bayesian statistical methods for data analysis with complex gene-environment and gene-gene interactions, as well as extending some existing methods for gene-environment interactions to other related areas. It includes three sections: (1) Deriving the Bayesian variable selection framework for the hierarchical gene-environment and gene-gene interactions; (2) Developing the Bayesian Natural and Orthogonal Interaction (NOIA) models for gene-environment interactions; and (3) extending the applications of two Bayesian statistical methods which were developed for gene-environment interaction studies, to other related types of studies such as adaptive borrowing historical data. We propose a Bayesian hierarchical mixture model framework that allows us to investigate the genetic and environmental effects, gene by gene interactions (epistasis) and gene by environment interactions in the same model. It is well known that, in many practical situations, there exists a natural hierarchical structure between the main effects and interactions in the linear model. Here we propose a model that incorporates this hierarchical structure into the Bayesian mixture model, such that the irrelevant interaction effects can be removed more efficiently, resulting in more robust, parsimonious and powerful models. We evaluate both of the 'strong hierarchical' and 'weak hierarchical' models, which specify that both or one of the main effects between interacting factors must be present for the interactions to be included in the model. The extensive simulation results show that the proposed strong and weak hierarchical mixture models control the proportion of false positive discoveries and yield a powerful approach to identify the predisposing main effects and interactions in the studies with complex gene-environment and gene-gene interactions. We also compare these two models with the 'independent' model that does not impose this hierarchical constraint and observe their superior performances in most of the considered situations. The proposed models are implemented in the real data analysis of gene and environment interactions in the cases of lung cancer and cutaneous melanoma case-control studies. The Bayesian statistical models enjoy the properties of being allowed to incorporate useful prior information in the modeling process. Moreover, the Bayesian mixture model outperforms the multivariate logistic model in terms of the performances on the parameter estimation and variable selection in most cases. Our proposed models hold the hierarchical constraints, that further improve the Bayesian mixture model by reducing the proportion of false positive findings among the identified interactions and successfully identifying the reported associations. This is practically appealing for the study of investigating the causal factors from a moderate number of candidate genetic and environmental factors along with a relatively large number of interactions. The natural and orthogonal interaction (NOIA) models of genetic effects have previously been developed to provide an analysis framework, by which the estimates of effects for a quantitative trait are statistically orthogonal regardless of the existence of Hardy-Weinberg Equilibrium (HWE) within loci. Ma et al. (2012) recently developed a NOIA model for the gene-environment interaction studies and have shown the advantages of using the model for detecting the true main effects and interactions, compared with the usual functional model. In this project, we propose a novel Bayesian statistical model that combines the Bayesian hierarchical mixture model with the NOIA statistical model and the usual functional model. The proposed Bayesian NOIA model demonstrates more power at detecting the non-null effects with higher marginal posterior probabilities. Also, we review two Bayesian statistical models (Bayesian empirical shrinkage-type estimator and Bayesian model averaging), which were developed for the gene-environment interaction studies. Inspired by these Bayesian models, we develop two novel statistical methods that are able to handle the related problems such as borrowing data from historical studies. The proposed methods are analogous to the methods for the gene-environment interactions on behalf of the success on balancing the statistical efficiency and bias in a unified model. By extensive simulation studies, we compare the operating characteristics of the proposed models with the existing models including the hierarchical meta-analysis model. The results show that the proposed approaches adaptively borrow the historical data in a data-driven way. These novel models may have a broad range of statistical applications in both of genetic/genomic and clinical studies.

L -Sox5 and Sox6: Architectural transcription factors in chondrogenesis

Transcription factors often determine cell fate and tissue development. Chondrogenesis is the developmental process by which cartilages form. Recently, gene targeting studies have shown that two transcription factors, L-Sox5 and Sox6, play essential and redundant roles in chondrogenesis in vivo by converting precartilaginous cell condensations into cartilages. Both are highly similar High-Mobility-Group (HMG)-domain proteins that bind and subsequently bend DNA containing the 7bp HMG site (A/T)(A/T)CAA(A/T)G. They have no transactivation domain, but homo- and hetero-dimerize and preferentially bind DNA containing two HMG sites. They are thought to play an architectural role in transactivation by facilitating long-range DNA and protein interactions. To understand their molecular mechanism of action, we investigated how phasing, orientation, and spacing between HMG sites affect L-Sox5 and Sox6 DNA-binding. We determined that L-Sox5 and Sox6 dimers bind with high affinity to paired HMG sites in DNA rather than a single HMG site. Binding of paired sites is independent of DNA helical phasing, orientation of paired HMG sites and independent of distance up to 255 base pairs between sites. Mutational analysis demonstrated that binding of L-Sox5 and Sox6, independent of orientation of the sites, is critically dependent on the presence of paired HMG sites rather than one HMG site alone. Our data support a unique and novel model whereby L-Sox5 and Sox6 dimerize and bind DNA with pronounced spatial flexibility, possibly by a flexible hinge, and act as architectural transcription factors that bring distant DNA sites and proteins together to form higher order transcriptional complexes that are essential for the activation of their target genes in chondrogenesis. ^

Water stable oxygen isotope records from six Antarctic ice core sites for the present and last interglacial periods

We compare the present and last interglacial periods as recorded in Antarctic water stable isotope records now available at various temporal resolutions from six East Antarctic ice cores: Vostok, Taylor Dome, EPICA Dome C (EDC), EPICA Dronning Maud Land (EDML), Dome Fuji and the recent TALDICE ice core from Talos Dome. We first review the different modern site characteristics in terms of ice flow, meteorological conditions, precipitation intermittency and moisture origin, as depicted by meteorological data, atmospheric reanalyses and Lagrangian moisture source diagnostics. These different factors can indeed alter the relationships between temperature and water stable isotopes. Using five records with sufficient resolution on the EDC3 age scale, common features are quantified through principal component analyses. Consistent with instrumental records and atmospheric model results, the ice core data depict rather coherent and homogenous patterns in East Antarctica during the last two interglacials. Across the East Antarctic plateau, regional differences, with respect to the common East Antarctic signal, appear to have similar patterns during the current and last interglacials. We identify two abrupt shifts in isotopic records during the glacial inception at TALDICE and EDML, likely caused by regional sea ice expansion. These regional differences are discussed in terms of moisture origin and in terms of past changes in local elevation histories, which are compared to ice sheet model results. Our results suggest that elevation changes may contribute significantly to inter-site differences. These elevation changes may be underestimated by current ice sheet models

Essential elements of postabortion care: origins, evolution and future directions

In this comment, we chronicle the development and expansion of a postabortion care model designed to promote interventions that address abortion-related public health concerns even when abortion laws and policies are restrictive. We review years of program experience with the original model, which led to the development of an expanded and updated model, Essential Elements of Postabortion Care (PAC). Implementing the model challenges global public health leaders, donors, technical assistance agencies and ministries of health to work with communities to ensure that all women who want to prevent or space pregnancies can obtain contraceptive services; that all women have access to services to manage complications from abortion, whether induced or spontaneous; and that all women receiving treatment also receive counseling and the reproductive and other health services they need at the treatment visit, as well as follow-up care and contraceptive resupply