39 research outputs found
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Questioning Voices: Dissention and Dialogue in the Poetry of Emily and Anne Brontë
No full textMy dissertation examines the roles of Emily and Anne Brontë as nineteenth-century women poets, composing in a literary form dominated by androcentric language and metaphor. The work of Mikhail Bakhtin, particularly concerning spoken and implied dialogue, and feminists who have pioneered an exploration of feminist dialogics provide crucial tools for examining the importance and uses of the dialogic form in the development of a powerful and creative feminine voice. As such, I propose to view Emily's Gondal poetry not as a series of loosely connected monologues, but as utterances in an inner dialogue between the dissenting and insistent female voice and the authoritative voice of the non-Gondal world. Emily's identification with her primary heroine, Augusta, enables her to challenge the controlling voice of the of the patriarchy that attempts to dictate and limit her creative and personal expression. The voice of Augusta in particular expresses the guilt, shame, and remorse that the woman-as-author must also experience when attempting to do battle with the patriarchy that attempts to restrict and reshape her utterances. While Anne was a part of the creation of Gondal, using it to mask her emotions through sustained dialogue with those who enabled and inspired such feelings, her interest in the mythical kingdom soon waned. However, it is in the dungeons and prisons of Gondal and within these early poems that Anne's distinct voice emerges and enters into a dialogue with her readers, her sister, and herself. The interior dialogues that her heroines engage in become explorations of the choices that Anne feels she must make as a woman within both society and the boundaries of her religious convictions. Through dialogue with the church, congregation, and religious doctrine, she attempts to relieve herself of the guilt of female creativity and justify herself and her creations through religious orthodoxy. Yet her seeming obedience belies the power of her voice that insists on being heard, even within the confines of androcentric social and religious power structures
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Problems in Variable Selection: False Discovery Rate Control and Variational Inference
No full textVariable selection plays a key role in modern high-dimensional statistics. This dissertation provides a comprehensive survey of theory and methods developed by the author and collaborators, with a specific focus on two areas: false discovery rate (FDR) control and Bayesian variable selection. In the domain of FDR control, we introduce a data-splitting method to asymptotically control the FDR while maintaining a high power. Furthermore,
a Multiple Data Splitting (MDS) method is proposed to stabilize the selection result and boost the power. In Chapter 1, we apply both DS and MDS to the generalized linear models, which appear to be more robust in finite-sample cases compared to existing methods. Chapter 2 provides some following discussions regarding the proposed method and Chapter 3 compares the power of the proposed method with two existing methods: the model-X knockoff and Gaussian mirror. In terms of the Bayesian variable selection, the posterior is typically high-dimensional and analytically intractable. Exact inference methods based on sampling, such as Markov Chain Monte Carlo (MCMC), can encounter challenges related to mixing. Variational inference has emerged as an attractive alternative for approximating the posterior distribution. By recasting the sampling problem as an optimization problem, variational inference can significantly reduce computational time. In chapter 4, we apply the variational inference to group variable selection with spike-and-slab prior and propose an efficient parameter-expanded coordinate-ascent algorithm to obtain the optimal variational Bayes approximation. The proposed method has demonstrated good performance in both simulations and a real data example
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Clustering of Single-Cell and Text Data
No full textIn recent years, we have witnessed the rapid growth of the data volume and a significant
fraction of the unlabeled data. We study the problems of subject clustering in bioinformatics
and document clustering in Natural Languague Processing (NLP). In these problems, the data
matrix is usually in very high dimension, but the useful signals for clustering are contained in
a low-dimensional latent structure, masked by complicated noise. This dissertation introduces
new methods and theory for such problems.
In Chapter 1, we study high-dimensional clustering under Rare and Weak signals (i.e., there
are only a small fraction of useful features and each useful feature contains very weak signals for
clustering). First, we theoretically investigate IF-PCA, a popular clustering method. We derive a
phase diagram – in the Possibility region, IF-PCA yields successful clustering; in the Impossibility
region, there exists no polynomial-time algorithm that can yield successful clustering. Next,
inspired by the appealing theoretical properties of IF-PCA, we combine it with recent unsupervised
deep learning methods, the variational auto-encoder (VAE), to simultaneously deal with
sparsity and non-linearity. We call this method IF-VAE. Last, we evaluate the performance of
IF-PCA and IF-VAE on 10 gene microarray data sets and 8 single-cell RNA-seq data sets, with
a comparison with popular methods for single-cell subject clustering (e.g., Seurat and SC3).
In Chapter 2, we study bi-gram topic modeling. The topic model is one of the most popular
uni-gram models (a.k.a., bag-of-words models) for text analysis. However, it ignores word orders
and the context of each word. Bi-gram models improve uni-gram models, but it is yet unclear
how to learn “topics” from the bi-grams. We propose two versions of bi-gram models. For each
model, we propose a tensor-decomposition approach to learn “topics”. These approaches yield
consistent topic estimation in simulations. As a related problem, we also study author clustering
based on the bi-grams of abstracts of statistical papers. We find evidence in real data where using
the bi-grams leads to more meaningful clusters than using the uni-grams.
In Chapter 3, we focus on a sub-problem that arises in many soft-clustering problems, such
as network mixed membership estimation, topic modeling, and hyperspectral remote sensing.
In these problems, one of the key steps is to estimate a simplex structure from a noisy point
cloud, which we call the vertex hunting (VH) problem. The existed VH algorithms, such as
successive projection (SP), are susceptible to outliers. We propose a robust VH algorithm that
properly shrinks estimated vertices towards the interior of data cloud, so as to mitigate the effect
of outliers. The level of shrinkage is determined by maximizing a pseudo likelihood and has no
tuning parameter. Under an idealized model, we show that the proposed method has a faster
rate of convergence than the existed VH algorithms
Effect of praziquantel treatment of Schistosoma mansoni during pregnancy on immune responses to schistosome antigens among the offspring: results of a randomised, placebo-controlled trial.
No full textBACKGROUND: Offspring of women with schistosomiasis may exhibit immune responsiveness to schistosomes due to in utero sensitisation or trans-placental transfer of antibodies. Praziquantel treatment during pregnancy boosts maternal immune responses to schistosome antigens and reduces worm burden. Effects of praziquantel treatment during pregnancy on responses among offspring are unknown. METHODS: In a trial of anthelminthic treatment during pregnancy in Uganda (ISRCTN32849447; http://www.controlled-trials.com/ISRCTN32849447/elliott), offspring of women with Schistosoma mansoni were examined for cytokine and antibody responses to schistosome worm (SWA) and egg (SEA) antigen, in cord blood and at age one year. Relationships to maternal responses and pre-treatment infection intensities were examined, and responses were compared between the offspring of women who did, or did not receive praziquantel treatment during pregnancy. RESULTS: Of 388 S. mansoni-infected women studied, samples were obtained at age one year from 215 of their infants. Stool examination for S. mansoni eggs was negative for all infants. Cord and infant samples were characterised by very low cytokine production in response to schistosome antigens with the exception of cord IL-10 responses, which were substantial. Cord and infant cytokine responses showed no association with maternal responses. As expected, cord blood levels of immunoglobulin (Ig) G to SWA and SEA were high and correlated with maternal antibodies. However, by age one year IgG levels had waned and were hardly detectable. Praziquantel treatment during pregnancy showed no effect on cytokine responses or antibodies levels to SWA or SEA either in cord blood or at age one year, except for IgG1 to SWA, which was elevated in infants of treated mothers, reflecting maternal levels. There was some evidence that maternal infection intensity was positively associated with cord blood IL-5 and IL-13 responses to SWA, and IL-5 responses to SEA, and that this association was modified by treatment with praziquantel. CONCLUSIONS: Despite strong effects on maternal infection intensity and maternal immune responses, praziquantel treatment of infected women during pregnancy had no effect on anti-schistosome immune responses among offspring by age one year. Whether the treatment will impact upon the offspring's responses on exposure to primary schistosome infection remains to be elucidated. TRIAL REGISTRATION: ISRCTN: ISRCTN32849447
Factors affecting the infant antibody response to measles immunisation in Entebbe-Uganda.
No full textBACKGROUND: Vaccine failure is an important concern in the tropics with many contributing elements. Among them, it has been suggested that exposure to natural infections might contribute to vaccine failure and recurrent disease outbreaks. We tested this hypothesis by examining the influence of co-infections on maternal and infant measles-specific IgG levels. METHODS: We conducted an observational analysis using samples and data that had been collected during a larger randomised controlled trial, the Entebbe Mother and Baby Study (ISRCTN32849447). For the present study, 711 pregnant women and their offspring were considered. Helminth infections including hookworm, Schistosoma mansoni and Mansonella perstans, along with HIV, malaria, and other potential confounding factors were determined in mothers during pregnancy and in their infants at age one year. Infants received their measles immunisation at age nine months. Levels of total IgG against measles were measured in mothers during pregnancy and at delivery, as well as in cord blood and from infants at age one year. RESULTS: Among the 711 pregnant women studied, 66% had at least one helminth infection at enrolment, 41% had hookworm, 20% M. perstans and 19% S. mansoni. Asymptomatic malaria and HIV prevalence was 8% and 10% respectively. At enrolment, 96% of the women had measles-specific IgG levels considered protective (median 4274 mIU/ml (IQR 1784, 7767)). IgG levels in cord blood were positively correlated to maternal measles-specific IgG levels at delivery (r = 0.81, p < 0.0001). Among the infants at one year of age, median measles-specific IgG levels were markedly lower than in maternal and cord blood (median 370 mIU/ml (IQR 198, 656) p < 0.0001). In addition, only 75% of the infants had measles-specific IgG levels considered to be protective. In a multivariate regression analysis, factors associated with reduced measles-specific antibody levels in infancy were maternal malaria infection, infant malaria parasitaemia, infant HIV and infant wasting. There was no association with maternal helminth infection. CONCLUSION: Malaria and HIV infection in mothers during pregnancy, and in their infants, along with infant malnutrition, may result in reduction of the antibody response to measles immunisation in infancy. This re-emphasises the importance of malaria and HIV control, and support for infant nutrition, as these interventions may have benefits for vaccine efficacy in tropical settings
Adaptive Evolution in the Glucose Transporter 4 Gene Slc2a4 in Old World Fruit Bats (Family: Pteropodidae)
No full textPMCID: PMC3320886This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Synthesis and Stability of Ceramic-Carbonate Dual-Phase Membrane for Carbon Dioxide Separation
No full textabstract: Of the potential technologies for pre-combustion capture, membranes offer the advantages of being temperature resistant, able to handle large flow rates, and having a relatively small footprint. A significant amount of research has centered on the use of polymeric and microporous inorganic membranes to separate CO2. These membranes, however, have limitations at high temperature resulting in poor permeation performance. To address these limitations, the use of a dense dual-phase membrane has been studied. These membranes are composed of conductive solid and conductive liquid phases that have the ability to selectively permeate CO2 by forming carbonate ions that diffuse through the membrane at high temperature. The driving force for transport through the membrane is a CO2 partial pressure gradient. The membrane provides a theoretically infinite selectivity. To address stability of the ceramic-carbonate dual-phase membrane for CO2 capture at high temperature, the ceramic phase of the membrane was studied and replaced with materials previously shown to be stable in harsh conditions. The permeation properties and stability of La0.6Sr0.4Co0.8Fe0.2O3-δ (LSCF)-carbonate, La0.85Ce0.1Ga0.3Fe0.65Al0.05O3-δ (LCGFA)-carbonate, and Ce0.8Sm0.2O1.9 (SDC)-carbonate membranes were examined under a wide range of experimental conditions at high temperature. LSCF-carbonate membranes were shown to be unstable without the presence of O2 due to reaction of CO2 with the ceramic phase. In the presence of O2, however, the membranes showed stable permeation behavior for more than one month at 900oC. LCGFA-carbonate membranes showed great chemical and permeation stability in the presence of various conditions including exposure to CH4 and H2, however, the permeation performance was quite low when compared to membranes in the literature. Finally, SDC-carbonate membranes showed great chemical and permeation stability both in a CO2:N2 environment for more than two weeks at 900oC as well as more than one month of exposure to simulated syngas conditions at 700oC. Ceramic phase chemical stability increased in the order of LSCF < LCGFA < SDC while permeation performance increased in the order of LCGFA < LSCF < SDC.Dissertation/ThesisPh.D. Chemical Engineering 201
[[alternative]]Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes (Nature, (2020), 586, 7831, (763-768), 10.1038/s41586-020-2819-2)
No full text[[abstract]]In this Article, Abhishek Niroula should have been listed as an author, with the affiliations: Broad Institute of MIT and Harvard, Cambridge, MA, USA; and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. They performed additional bioinformatic analyses (see ‘Author contributions’). The original Article has been corrected online. *A list of authors and their affiliations appears online
Rate of telomere shortening and cardiovascular damage: a longitudinal study in the 1946 British Birth Cohort.
No full textCross-sectional studies reported associations between short leucocyte telomere length (LTL) and measures of vascular and cardiac damage. However, the contribution of LTL dynamics to the age-related process of cardiovascular (CV) remodelling remains unknown. In this study, we explored whether the rate of LTL shortening can predict CV phenotypes over 10-year follow-up and the influence of established CV risk factors on this relationship
Wave generation, dissipation, and disequilibrium in an embayment with complex bathymetry
No full textAuthor Posting. © American Geophysical Union, 2018. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Wave generation, dissipation, and disequilibrium in an embayment with complex bathymetry. Journal of Geophysical Research-Oceans, 123(11), (2018): 7856-7876, doi:10.1029/2018JC014381.Heterogeneous, sharply varying bathymetry is common in estuaries and embayments, and complex interactions between the bathymetry and wave processes fundamentally alter the distribution of wave energy. The mechanisms that control the generation and dissipation of wind waves in an embayment with heterogeneous, sharply varying bathymetry are evaluated with an observational and numerical study of the Delaware Estuary. Waves in the lower bay depend on both local wind forcing and remote wave forcing from offshore, but elsewhere in the estuary waves are controlled by the local winds and the response of the wavefield to bathymetric variability. Differences in the wavefield with wind direction highlight the impacts of heterogeneous bathymetry and limited fetch. Under the typical winter northwest wind conditions waves are fetch‐limited in the middle estuary and reach equilibrium with local water depth only in the lower bay. During southerly wind conditions typical of storms, wave energy is near equilibrium in the lower bay, and midestuary waves are attenuated by the combination of whitecapping and bottom friction, particularly over the steep, longitudinal shoals. Although the energy dissipation due to bottom friction is generally small relative to whitecapping, it becomes significant where the waves shoal abruptly due to steep bottom topography. In contrast, directional spreading keeps wave heights in the main channel significantly less than local equilibrium. The wave disequilibrium in the deep navigational channel explains why the marked increase in depth by dredging of the modern channel has had little impact on wave conditions.Funding was provided by National Science Foundation Coastal SEES: Toward Sustainable Urban Estuaries in the Anthropocene (OCE 1325136) and Ministry of Science and Technology (MOST 107‐2611‐M‐006‐004). We thank James Kirby, Fengyan Shi, and the two anonymous reviewers for their careful reading of our manuscript and their insightful comments. We thank Tracy Quirk for providing wave measurements in Bombay Hook, DE and Stow Creek, NJ. We thank Katie Pijanowski for compiling historical and modern bathymetric data for the estuary. Data supporting this study are posted to Zenodo (http://doi.org/10.5281/zenodo.1433055).2019-04-0
