Modeling the dynamics of bivalent histone modifications

Epigenetic modifications to histones may promote either activation or repression of the transcription of nearby genes. Recent experimental studies show that the promoters of many lineage-control genes in stem cells have "bivalent domains" in which the nucleosomes contain both active (H3K4me3) and repressive (H3K27me3) marks. It is generally agreed that bivalent domains play an important role in stem cell differentiation, but the underlying mechanisms remain unclear. Here we formulate a mathematical model to investigate the dynamic properties of histone modification patterns. We then illustrate that our modeling framework can be used to capture key features of experimentally observed combinatorial chromatin states.Comment: 23 pages, 10 figure

Carbon in Red Giants in Globular Clusters and Dwarf Spheroidal Galaxies

We present carbon abundances of red giants in Milky Way globular clusters and dwarf spheroidal galaxies (dSphs). Our sample includes measurements of carbon abundances for 154 giants in the clusters NGC 2419, M68, and M15 and 398 giants in the dSphs Sculptor, Fornax, Ursa Minor, and Draco. This sample doubles the number of dSph stars with measurements of [C/Fe]. The [C/Fe] ratio in the clusters decreases with increasing luminosity above log(L/L_sun) ~= 1.6, which can be explained by deep mixing in evolved giants. The same decrease is observed in dSphs, but the initial [C/Fe] of the dSph giants is not uniform. Stars in dSphs at lower metallicities have larger [C/Fe] ratios. We hypothesize that [C/Fe] (corrected to the initial carbon abundance) declines with increasing [Fe/H] due to the metallicity dependence of the carbon yield of asymptotic giant branch stars and due to the increasing importance of Type Ia supernovae at higher metallicities. We also identified 11 very carbon-rich giants (8 previously known) in three dSphs. However, our selection biases preclude a detailed comparison to the carbon-enhanced fraction of the Milky Way stellar halo. Nonetheless, the stars with [C/Fe] < +1 in dSphs follow a different [C/Fe] track with [Fe/H] than the halo stars. Specifically, [C/Fe] in dSphs begins to decline at lower [Fe/H] than in the halo. The difference in the metallicity of the [C/Fe] "knee" adds to the evidence from [alpha/Fe] distributions that the progenitors of the halo had a shorter timescale for chemical enrichment than the surviving dSphs.Comment: accepted to ApJ; 20 pages, 11 figures, 2 machine-readable table

Knowledge Distillation for Small-footprint Highway Networks

Deep learning has significantly advanced state-of-the-art of speech recognition in the past few years. However, compared to conventional Gaussian mixture acoustic models, neural network models are usually much larger, and are therefore not very deployable in embedded devices. Previously, we investigated a compact highway deep neural network (HDNN) for acoustic modelling, which is a type of depth-gated feedforward neural network. We have shown that HDNN-based acoustic models can achieve comparable recognition accuracy with much smaller number of model parameters compared to plain deep neural network (DNN) acoustic models. In this paper, we push the boundary further by leveraging on the knowledge distillation technique that is also known as {\it teacher-student} training, i.e., we train the compact HDNN model with the supervision of a high accuracy cumbersome model. Furthermore, we also investigate sequence training and adaptation in the context of teacher-student training. Our experiments were performed on the AMI meeting speech recognition corpus. With this technique, we significantly improved the recognition accuracy of the HDNN acoustic model with less than 0.8 million parameters, and narrowed the gap between this model and the plain DNN with 30 million parameters.Comment: 5 pages, 2 figures, accepted to icassp 201

What Women With Disabilities Write in Personal Blogs About Pregnancy and Early Motherhood: Qualitative Analysis of Blogs.

BackgroundMore than 1 in 10 women of reproductive age identify as having some type of disability. Most of these women are able to become pregnant and have similar desires for motherhood as women without disability. Women with disability, however, face greater stigma and stereotyping, additional risk factors, and may be less likely to receive adequate reproductive health care compared with their peers without disability. More and more individuals, including those with disability, are utilizing the internet to seek information and peer support. Blogs are one source of peer-to-peer social media engagement that may provide a forum for women with disability to both share and obtain peer-to-peer information and support. Nevertheless, it is not clear what content about reproductive health and pregnancy and/or motherhood is featured in personal blogs authored by women with spinal cord injury (SCI), traumatic brain injury (TBI), spina bifida, and autism.ObjectiveThe objective of this study was twofold: (1) to examine the information being shared in blogs by women with 4 types of disabilities, namely, SCI, TBI, spina bifida, and autism, about reproductive health, disability, health care, pregnancy, and motherhood; and (2) to classify the content of reproductive health experiences addressed by bloggers to better understand what they viewed as important.MethodsPersonal blogs were identified by searching Google with keywords related to disabilities, SCI, TBI, spina bifida, and autism, and a variety of keywords related to reproductive health. The first 10 pages of each database search in Google, based on the relevance of the search terms, were reviewed and all blogs in these pages were included. Blog inclusion criteria were as follows: (1) written by a woman or care partner (ie, parent or spouse) of a woman with a self-identified diagnosis of SCI, TBI, spina bifida, or autism; (2) focused on the personal experience of health and health care during the prepregnancy, prenatal, antepartum, intrapartum, and/or postpartum periods; (3) written in English; and (4) published between 2013 and 2017. A descriptive and thematic qualitative analysis of blogs and corresponding comments was facilitated with NVivo software and matrix analysis.ResultsOur search strategy identified 125 blogs that met all the inclusion criteria; no blogs written by women with spina bifida were identified. We identified 4 reproductive health themes featured in the blog of women with disabilities: (1) (in)accessible motherhood, (2) (un)supportive others, (3) different, but not different, and (4) society questioning motherhood.ConclusionsThis analysis of personal blogs about pregnancy and health care written by women with SCI, TBI, and autism provides a glimpse into their experiences. The challenges faced by these women and the adaptations they made to successfully navigate pregnancy and early motherhood provide insights that can be used to shape future research

Parental Co‐Construction of 5‐ to 13‐Year‐Olds\u27 Global Self‐Esteem Through Reminiscing About Past Events

The current study explored parental processes associated with children\u27s global self‐esteem development. Eighty 5‐ to 13‐year‐olds and one of their parents provided qualitative and quantitative data through questionnaires, open‐ended questions, and a laboratory‐based reminiscing task. Parents who included more explanations of emotions when writing about the lowest points in their lives were more likely to discuss explanations of emotions experienced in negative past events with their child, which was associated with child attachment security. Attachment was associated with concurrent self‐esteem, which predicted relative increases in self‐esteem 16 months later, on average. Finally, parent support also predicted residual increases in self‐esteem. Findings extend prior research by including younger ages and uncovering a process by which two theoretically relevant parenting behaviors impact self‐esteem development