The Impact of a Regulatory Intervention on Resident-Centered Nursing Home Care: Rhode Island's Individualized Care Pilot

Evaluates a pilot project to promote resident-centered care through activities integrated with recertification inspections, including visits from a nonregulatory entity, and its impact on understanding, consideration, and implementation of practices

Modeling Persistent Trends in Distributions

We present a nonparametric framework to model a short sequence of probability distributions that vary both due to underlying effects of sequential progression and confounding noise. To distinguish between these two types of variation and estimate the sequential-progression effects, our approach leverages an assumption that these effects follow a persistent trend. This work is motivated by the recent rise of single-cell RNA-sequencing experiments over a brief time course, which aim to identify genes relevant to the progression of a particular biological process across diverse cell populations. While classical statistical tools focus on scalar-response regression or order-agnostic differences between distributions, it is desirable in this setting to consider both the full distributions as well as the structure imposed by their ordering. We introduce a new regression model for ordinal covariates where responses are univariate distributions and the underlying relationship reflects consistent changes in the distributions over increasing levels of the covariate. This concept is formalized as a "trend" in distributions, which we define as an evolution that is linear under the Wasserstein metric. Implemented via a fast alternating projections algorithm, our method exhibits numerous strengths in simulations and analyses of single-cell gene expression data.Comment: To appear in: Journal of the American Statistical Associatio

NF-KB protein purification from bovine spleen: Nucleotide stimulation and binding site specificity

The activity of the enhancer for the κ immunoglobulin light chain gene critically depends on the presence in the nucleus of the NF-κB protein. We purified NF-κB over 50,000-fold and identified two protein species, 42 and 44 kDa, that could be eluted and renatured from a sodium dodecyl sulfate/polyacrylamide gel to give specific DNA-binding activity. Binding of the purified bovine NF-κB as well as that from human and murine B- or T-lymphoid cell extracts was dramatically stimulated by nucleoside triphosphates. This effect distinguished NF-κB from a related factor, H2-TF1. Purified NF-κB interacted efficiently with regulatory sequences that function during either B- or T-lymphocyte activation, including the human immunodeficiency virus enhancer and a NF-κB binding site we detected in the interleukin 2 enhancer

The In Situ Meaning of to Observe All in Matthew 28:20 (NASB)

Christian leaders often bemoan the typical American believer for his lack of commitment to Jesus\u27 commands. Wanting the blessing of God, she looks for it in all the wrong places. The Great Commission, however, commands Church leaders to teach their disciples to observe all (terein panta) that Jesus commanded. This thesis has the underlying assumption, therefore, that diminished faithfulness to commandments may stem from exegetical oversight. First, Christians may be overlooking the full meaning and significance of the verb terein. A literature review revealed that the word implies four independent concepts, the primary one being observation; the others are guardianship, cognition, and obedience. Because of this etymological link with the sense of sight, and fully supported by scripture, this thesis proposes that disciplers must personify Jesus\u27 commands so their students can observe them optically and behaviorally. The second exegetical oversight this thesis proposes is that Church leaders may be incorrectly identifying the Great Commission\u27s core curriculum. A literature review discovered that there is no consensus surrounding the content of all. Many theologians simply assume their readers already know what it means. Of those that directly address this issue, however, a multitude of views exist. Some scholars, nevertheless, do rally around Jesus\u27 commands in Matthew as the content of all --but even these have a variety of interpretations. One major issue they disagree over is Jesus\u27 support for commandments in the Law and the Prophets. Based on a variety of factors, this thesis concludes that the in situ meaning of to observe all in Matthew 28.20 is that Jesus\u27 disciples shall observe (and keep, heed, and obey) all that Jesus commanded in the Gospel of Matthew. Because of Matthew 5.17-48, this also includes observing everything commanded in the Old Testament as reinterpreted in the light of Christ

Roasted: Coffee, Insult, Rhetoric

While insult has been a frequent topic for rhetorical study in the past, little if any work has gone toward the formation of a systematic theory of insult. Karina Korostelina has proposed a theory of intergroup identity insults, which appears promising from a socio-cultural perspective. However, her theory does not address the particularly rhetorical characteristics of insults, preferring instead to analyze them with reference to their socio-historic context. While her theory proves sound under scrutiny, it does little to shed light on pejorative rhetoric as rhetoric. In what follows, I would like to propose certain characteristics of pejorative rhetoric that may prove useful in developing a rhetorical understanding of insult. I will be using Korostelina’s theory as a starting place to ground my discussion of insult, but I will go beyond the socio-historic contexts to suggest a purely rhetorical aspect of insults that creates new meanings and associations independent of larger cultural contexts. While independent of cultural contexts, these new associations are still informed by cultural contexts. As such, I will be using coffee, a cultural artifact with a variety of social and culture meanings, as a lens from which to examine pejorative rhetoric. Ultimately, I propose that insult functions by drawing from the associations inherent in cultural artifacts in order to transform those associations into purely rhetorical associations, that is, associations that could not exist without the influence of pejorative rhetoric, thereby creating a rhetorical context independent of large cultural contexts

Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding

Background The combinatorial binding of trans-acting factors (TFs) to the DNA is critical to the spatial and temporal specificity of gene regulation. For certain regulatory regions, more than one regulatory module (set of TFs that bind together) are combined to achieve context-specific gene regulation. However, previous approaches are limited to either pairwise TF co-association analysis or assuming that only one module is used in each regulatory region. Results We present a new computational approach that models the modular organization of TF combinatorial binding. Our method learns compact and coherent regulatory modules from in vivo binding data using a topic model. We found that the binding of 115 TFs in K562 cells can be organized into 49 interpretable modules. Furthermore, we found that tens of thousands of regulatory regions use multiple modules, a structure that cannot be observed with previous hard clustering based methods. The modules discovered recapitulate many published protein-protein physical interactions, have consistent functional annotations of chromatin states, and uncover context specific co-binding such as gene proximal binding of NFY + FOS + SP and distal binding of NFY + FOS + USF. For certain TFs, the co-binding partners of direct binding (motif present) differs from those of indirect binding (motif absent); the distinct set of co-binding partners can predict whether the TF binds directly or indirectly with up to 95% accuracy. Joint analysis across two cell types reveals both cell-type-specific and shared regulatory modules. Conclusions Our results provide comprehensive cell-type-specific combinatorial binding maps and suggest a modular organization of combinatorial binding. Keywords Computational genomics Transcription factor Combinatorial binding Direct and indirect binding Topic modelNational Institutes of Health (U.S.) (grant 1U01HG007037-01

Training Data Attribution for Diffusion Models

Diffusion models have become increasingly popular for synthesizing high-quality samples based on training datasets. However, given the oftentimes enormous sizes of the training datasets, it is difficult to assess how training data impact the samples produced by a trained diffusion model. The difficulty of relating diffusion model inputs and outputs poses significant challenges to model explainability and training data attribution. Here we propose a novel solution that reveals how training data influence the output of diffusion models through the use of ensembles. In our approach individual models in an encoded ensemble are trained on carefully engineered splits of the overall training data to permit the identification of influential training examples. The resulting model ensembles enable efficient ablation of training data influence, allowing us to assess the impact of training data on model outputs. We demonstrate the viability of these ensembles as generative models and the validity of our approach to assessing influence.Comment: 14 pages, 6 figure