Matrix prior for data transfer between single cell data types in latent Dirichlet allocation

Single cell ATAC-seq (scATAC-seq) enables the mapping of regulatory elements in fine-grained cell types. Despite this advance, analysis of the resulting data is challenging, and large scale scATAC-seq data are difficult to obtain and expensive to generate. This motivates a method to leverage information from previously generated large scale scATAC-seq or scRNA-seq data to guide our analysis of new scATAC-seq datasets. We analyze scATAC-seq data using latent Dirichlet allocation (LDA), a Bayesian algorithm that was developed to model text corpora, summarizing documents as mixtures of topics defined based on the words that distinguish the documents. When applied to scATAC-seq, LDA treats cells as documents and their accessible sites as words, identifying "topics" based on the cell type-specific accessible sites in those cells. Previous work used uniform symmetric priors in LDA, but we hypothesized that nonuniform matrix priors generated from LDA models trained on existing data sets may enable improved detection of cell types in new data sets, especially if they have relatively few cells. In this work, we test this hypothesis in scATAC-seq data from whole C. elegans nematodes and SHARE-seq data from mouse skin cells. We show that nonsymmetric matrix priors for LDA improve our ability to capture cell type information from small scATAC-seq datasets.

Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome

The human epigenome has been experimentally characterized by thousands of measurements for every basepair in the human genome. We propose a deep neural network tensor factorization method, Avocado, that compresses this epigenomic data into a dense, information-rich representation. We use this learned representation to impute epigenomic data more accurately than previous methods, and we show that machine learning models that exploit this representation outperform those trained directly on epigenomic data on a variety of genomics tasks. These tasks include predicting gene expression, promoter-enhancer interactions, replication timing, and an element of 3D chromatin architecture.

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

Here, we present Scribe (https://github.com/aristoteleo/Scribe-py), a toolkit for detecting and visualizing causal regulatory interactions between genes and explore the potential for single-cell experiments to power network reconstruction. Scribe employs restricted directed information to determine causality by estimating the strength of information transferred from a potential regulator to its downstream target. We apply Scribe and other leading approaches for causal network reconstruction to several types of single-cell measurements and show that there is a dramatic drop in performance for "pseudotime"-ordered single-cell data compared with true time-series data. We demonstrate that performing causal inference requires temporal coupling between measurements. We show that methods such as "RNA velocity" restore some degree of coupling through an analysis of chromaffin cell fate commitment. These analyses highlight a shortcoming in experimental and computational methods for analyzing gene regulation at single-cell resolution and suggest ways of overcoming it.

Functional characterization of enhancer evolution in the primate lineage

BACKGROUND

Enhancers play an important role in morphological evolution and speciation by controlling the spatiotemporal expression of genes. Previous efforts to understand the evolution of enhancers in primates have typically studied many enhancers at low resolution, or single enhancers at high resolution. Although comparative genomic studies reveal large-scale turnover of enhancers, a specific understanding of the molecular steps by which mammalian or primate enhancers evolve remains elusive.

RESULTS

We identified candidate hominoid-specific liver enhancers from H3K27ac ChIP-seq data. After locating orthologs in 11 primates spanning around 40 million years, we synthesized all orthologs as well as computational reconstructions of 9 ancestral sequences for 348 active tiles of 233 putative enhancers. We concurrently tested all sequences for regulatory activity with STARR-seq in HepG2 cells. We observe groups of enhancer tiles with coherent trajectories, most of which can be potentially explained by a single gain or loss-of-activity event per tile. We quantify the correlation between the number of mutations along a branch and the magnitude of change in functional activity. Finally, we identify 84 mutations that correlate with functional changes; these are enriched for cytosine deamination events within CpGs.

CONCLUSIONS

We characterized the evolutionary-functional trajectories of hundreds of liver enhancers throughout the primate phylogeny. We observe subsets of regulatory sequences that appear to have gained or lost activity. We use these data to quantify the relationship between sequence and functional divergence, and to identify CpG deamination as a potentially important force in driving changes in enhancer activity during primate evolution.

Genome-wide chromatin state transitions associated with developmental and environmental cues

Differences in chromatin organization are key to the multiplicity of cell states that arise from a single genetic background, yet the landscapes of in vivo tissues remain largely uncharted. Here, we mapped chromatin genome-wide in a large and diverse collection of human tissues and stem cells. The maps yield unprecedented annotations of functional genomic elements and their regulation across developmental stages, lineages, and cellular environments. They also reveal global features of the epigenome, related to nuclear architecture, that also vary across cellular phenotypes. Specifically, developmental specification is accompanied by progressive chromatin restriction as the default state transitions from dynamic remodeling to generalized compaction. Exposure to serum in vitro triggers a distinct transition that involves de novo establishment of domains with features of constitutive heterochromatin. We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming.

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure. Here, we present a systematic approach to infer CR function. We developed ChIP-string, a meso-scale assay that combines chromatin immunoprecipitation with a signature readout of 487 representative loci. We applied ChIP-string to screen 145 antibodies, thereby identifying effective reagents, which we used to map the genome-wide binding of 29 CRs in two cell types. We found that specific combinations of CRs colocalize in characteristic patterns at distinct chromatin environments, at genes of coherent functions, and at distal regulatory elements. When comparing between cell types, CRs redistribute to different loci but maintain their modular and combinatorial associations. Our work provides a multiplex method that substantially enhances the ability to monitor CR binding, presents a large resource of CR maps, and reveals common principles for combinatorial CR function.

Oral care for special needs patients: a survey of Nebraska general dentists

PURPOSE

The purpose of this survey was to assess the attitudes, behavior, and demographics of general dentists in Nebraska regarding their providing oral health care to patients with special health care needs (PSHCN).

METHODS

A 14-item questionnaire and accompanying cover letter were sent to 800 licensed general dentists in Nebraska. The survey asked for the dentists' demographic information and questions about their PSCHN. Responses to the questionnaire were tabulated, and percent frequency distributions for responses to each item were computed.

RESULTS

Of the 800 surveys sent, 371 (approximately 46%) were returned. Solo practitioners were more likely to report seeing PSCHN (P<.001). Most respondents see all ages, but approximately 10% see only PSCHN over 18-years-old. The most common reasons given to improve the practitioners' ability to care for PSCHN were improved reimbursement (approximately 35%) and more continuing education (approximately 36%).

CONCLUSIONS

These data indicate that most general dentists surveyed in Nebraska see special needs patients of all ages. The most common reasons for not seeing more special needs patients were the level of the patient's disease, the patient's behavior, and insufficient training/experience.

Minimal genomes, maximal productivity: comparative genomics of the photosystem and light-harvesting complexes in the marine cyanobacterium, Prochlorococcus

Although Prochlorococcus isolates possess the smallest genomes of any extant photosynthetic organism, this genus numerically dominates vast regions of the world's subtropical and tropical open oceans and has evolved to become an important contributor to global biogeochemical cycles. The sequencing of 12 Prochlorococcus genomes provides a glimpse of the extensive genetic heterogeneity and, thus, physiological potential of the lineage. In this study, we present an up-to-date comparative analysis of major proteins of the photosynthetic apparatus in 12 Prochlorococcus genomes. Our analyses reveal a striking diversity within the Prochlorococcus lineage in the major protein complexes of the photosynthetic apparatus. The heterogeneity that has evolved in the photosynthetic apparatus suggests versatility in strategies for optimizing photosynthesis under conditions of environmental variability and stress. This diversity could be particularly important in ensuring the survival of a lineage whose individuals have evolved minimal genomes and, thus, relatively limited repertoires for responding to environmental challenges.

Three quantitative approaches to the diagnosis of abdominal pain in children: practical applications of decision theory

BACKGROUND/PURPOSE

The authors compared 3 quantitative methods for assisting clinicians in the differential diagnosis of abdominal pain in children, where the most common important endpoint is whether the patient has appendicitis. Pretest probability in different age and sex groups were determined to perform Bayesian analysis, binary logistic regression was used to determine which variables were statistically significantly likely to contribute to a diagnosis, and recursive partitioning was used to build decision trees with quantitative endpoints.

METHODS

The records of all children (1,208) seen at a large urban emergency department (ED) with a chief complaint of abdominal pain were immediately reviewed retrospectively (24 to 72 hours after the encounter). Attempts were made to contact all the patients' families to determine an accurate final diagnosis. A total of 1,008 (83%) families were contacted. Data were analyzed by calculation of the posttest probability, recursive partitioning, and binary logistic regression.

RESULTS

In all groups the most common diagnosis was abdominal pain (ICD-9 Code 789). After this, however, the order of the most common final diagnoses for abdominal pain varied significantly. The entire group had a pretest probability of appendicitis of 0.06. This varied with age and sex from 0.02 in boys 2 to 5 years old to 0.16 in boys older than 12 years. In boys age 5 to 12, recursive partitioning and binary logistic regression agreed on guarding and anorexia as important variables. Guarding and tenderness were important in girls age 5 to 12. In boys age greater than 12, both agreed on guarding and anorexia. Using sensitivities and specificities from the literature, computed tomography improved the posttest probability for the group from.06 to.33; ultrasound improved it from.06 to.48; and barium enema improved it from.06 to.58.

CONCLUSIONS

Knowing the pretest probabilities in a specific population allows the physician to evaluate the likely diagnoses first. Other quantitative methods can help judge how much importance a certain criterion should have in the decision making and how much a particular test is likely to influence the probability of a correct diagnosis. It now should be possible to make these sophisticated quantitative methods readily available to clinicians via the computer.

The cellular intake kinetics and acute biological effects of various oxovanadium species: a comparative study

It is well known that different oxovanadium species can have significantly different biopotencies, including hypoglycemic actions. The basis for the observed differences in the biopotency of different oxovanadium species: vanadate, vanadyl, 1,10-phenanthroline bisperoxovanadate (phen-bpv), 4-methyl 1,10-phenanthroline bisperoxovanadate (mpv) and 4,7-dimethyl 1,10-phenanthroline bisperoxovanadate (dpv), was examined in this study. The cellular uptake kinetics for these oxovanadium species was measured. Phen-bpv and vandyl had the most rapid cellular uptake. Mpv, dpv and vanadate exhibited a much slower uptake kinetics. Stimulation of protein tyrosine phosphorylation (PTP), both the time dependency and the dose dependency, was used as an index for biopotency. Although phen-bpv and vanadyl had the same cellular uptake kinetics, they differed markedly in their ability to stimulate PTP. Structurally similar oxovanadium species, phen-bpv, mpv and dpv demonstrated different uptake kinetics and effects on stimulating PTP. Bioavailability, both in term of cellular uptake and migration or transport to the active site, has been shown to be an important factor, in addition to intrinsic activity of the oxovanadium species, in determining the overall biopotency. Finally, this study demonstrates that variation of the chelating ligand has a profound effect on the physiochemical properties and biological effects of the oxovanadium species.

Mercury determination in nursing home patients with Alzheimer's disease

Trace-element neurotoxicity contributing to the development of Alzheimer's disease (AD) may be an important etiologic factor for this disorder. This clinical study was conducted to determine the urine concentrations of mercury (Hg) from patients with AD disorders. Within the confines of a nursing home, all subjects were exposed to the same environment and a diet that excluded seafood. The results of this study do not indicate that subjects with AD have a greater body burden of Hg, according to urinary excretion. This can be further evidence that Hg from amalgam restorations or diet is not related to etiology and pathogenesis of AD.

Determination of blood mercury concentrations in Alzheimer's patients

Trace element neurotoxicity can be an etiologic factor for Alzheimer's disease. This cross sectional clinical study determined blood mercury in patients with diagnosed Alzheimer's disease as compared to control subjects without known central nervous system and renal disorders. Unique within the confines of a nursing home, all subjects were exposed to the same environment and consumed a diet without fish and seafood for a period of three months prior to the study. The results of this study show that blood mercury concentrations detected in subjects with Alzheimer's disease were not statistically different than that of control subjects. Ratios of blood mercury to blood selenium were also determined and no statistical difference was found between these two groups.

Oral histoplasmosis in a patient infected with HIV. A case report

Histoplasmosis is a frequent complication of HIV infection and is usually the result of reactivation. In the immunocompromised host, histoplasmosis may cause a chronic pulmonary infection or disseminated disease. In the setting of disseminated disease, oral lesions are present in 30% to 50% of patients and may occur in almost every part of the oral mucosa. The most common sites are the tongue, palate, and buccal mucosa. In some cases, oral lesions appear to be the primary or only manifestation of disease. We have been able to find only five case reports in the literature of histoplasmosis in HIV infection with oral lesions. In two of the cases, histoplasmosis was apparently localized to the oral cavity, whereas two cases also had evidence of disseminated disease, the fifth was undetermined. We report one such case of apparently localized oral histoplasmosis in a patient with HIV infection.

Effects of olfactory bulbectomy on social behavior of male guinea pigs (Cavia procellus)

Effects of olfactory bulbectomy on social behavior in male guinea pigs were studied. Both brief-exposure pairing techniques and a group-living observation period were employed to test for disruption. During short-term testing sessions bulbectomized animals courted females less than but mounted them as frequently as control subjects. While the groups did not differ in fighting behavior during short-term tests, control subjects scent-marked more frequently. Subsequently, animals were observed as same-treatment pairs living continuously with females, and behavior was sampled over a 3-wk period. Under these conditions bulbectomized males, unlike controls, failed to form dominance orders, exhibited virtually no intermale aggressive activity, had markedly depressed sexual activity, and scent-marked rarely. It is concluded that olfactory bulbectomy profoundly alters the behavior of male domestic guinea pigs and that hose alterations are most evident when experimental subjects are observed in a species-typical group-living environment.

Genetic Control by the H-2 Gene Complex of the Alloantibody Response to an H-2 Antigen

The genetic control of the immune response against an H-2 antigenic specificity was investigated. With the aid of five congenic mouse strains, B10.A, C57BL/10, B10.A(2R), B10.A(3R) and B10.A(5R), it was demonstrated that a genetic factor, possibly Ir-1, associated with the H-2(K) subdivision of the H-2b chromosome, exerts a regulatory effect on a recipient's capacity to respond to H-2.2, an antigenic specificity determined by the H-2(D) subdivision of the H-2 gene complex.