CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features

CTCF DNA binding sites are classified into distinct functional classes, with distinct biological properties, shedding light on the differing functional roles of CTCF binding

Declarative Representations of Multiagent Systems

This paper explores the specification and semantics of multiagent problem-solving systems, focusing on the representations that agents have of each other. It provides a declarative representation for such systems. Several procedural solutions to a well-known test-bed problem are considered, and the requirements they impose on different agents are identified. A study of these requirements yields a representational scheme based on temporal logic for specifying the acting, perceiving, communicating, and reasoning abilities of computational agents. A formal semantics is provided for this scheme. The resulting representation is highly declarative, and useful for describing systems of agents solving problems reactively

A Knowledge-Based Expert System for Managing Underground Coal Mines in the U.S.

The Mine Management Support System which is being developed as a knowledge-based expert system for better management of underground coal mines, is presented. Concentrating on capturing the complex body of knowledge needed to enhance efficient management of a mine, it will encompass information and preferred rules on work scheduling, work practices, regulations impinging on the accomplishment of work, responses to operating problems, and the labor-management work agreement. Different components of the mine system, modeled using an object-oriented layering technique, are displayed graphically to aid in coordinating work plans and to present locations of equipment, supplies, and proposed subsystem components

High Resolution Helium Ion Scanning Microscopy of the Rat Kidney

Helium ion scanning microscopy is a novel imaging technology with the potential to provide sub-nanometer resolution images of uncoated biological tissues. So far, however, it has been used mainly in materials science applications. Here, we took advantage of helium ion microscopy to explore the epithelium of the rat kidney with unsurpassed image quality and detail. In addition, we evaluated different tissue preparation methods for their ability to preserve tissue architecture. We found that high contrast, high resolution imaging of the renal tubule surface is possible with a relatively simple processing procedure that consists of transcardial perfusion with aldehyde fixatives, vibratome tissue sectioning, tissue dehydration with graded methanol solutions and careful critical point drying. Coupled with the helium ion system, fine details such as membrane texture and membranous nanoprojections on the glomerular podocytes were visualized, and pores within the filtration slit diaphragm could be seen in much greater detail than in previous scanning EM studies. In the collecting duct, the extensive and striking apical microplicae of the intercalated cells were imaged without the shrunken or distorted appearance that is typical with conventional sample processing and scanning electron microscopy. Membrane depressions visible on principal cells suggest possible endo- or exocytotic events, and central cilia on these cells were imaged with remarkable preservation and clarity. We also demonstrate the use of colloidal gold probes for highlighting specific cell-surface proteins and find that 15 nm gold labels are practical and easily distinguishable, indicating that external labels of various sizes can be used to detect multiple targets in the same tissue. We conclude that this technology represents a technical breakthrough in imaging the topographical ultrastructure of animal tissues. Its use in future studies should allow the study of fine cellular details and provide significant advances in our understanding of cell surface structures and membrane organization

Myeloid cell interferon responses correlate with clearance of SARS-CoV-2

Emergence of mutant SARS-CoV-2 strains associated with an increased risk of COVID-19-related death necessitates better understanding of the early viral dynamics, host responses and immunopathology. Single cell RNAseq (scRNAseq) allows for the study of individual cells, uncovering heterogeneous and variable responses to environment, infection and inflammation. While studies have reported immune profiling using scRNAseq in terminal human COVID-19 patients, performing longitudinal immune cell dynamics in humans is challenging. Macaques are a suitable model of SARS-CoV-2 infection. Our longitudinal scRNAseq of bronchoalveolar lavage (BAL) cell suspensions from young rhesus macaques infected with SARS-CoV-2 (n = 6) demonstrates dynamic changes in transcriptional landscape 3 days post- SARS-CoV-2-infection (3dpi; peak viremia), relative to 14-17dpi (recovery phase) and pre-infection (baseline) showing accumulation of distinct populations of both macrophages and T-lymphocytes expressing strong interferon-driven inflammatory gene signature at 3dpi. Type I interferon response is induced in the plasmacytoid dendritic cells with appearance of a distinct HLAD

The role of urgent care centers in headache management: a quality improvement project

BACKGROUND: Patients with headache often seek urgent medical care to treat pain and associated symptoms that do not respond to therapeutic options at home. Urgent Cares (UCs) may be suitable for the evaluation and treatment of such patients but there is little data on how headache is evaluated in UC settings and what types of treatments are available. We conducted a study to evaluate the types of care available for patients with headache presenting to UCs. DESIGN: Cross-Sectional. METHODS: Headache specialists across the United States contacted UCs to collect data on a questionnaire. Questions asked about UC staffing (e.g. number and backgrounds of staff, hours of operation), average length of UC visits for headache, treatments and tests available for patients presenting with headache, and disposition including to the ED. RESULTS: Data from 10 UC programs comprised of 61 individual UC sites revealed: The vast majority (8/10; 80%) had diagnostic testing onsite for headache evaluation. A small majority (6/10; 60%) had the American Headache Society recommended intravenous medications for acute migraine available. Half (5/10) had a headache protocol in place. The majority (6/10; 60%) had no follow up policy after UC discharge. CONCLUSIONS: UCs have the potential to provide expedited care for patients presenting for evaluation and treatment of headache. However, considerable variability exists amongst UCs in their abilities to manage headaches. This study reveals many opportunities for future research including the development of protocols and professional partnerships to help guide the evaluation, triage, and treatment of patients with headache in UC settings

Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families

Gene duplication is integral to evolution, providing novel opportunities for organisms to diversify in function. One fundamental pathway of functional diversification among initially redundant gene copies, or paralogs, is via alterations in their expression patterns. Although the mechanisms underlying expression divergence are not completely understood, transcription factor binding sites and nucleosome occupancy are known to play a significant role in the process. Previous attempts to detect genomic variations mediating expression divergence in orthologs have had limited success for two primary reasons. First, it is inherently challenging to compare expressions among orthologs due to variable trans-acting effects and second, previous studies have quantified expression divergence in terms of an overall similarity of expression profiles across multiple samples, thereby obscuring condition-specific expression changes. Moreover, the inherently inter-correlated expressions among homologs present statistical challenges, not adequately addressed in many previous studies. Using rigorous statistical tests, here we characterize the relationship between cis element divergence and condition-specific expression divergence among paralogous genes in Saccharomyces cerevisiae. In particular, among all combinations of gene family and TFs analyzed, we found a significant correlation between TF binding and the condition-specific expression patterns in over 20% of the cases. In addition, incorporating nucleosome occupancy reveals several additional correlations. For instance, our results suggest that GAL4 binding plays a major role in the expression divergence of the genes in the sugar transporter family. Our work presents a novel means of investigating the cis regulatory changes potentially mediating expression divergence in paralogous gene families under specific conditions

TREMOR—a tool for retrieving transcriptional modules by incorporating motif covariance

A transcriptional module (TM) is a collection of transcription factors (TF) that as a group, co-regulate multiple, functionally related genes. The task of identifying TMs poses an important biological challenge. Since TFs belong to evolutionarily and structurally related families, TF family members often bind to similar DNA motifs and can confound sequence-based approaches to TM identification. A previous approach to TM detection addresses this issue by pre-selecting a single representative from each TF family. One problem with this approach is that closely related transcription factors can still target sufficiently distinct genes in a biologically meaningful way, and thus, pre-selecting a single family representative may in principle miss certain TMs. Here we report a method—TREMOR (Transcriptional Regulatory Module Retriever). This method uses the Mahalanobis distance to assess the validity of a TM and automatically incorporates the inter-TF binding similarity without resorting to pre-selecting family representatives. The application of TREMOR on human muscle-specific, liver-specific and cell-cycle-related genes reveals TFs and TMs that were validated from literature and also reveals additional related genes

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin