Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.

The advent of high-resolution chromosome conformation capture assays (such as 5C, Hi-C and Pore-C) has allowed for unprecedented sequence-level investigations into the structure-function relationship of the genome. In order to comprehensively understand this relationship, computational tools are required that utilize data generated from these assays to predict 3D genome organization (the 3D genome reconstruction problem). Many computational tools have been developed that answer this need, but a comprehensive comparison of their underlying algorithmic approaches has not been conducted.

The influence of posture variation on electromyographic signals in females obtained during maximum voluntary isometric contractions: A shoulder example.

Surface electromyography (sEMG) is commonly used to estimate muscle demands in occupational tasks. To allow for comparisons, sEMG amplitude is normalized to muscle specific maximum voluntary contractions (MVCs) performed in a standardized set of postures. However, maximal sEMG amplitude in shoulder muscles is highly dependent on arm posture and therefore, normalizing task related muscular activity to standard MVCs may lead to misinterpretation of task specific muscular demands.

GrapHi-C: graph-based visualization of Hi-C datasets.

Objectives: Hi-C is a proximity-based ligation reaction used to detect regions of the genome that are close in 3D space (or "interacting"). Typically, results from Hi-C experiments (contact maps) are visualized as heatmaps or Circos plots. While informative, these visualizations do not directly represent genomic structure and folding, making the interpretation of the underlying 3D genomic organization obscured.

Rapamycin reduces fibroblast proliferation without causing quiescence and induces STAT5A/B-mediated cytokine production.

Rapamycin is a well-known inhibitor of the Target of Rapamycin (TOR) signaling cascade; however, the impact of this drug on global genome function and organization in normal primary cells is poorly understood. To explore this impact, we treated primary human foreskin fibroblasts with rapamycin and observed a decrease in cell proliferation without causing cell death. Upon rapamycin treatment chromosomes 18 and 10 were repositioned to a location similar to that of fibroblasts induced into quiescence by serum reduction.

Detection and molecular characterization of two FAD3 genes controlling linolenic acid content and development of allele-specific markers in yellow mustard (Sinapis alba).

Development of yellow mustard (Sinapis alba L.) with superior quality traits (low erucic and linolenic acid contents, and low glucosinolate content) can make this species as a potential oilseed crop. We have recently isolated three inbred lines Y1127, Y514 and Y1035 with low (3.

Clinical outcomes of a veterans affairs outpatient antimicrobial treatment program.

Objectives: The outpatient parenteral antibiotic therapy (OPAT) program of the Portland Veterans Affairs Medical Center (PVAMC), which has a self-administration model, is staffed by visiting nurses from a specialist infusion company. This study evaluates the clinical outcomes of these patients.

Methods: This study was a retrospective chart review of 262 patients at PVAMC who had received OPAT between 2007 and 2009.

Management of gram-positive coccal bacteremia and hemodialysis.

Gram-positive cocci are the most common cause of bloodstream infections in hemodialysis patients, with Staphylococcus aureus and coagulase-negative staphylococci causing most infections. Management of these infections often is complicated by limited vascular access options, as well as an increasing prevalence of drug-resistant bacteria in hemodialysis centers, including the emergence of strains of methicillin-resistant S aureus with vancomycin heteroresistance and increasing rates of vancomycin-resistant enterococci, both of which have limited antibiotic treatment options. This article describes the management of these infections based on the organism and its susceptibility profile, including catheter management, antibiotic lock therapies, and systemic antibiotic choices.