Baryons Still Trace Dark Matter: Probing CMB Lensing Maps For Hidden Isocurvature

Compensated isocurvature perturbations (CIPs) are primordial fluctuations that balance baryon and dark-matter isocurvature to leave the total matter density unperturbed. The effects of CIPs on the cosmic microwave background (CMB) anisotropies are similar to those produced by weak lensing of the CMB: smoothing of the power spectrum and generation of non-Gaussian features. Here, an entirely new CIP contribution to the standard estimator for the lensing-potential power spectrum is derived. Planck measurements of the temperature and polarization power spectrum, as well as estimates of CMB lensing, are used to place limits on the variance of the CIP fluctuations on CMB scales, Δ2rms(RCMB). The resulting constraint of Δ2rms(RCMB)\u3c4.3×10−3 at 95% confidence level (CL) using this new technique improves on past work by a factor of ∼3. We find that for Planck data our constraints almost reach the sensitivity of the optimal CIP estimator. The method presented here is currently the most sensitive probe of the amplitude of a scale-invariant CIP power spectrum, ACIP, placing an upper limit of ACIP\u3c0.017 at 95% CL. Future measurements of the large-scale CMB lensing-potential power spectrum could probe CIP amplitudes as low as Δ2rms(RCMB)=8×10−5 at 95% CL (corresponding to ACIP=3.2×10−4)

Isostaticity of Constraints in Jammed Systems of Soft Frictionless Platonic Solids

The average number of constraints per particle $$ in mechanically stable systems of Platonic solids (except cubes) approaches the isostatic limit at the jamming point ($\rightarrow 12$), though average number of contacts are hypostatic. By introducing angular alignment metrics to classify the degree of constraint imposed by each contact, constraints are shown to arise as a direct result of local orientational order reflected in edge-face and face-face alignment angle distributions. With approximately one face-face contact per particle at jamming chain-like face-face clusters with finite extent form in these systems.Comment: 4 pages, 3 figures, 4 tabl

The Development of a Human Well-Being Index for the United States

The US Environmental Protection Agency (EPA) has developed a human well-being index (HWBI) that assesses the over-all well-being of its population at the county level. The HWBI contains eight domains representing social, economic and environmental well-being. These domains include 25 indicators comprised of 80 metrics and 22 social, economic and environmental services. The application of the HWBI has been made for the nation as a whole at the county level and two alternative applications have been made to represent key populations within the overall US population—Native Americans and children. A number of advances have been made to estimate the values of metrics for counties where no data is available and one such estimator—MERLIN—is discussed. Finally, efforts to make the index into an interactive web site are described

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

Abstract Background Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls. Results With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC) elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample. Conclusion Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, Decon2LS is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs. Decon2LS source code, installer, and tutorials may be downloaded free of charge at http://http:/ncrr.pnl.gov/software/

Comparative genomics and phylogenomic investigation of the class Geoglossomycetes provide insights into ecological specialization and the systematics of Pezizomycotina

Despite their global presence and ubiquity, members of the class Geoglossomycetes (Pezizomycotina, Ascomycota) are understudied systematically and ecologically. These fungi have long been presumed saprobic due to their occurrence in or near leaf litter and soils. Additionally, they lack an apparent association with other organisms, reinforcing this perception. However, observations of sporocarps near ericaceous shrubs have given rise to an alternative hypothesis that members of Geoglossomycetes may form ericoid mycorrhizae or ectomycorrhizae. This claim, however, has yet to be confirmed via microscopy or amplicon-based studies examining root communities. As a result, our current understanding of their ecology is based on cursory observations. This study presents a comparative analysis of genomic signatures related to ecological niche to investigate the hypothesis of an ericoid mycorrhizal or ectomycorrhizal ecology in the class. We compared the carbohydrate-active enzyme (CAZyme) and secondary metabolite contents of six newly sequenced Geoglossomycetes genomes with those of fungi representing specific ecologies across Pezizomycotina. Our analysis reveals CAZyme and secondary metabolite content patterns consistent with ectomycorrhizal (EcM) members of Pezizomycotina. Specifically, we found a reduction in CAZyme-encoding genes and secondary metabolite clusters that suggests a mutualistic ecology. Our work includes the broadest taxon sampling for a phylogenomic study of Pezizomycotina to date. It represents the first functional genomic and genome-scale phylogenetic study of the class Geoglossomycetes and improves the foundational knowledge of the ecology and evolution of these understudied fungi

Comparison of Direct Staffing Costs of Advanced Practice Providers and Residents in a High Acuity Area of a Community Emergency Department

Background: Resident physicians and advanced practice providers (APPs) both have roles in providing care within emergency departments (ED). While both bring unique skill sets and capabilities to the health care team, little is known about the comparative financial impact of APPs and residents in a community ED. The objective of this study was to compare direct staffing costs per relative value unit (RVU) generated of emergency medicine (EM) residents and APPs in a community ED setting. Methods: This was a retrospective, observational analysis of RVU productivity of resident physicians and APPs in the high acuity area of a community ED. Billing data was acquired to determine RVUs generated by both APPs and residents when supervised by an attending physician. Direct costs and hours worked were used to calculate RVUs/hour and direct costs/hour. Direct cost/RVU generated were calculated for the four specific groups of providers (PGY1, PGY2, PGY3, and APP). Results: During the study period, APPs generated 2.88 RVUs/hour. Residents generated 2.01, 3.00, and 3.49 RVUs/hour respectively from PGY1 to PGY3. When the RVU data was combined with scheduled hours and direct costs for both groups, APPs were found to cost $22.46 per RVU generated. The average cost of a resident throughout three years of residency training is approximately$12.38 per RVU generated. Conclusion: In a high acuity area of a community ED, EM residents generate more RVUs/hour than APPs after completion of their PGY1 year. Given the lower direct hourly cost of a resident compared with an APP, the direct cost of a resident to assist an attending to generate RVUs is less than that of their APP counterparts during all three years of training. This suggests that community hospitals should consider sponsoring EM residency positions over hiring APPs for use in the high acuity setting

Regulatory T Cell Induction and Retention in the Lungs Drives Suppression of Detrimental Type 2 Th Cells During Pulmonary Cryptococcal Infection

Lethal disease caused by the fungus, Cryptococcus neoformans, is a consequence of the combined failure to control pulmonary fungal replication and immunopathology caused by induced type-2 helper T (Th2) cell responses in animal models. In order to gain incites into immune regulatory networks, we examined the role of regulatory T (Treg) cells in suppression of Th2 cells, using a mouse model of experimental cryptococcosis. Upon pulmonary infection with Cryptococcus, Treg cells accumulated in the lung parenchyma independently of priming in the draining lymph node. Using peptide-MHCII molecules to identify Cryptococcus-specific Treg cells combined with genetic fate-mapping, we noted that a majority of the Treg cells found in the lungs were induced during the infection. Additionally, we found that Treg cells utilized the transcription factor, Interferon Regulatory Factor 4 (IRF4), to dampen harmful Th2 cell responses, as well as mediate chemokine retention of Treg cells in the lungs. Taken together, induction and IRF4-dependent localization of Treg cells in the lungs allow Treg cells to suppress the deleterious effects of Th2 cells during cryptococcal infection