Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.

Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific subgroups in supporting fibrogenesis has not been investigated in vivo. Here, we used single-cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of macrophages in bleomycin-induced lung fibrosis in mice. A novel computational framework for the annotation of scRNA-seq by reference to bulk transcriptomes (SingleR) enabled the subclustering of macrophages and revealed a disease-associated subgroup with a transitional gene expression profile intermediate between monocyte-derived and alveolar macrophages. These CX3CR1+SiglecF+ transitional macrophages localized to the fibrotic niche and had a profibrotic effect in vivo. Human orthologs of genes expressed by the transitional macrophages were upregulated in samples from patients with idiopathic pulmonary fibrosis. Thus, we have identified a pathological subgroup of transitional macrophages that are required for the fibrotic response to injury

An interactive geometry modeling and parametric design platform for isogeometric analysis

In this paper an interactive parametric design-through-analysis platform is proposed to help design engineers and analysts make more effective use of Isogeometric Analysis (IGA) to improve their product design and performance. We develop several Rhinoceros (Rhino) plug-ins to take input design parameters through a user-friendly interface, generate appropriate surface and/or volumetric models, perform mechanical analysis, and visualize the solution fields, all within the same Computer-Aided Design (CAD) program. As part of this effort we propose and implement graphical generative algorithms for IGA model creation and visualization based on Grasshopper, a visual programming interface to Rhino. The developed platform is demonstrated on two structural mechanics examples—an actual wind turbine blade and a model of an integrally bladed rotor (IBR). In the latter example we demonstrate how the Rhino functionality may be utilized to create conforming volumetric models for IGA

Hydrogen is neuroprotective against surgically induced brain injury

<p>Abstract</p> <p>Background</p> <p>Neurosurgical operations cause unavoidable damage to healthy brain tissues. Direct surgical injury as well as surgically induced oxidative stress contributes to the subsequent formation of brain edema. Therefore, we tested the neuroprotective effects of hydrogen (H₂) in an established surgical brain injury (SBI) model in rats.</p> <p>Materials and methods</p> <p>Adult male Sprague - Dawley rats (weight 300-350g) were divided into three groups to serve as sham operated, SBI without treatment, and SBI treated with H₂(2.9%). Brain water content, myeloperoxidase (MPO) assay, lipid peroxidation (LPO), and neurological function were measured at 24 hrs after SBI.</p> <p>Results</p> <p>SBI resulted in localized brain edema (p = < 0.001). Hydrogen (2.9%) administered concurrently with surgery significantly decreased the formation of cerebral edema (p = 0.028) and improved neurobehavioral score (p = 0.022). However, hydrogen treatment failed to reduce oxidative stress (LPO assay) or inflammation (MPO assay) in brain tissues.</p> <p>Conclusions</p> <p>Hydrogen appears to be promising as an effective, yet inexpensive way to reduce cerebral edema caused by surgical procedures. Hydrogen has the potential to improve clinical outcome, decrease hospital stay, and reduce overall cost to patients and the health care system.</p

Direct immersogeometric fluid flow analysis using B-rep CAD models

We present a new method for immersogeometric fluid flow analysis that directly uses the CAD boundary representation (B-rep) of a complex object and immerses it into a locally refined, non-boundary-fitted discretization of the fluid domain. The motivating applications include analyzing the flow over complex geometries, such as moving vehicles, where the detailed geometric features usually require time-consuming, labor-intensive geometry cleanup or mesh manipulation for generating the surrounding boundary-fitted fluid mesh. The proposed method avoids the challenges associated with such procedures. A new method to perform point membership classification of the background mesh quadrature points is also proposed. To faithfully capture the geometry in intersected elements, we implement an adaptive quadrature rule based on the recursive splitting of elements. Dirichlet boundary conditions in intersected elements are enforced weakly in the sense of Nitsche\u27s method. To assess the accuracy of the proposed method, we perform computations of the benchmark problem of flow over a sphere represented using B-rep. Quantities of interest such as drag coefficient are in good agreement with reference values reported in the literature. The results show that the density and distribution of the surface quadrature points are crucial for the weak enforcement of Dirichlet boundary conditions and for obtaining accurate flow solutions. Also, with sufficient levels of surface quadrature element refinement, the quadrature error near the trim curves becomes insignificant. Finally, we demonstrate the effectiveness of our immersogeometric method for high-fidelity industrial scale simulations by performing an aerodynamic analysis of an agricultural tractor directly represented using B-rep

Exploring reasons for state-level variation in incidence of dialysis-requiring acute kidney injury (AKI-D) in the United States

Background: There is considerable state-level variation in the incidence of dialysis-requiring acute kidney injury (AKI-D). However, little is known about reasons for this geographic variation. Methods: National cross-sectional state-level ecological study based on State Inpatient Databases (SID) and the Behavioral Risk Factor Surveillance System (BRFSS) in 2011. We analyzed 18 states and six chronic health conditions (diabetes mellitus [diabetes], hypertension, chronic kidney disease [CKD], arteriosclerotic heart disease [ASHD], cancer (excluding skin cancer), and chronic obstructive pulmonary disease [COPD]). Associations between each of the chronic health conditions and AKI-D incidence was assessed using Pearson correlation and multiple regression adjusting for mean age, the proportion of males, and the proportion of non-Hispanic whites in each state. Results: The state-level AKI-D incidence ranged from 190 to 1139 per million population. State-level differences in rates of hospitalization with chronic health conditions (mostly \u3c 3-fold difference in range) were larger than the state-level differences in prevalence for each chronic health condition (mostly \u3c 2.5-fold difference in range). A significant correlation was shown between AKI-D incidence and prevalence of diabetes, ASHD, and COPD, as well as between AKI-D incidence and rate of hospitalization with hypertension. In regression models, after adjusting for age, sex, and race, AKI-D incidence was associated with prevalence of and rates of hospitalization with five chronic health conditions - diabetes, hypertension, CKD, ASHD and COPD - and rates of hospitalization with cancer. Conclusions: Results from this ecological analysis suggest that state-level variation in AKI-D incidence may be influenced by state-level variations in prevalence of and rates of hospitalization with several chronic health conditions. For most of the explored chronic conditions, AKI-D correlated stronger with rates of hospitalizations with the health conditions rather than with their prevalences, suggesting that better disease management strategies that prevent hospitalizations may translate into lower incidence of AKI-D

Inherited susceptibility to bleomycin-induced chromatid breaks in cultured peripheral blood lymphocytes

Background: Susceptibility to bleomycin-induced chromatid breaks in cultured peripheral blood lymphocytes may reflect the way a person deals with carcinogenic challenges. This susceptibility (also referred to as mutagen sensitivity) has been found to be increased in patients with environmentally related cancers, including cancers of the head and neck, lung, and colon, and, in combination with carcinogenic exposure, this susceptibility can greatly influence cancer risk. The purpose of this study was to assess the heritability of mutagen sensitivity. Methods: Heritability was determined by use of a maximum likelihood method that employed the FISHER package of pedigree analysis. Bleomycin-induced breaks per cell values for 135 healthy volunteers without cancer were determined. These individuals were from 53 different pedigrees and included 25 monozygotic twin pairs (n = 50), 14 pairs of dizygotes (twin pairs and siblings, n = 28), and 14 families selected on the basis of a first-degree relative who was successfully treated for head and neck cancer and who had no sign of recurrence for at least 1 year. All data were analyzed simultaneously, and different models of familial resemblance were fitted to the data. All P values are two-sided. Results: Our results showed no evidence for the influence of a shared family environment on bleomycin-induced chromatid breaks. Genetic influences, however, were statistically significant (P = .036) and accounted for 75% of the total variance. Conclusions: The high heritability estimate of the susceptibility to bleomycin-induced chromatid breaks indicates a clear genetic basis. The findings of this study support the notion that a common genetic susceptibility to DNA damage - and thereby a susceptibility to cancer - may exist in the general population

Expression Profiling of MAP Kinase–Mediated Meiotic Progression in Caenorhabditis elegans

The LET-60 (Ras)/LIN-45 (Raf)/MPK-1 (MAP kinase) signaling pathway plays a key role in the development of multiple tissues in Caenorhabditis elegans. For the most part, the identities of the downstream genes that act as the ultimate effectors of MPK-1 signaling have remained elusive. A unique allele of mpk-1, ga111, displays a reversible, temperature-sensitive, tissue-specific defect in progression through meiotic prophase I. We performed gene expression profiling on mpk-1(ga111) animals to identify candidate downstream effectors of MPK-1 signaling in the germ line. This analysis delineated a cohort of genes whose expression requires MPK-1 signaling in germ cells in the pachytene stage of meiosis I. RNA in situ hybridization analysis shows that these genes are expressed in the germ line in an MPK-1-dependent manner and have a spatial expression pattern consistent with the location of activated MPK-1. We found that one MPK-1 signaling-responsive gene encoding a C(2)H(2) zinc finger protein plays a role in meiotic chromosome segregation downstream of MPK-1. Additionally, discovery of genes responsive to MPK-1 signaling permitted us to order MPK-1 signaling relative to several events occurring in pachytene, including EFL-1/DPL-1 gene regulation and X chromosome reactivation. This study highlights the utility of applying global gene expression methods to investigate genes downstream of commonly used signaling pathways in vivo

Coatomer and dimeric ADP ribosylation factor 1 promote distinct steps in membrane scission

During membrane budding, coatomer drives initial curvature of the bud, whereas dimeric Arf1 is necessary for membrane scission