Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes.

BackgroundCharacterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic.ResultsWe find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method.ConclusionUse of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples

Computational Simulations for Aortic Coarctation: Representative Results From a Sampling of Patients

Treatments for coarctation of the aorta (CoA) can alleviate blood pressure (BP) gradients(D), but long-term morbidity still exists that can be explained by altered indices of hemodynamics and biomechanics. We introduce a technique to increase our understanding of these indices for CoA under resting and nonresting conditions, quantify their contribution to morbidity, and evaluate treatment options. Patient-specific computational fluid dynamics (CFD) models were created from imaging and BP data for one normal and four CoA patients (moderate native CoA: D12 mmHg, severe native CoA: D25 mmHg and postoperative end-to-end and end-to-side patients: D0 mmHg). Simulations incorporated vessel deformation, downstream vascular resistance and compliance. Indices including cyclic strain, time-averaged wall shear stress (TAWSS), and oscillatory shear index (OSI) were quantified. Simulations replicated resting BP and blood flow data. BP during simulated exercise for the normal patient matched reported values. Greatest exercise-induced increases in systolic BP and mean and peak DBP occurred for the moderate native CoA patient (SBP: 115 to 154 mmHg; mean and peak DBP: 31 and 73 mmHg). Cyclic strain was elevated proximal to the coarctation for native CoA patients, but reduced throughout the aorta after treatment. A greater percentage of vessels was exposed to subnormal TAWSS or elevated OSI for CoA patients. Local patterns of these indices reported to correlate with atherosclerosis in normal patients were accentuated by CoA. These results apply CFD to a range of CoA patients for the first time and provide the foundation for future progress in this area

Cognition and education benefits of increased hemoglobin and blood oxygenation in children with sickle cell disease

BACKGROUND: Among individuals with sickle cell disease (SCD), decreased hemoglobin is associated with lower oxygen saturation (SpO2) and increased risk of stroke, both of which are associated with lower intelligence quotient (IQ) scores. Thus, increasing hemoglobin and SpO2 in individuals with SCD may increase IQ and educational attainment. METHODS: A cohort simulation model was built to determine academic performance and educational attainment based on cognitive function (measured by IQ) of a pediatric SCD cohort randomly assigned to treatment and control groups. The model contained two key stages: childhood (\u3c10 years) and adolescence (≥10 years). In stage 1, increased hemoglobin and increased SpO2 (assigned to the treatment group) were determinants of higher IQ, prevention of IQ deterioration over time. Increased hemoglobin was also a determinant of decreased stroke risk. In stage 2, improvement in adolescent IQ as a result of treatment was a determinant of academic performance. RESULTS: In a simulated cohort of 2000 children and adolescents with SCD (52.5% female, 50% treated), stroke incidence was predicted to be 44.4% lower among the treated group than the untreated group (4.5% versus 8.1%, respectively). The average IQ among the treated group was estimated to be 91.1 compared with 82.9 in the untreated group (a 9.9% difference; P\u3c0.001). Finally, high school (≥12 years of education) completion rates were estimated to be 64.7% higher among the treated group: 76.1% of the treated group was projected to complete high school compared with 46.2% of the untreated group. CONCLUSIONS: Our model predicts that an average improvement in hemoglobin of 1.1 g/dL (11 g/L) among individuals with SCD may be associated with improved neurocognition and educational outcomes. These improvements may also generate benefits not captured by our model, including improved quality of life, employment, and income

Lipopolysaccharide-enhanced, Toll-like Receptor 4–dependent T Helper Cell Type 2 Responses to Inhaled Antigen

Allergic asthma is an inflammatory lung disease initiated and directed by T helper cells type 2 (Th2). The mechanism involved in generation of Th2 responses to inert inhaled antigens, however, is unknown. Epidemiological evidence suggests that exposure to lipopolysaccharide (LPS) or other microbial products can influence the development and severity of asthma. However, the mechanism by which LPS influences asthma pathogenesis remains undefined. Although it is known that signaling through Toll-like receptors (TLR) is required for adaptive T helper cell type 1 (Th1) responses, it is unclear if TLRs are needed for Th2 priming. Here, we report that low level inhaled LPS signaling through TLR4 is necessary to induce Th2 responses to inhaled antigens in a mouse model of allergic sensitization. The mechanism by which LPS signaling results in Th2 sensitization involves the activation of antigen-containing dendritic cells. In contrast to low levels, inhalation of high levels of LPS with antigen results in Th1 responses. These studies suggest that the level of LPS exposure can determine the type of inflammatory response generated and provide a potential mechanistic explanation of epidemiological data on endotoxin exposure and asthma prevalence

On Coupling a Lumped Parameter Heart Model and a Three-Dimensional Finite Element Aorta Model

Aortic flow and pressure result from the interactions between the heart and arterial system. In this work, we considered these interactions by utilizing a lumped parameter heart model as an inflow boundary condition for three-dimensional finite element simulations of aortic blood flow and vessel wall dynamics. The ventricular pressure–volume behavior of the lumped parameter heart model is approximated using a time varying elastance function scaled from a normalized elastance function. When the aortic valve is open, the coupled multidomain method is used to strongly couple the lumped parameter heart model and three-dimensional arterial models and compute ventricular volume, ventricular pressure, aortic flow, and aortic pressure. The shape of the velocity profiles of the inlet boundary and the outlet boundaries that experience retrograde flow are constrained to achieve a robust algorithm. When the aortic valve is closed, the inflow boundary condition is switched to a zero velocity Dirichlet condition. With this method, we obtain physiologically realistic aortic flow and pressure waveforms. We demonstrate this method in a patient-specific model of a normal human thoracic aorta under rest and exercise conditions and an aortic coarctation model under pre- and post-interventions

Therapeutic target-site variability in α1-antitrypsin characterized at high resolution

The intrinsic propensity of [alpha]1-antitrypsin to undergo conformational transitions from its metastable native state to hyperstable forms provides a motive force for its antiprotease function. However, aberrant conformational change can also occur via an intermolecular linkage that results in polymerization. This has both loss-of-function and gain-of-function effects that lead to deficiency of the protein in human circulation, emphysema and hepatic cirrhosis. One of the most promising therapeutic strategies being developed to treat this disease targets small molecules to an allosteric site in the [alpha]1-antitrypsin molecule. Partial filling of this site impedes polymerization without abolishing function. Drug development can be improved by optimizing data on the structure and dynamics of this site. A new 1.8 Å resolution structure of [alpha]1-antitrypsin demonstrates structural variability within this site, with associated fluctuations in its upper and lower entrance grooves and ligand-binding characteristics around the innermost stable enclosed hydrophobic recess. These data will allow a broader selection of chemotypes and derivatives to be tested in silico and in vitro when screening and developing compounds to modulate conformational change to block the pathological mechanism while preserving function

Where Are You From? A Validation of the Foreigner Objectification Scale and the Psychological Correlates of Foreigner Objectification Among Asian Americans and Latinos

Many ethnic minorities in the United States consider themselves to be just as American as their European American counterparts. However, there is a persistent cultural stereotype of ethnic minorities as foreigners (i.e., the perpetual foreigner stereotype) that may be expressed during interpersonal interactions (i.e., foreigner objectification). The goal of the present study was to validate the Foreigner Objectification Scale, a brief self-report measure of perceived foreigner objectification, and to examine the psychological correlates of perceived foreigner objectification. Results indicated that the Foreigner Objectification Scale is structurally (i.e., factor structure) and metrically (i.e., factor loadings) invariant across foreign-born and U.S.-born Asian Americans and Latinos. Scalar (i.e., latent item intercepts) invariance was demonstrated for the two foreign-born groups and the two U.S.-born groups, but not across foreign-born and U.S.-born individuals. Multiple-group structural equation models indicated that, among U.S.-born individuals, perceived foreigner objectification was associated with less life satisfaction and more depressive symptoms, and was indirectly associated with lower self-esteem via identity denial, operationalized as the perception that one is not viewed by others as American. Among foreign-born individuals, perceived foreigner objectification was not significantly associated directly with self-esteem, life satisfaction, or depressive symptoms. However, perceived foreigner objectification was positively associated with identity denial, and identity denial was negatively associated with life satisfaction. This study illustrates the relevance of perceived foreigner objectification to the psychological well-being of U.S.-born Asian Americans and Latinos

Low-dimensional perovskite nanoplatelet synthesis using in situ photophysical monitoring to establish controlled growth.

Perovskite nanoparticles have attracted the attention of research groups around the world for their impressive photophysical properties, facile synthesis and versatile surface chemistry. Here, we report a synthetic route that takes advantage of a suite of soluble precursors to generate CsPbBr3 perovskite nanoplatelets with fine control over size, thickness and optical properties. We demonstrate near unit cell precision, creating well characterized materials with sharp, narrow emission lines at 430, 460 and 490 nm corresponding to nanoplatelets that are 2, 4, and 6 unit cells thick, respectively. Nanoplatelets were characterized with optical spectroscopy, atomic force microscopy, scanning electron microscopy and transmission electron microscopy to explicitly correlate growth conditions, thickness and resulting photophysical properties. Detailed in situ photoluminescence spectroscopic studies were carried out to understand and optimize particle growth by correlating light emission with nanoplatelet growth across a range of synthetic conditions. It was found that nanoplatelet thickness and emission wavelength increase as the ratio of oleic acid to oleyl amine or the reaction temperature is increased. Using this information, we control the lateral size, width and corresponding emission wavelength of the desired nanoplatelets by modulating the temperature and ratios of the ligand

Electromagnetic Enhancement in Lossy Optical Transition Metamaterials

We investigate the effect of anomalous field enhancement in metamaterials where the effective refractive index gradually changes from positive to negative values, i.e. transition metamaterials. We demonstrate that considerable field enhancement can be achieved in lossy optical transition metamaterials that have electromagnetic material properties obtained from experimental data. The field enhancement factor is found to be polarization-dependent and largely determined by the material parameters and the width of the transition layer

Aortoiliac hemodynamic and morphologic adaptation to chronic spinal cord injury

BackgroundReduced lower limb blood flow and resistive hemodynamic conditions potentially promote aortic inflammation and aneurysmal degeneration. We used abdominal ultrasonography, magnetic resonance imaging, and computational flow modeling to determine the relationship between reduced infrarenal aortic blood flow in chronic spinal cord injury (SCI) subjects and risk for abdominal aortic aneurysm (AAA) disease.MethodsAortic diameter in consecutive SCI subjects (n = 123) was determined via transabdominal ultrasonography. Aortic anatomic and physiologic data were acquired via magnetic resonance angiography (MRA; n = 5) and cine phase-contrast magnetic resonance flow imaging (n = 4) from SCI subjects whose aortic diameter was less than 3.0 cm by ultrasonography. Computational flow models were constructed from magnetic resonance data sets. Results were compared with those obtained from ambulatory control subjects (ultrasonography, n = 129; MRA/phase-contrast magnetic resonance flow imaging, n = 6) who were recruited at random from a larger pool of risk factor–matched individuals without known AAA disease.ResultsAge, sex distribution, and smoking histories were comparable between the SCI and control groups. In the SCI group, time since injury averaged 26 ± 13 years (mean ± SD). Aortic diameter was larger (P < .01), and the prevalence of large (≥2.5 cm; P < .01) or aneurysmal (≥3.0 cm; P < .05) aortas was greater in SCI subjects. Paradoxically, common iliac artery diameters were reduced in SCI subjects (<1.0 cm; 48% SCI vs 26% control; P < .0001). Focal preaneurysmal enlargement was noted in four of five SCI subjects by MRA. Flow modeling revealed normal flow volume, biphasic and reduced oscillatory flow, slower pressure decay, and reduced wall shear stress in the SCI infrarenal aorta.ConclusionsCharacteristic aortoiliac hemodynamic and morphologic adaptations occur in response to chronic SCI. Slower aortic pressure decay and reduced wall shear stress after SCI may contribute to mural degeneration, enlargement, and an increased prevalence of AAA disease