Development of a linearized unsteady Euler analysis for turbomachinery blade rows

A linearized unsteady aerodynamic analysis for axial-flow turbomachinery blading is described in this report. The linearization is based on the Euler equations of fluid motion and is motivated by the need for an efficient aerodynamic analysis that can be used in predicting the aeroelastic and aeroacoustic responses of blade rows. The field equations and surface conditions required for inviscid, nonlinear and linearized, unsteady aerodynamic analyses of three-dimensional flow through a single, blade row operating within a cylindrical duct, are derived. An existing numerical algorithm for determining time-accurate solutions of the nonlinear unsteady flow problem is described, and a numerical model, based upon this nonlinear flow solver, is formulated for the first-harmonic linear unsteady problem. The linearized aerodynamic and numerical models have been implemented into a first-harmonic unsteady flow code, called LINFLUX. At present this code applies only to two-dimensional flows, but an extension to three-dimensions is planned as future work. The three-dimensional aerodynamic and numerical formulations are described in this report. Numerical results for two-dimensional unsteady cascade flows, excited by prescribed blade motions and prescribed aerodynamic disturbances at inlet and exit, are also provided to illustrate the present capabilities of the LINFLUX analysis

Facile collection of two-dimensional electronic spectra using femtosecond pulse-shaping technology

This letter reports a straightforward means of collecting two-dimensional electronic (2D-E) spectra using optical tools common to many research groups involved in ultrafast spectroscopy and quantum control. In our method a femtosecond pulse shaper is used to generate a pair of phase stable collinear laser pulses which are then incident on a gas or liquid sample. The pulse pair is followed by an ultrashort probe pulse that is spectrally resolved. The delay between the collinear pulses is incremented using phase and amplitude shaping and a 2D-E spectrum is generated following Fourier transformation. The partially collinear beam geometry results in perfectly phased absorptive spectra without phase twist. Our approach is much simpler to implement than standard non-collinear beam geometries, which are challenging to phase stabilize and require complicated calibrations. Using pulse shaping, many new experiments are now also possible in both 2D-E spectroscopy and coherent control.open798

Differential var gene expression in the organs of patients dying of falciparum malaria

Sequestration of parasitized erythrocytes in the microcirculation of tissues is thought to be important in the pathogenesis of severe falciparum malaria. A major variant surface antigen, var/Plasmodium falciparum erythrocyte membrane protein 1, expressed on the surface of the infected erythrocyte, mediates cytoadherence to vascular endothelium. To address the question of tissue-specific accumulation of variant types, we used the unique resource generated by the clinicopathological study of fatal paediatric malaria in Blantyre, Malawi, to analyse var gene transcription in patients dying with falciparum malaria. Despite up to 102 different var genes being expressed by P. falciparum populations in a single host, only one to two of these genes were expressed at high levels in the brains and hearts of these patients. These major var types differed between organs. However, identical var types were expressed in the brains of multiple patients from a single malaria season. These results provide the first evidence of organ-specific accumulation of P. falciparum variant types and suggest that parasitized erythrocytes can exhibit preferential binding in the body, supporting the hypothesis of cytoadherence-linked pathogenesis

Mucin binding reduces colistin antimicrobial activity

Colistin has found increasing use in treating drug-resistant bacterial lung infections, but potential interactions with pulmonary biomolecules have not been investigated. We postulated that colistin, like aminoglycoside antibiotics, may bind to secretory mucin in sputum or epithelial mucin that lines airways, reducing free drug levels. To test this hypothesis, we measured binding of colistin and other antibiotics to porcine mucin, a family of densely glycosylated proteins used as a surrogate for human sputum and airway mucin. Antibiotics were incubated in dialysis tubing with or without mucin, and concentrations of unbound antibiotics able to penetrate the dialysis tubing were measured over time using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The percentage of antibiotic measured in the dialysate after 4 h in the presence of mucin, relative to the amount without mucin, was 15% for colistin, 16% for polymyxin B, 19% for tobramycin, 52% for ciprofloxacin, and 78% for daptomycin. Antibiotics with the strongest mucin binding had an overall polybasic positive charge, whereas those with comparatively little binding were less basic. When comparing MICs measured with or without added mucin, colistin and polymyxin B showed >100-fold increases in MICs for multiple Gram-negative bacteria. Preclinical evaluation of mucin binding should become a standard procedure when considering the potential pulmonary use of new or existing antibiotics, particularly those with a polybasic overall charge. In the airways, mucin binding may reduce the antibacterial efficacy of inhaled or intravenously administered colistin, and the presence of sub-MIC effective antibiotic concentrations could result in the development of antibiotic resistance

The many faces of fear:A synthesis of methodological variation in characterizing predation risk from carnivores

Predators affect prey by killing them directly (lethal effects) and by inducing costly antipredator behaviours in living prey (risk effects). Risk effects can strongly influence prey populations and cascade through trophic systems. A prerequisite for assessing risk effects is characterizing the spatiotemporal variation in predation risk. Risk effects research has experienced rapid growth in the last several decades. However, preliminary assessments of the resultant literature suggest that researchers characterize predation risk using a variety of techniques. The implications of this methodological variation for inference and comparability among studies have not been well recognized or formally synthesized. We couple a literature survey with a hierarchical framework, developed from established theory, to quantify the methodological variation in characterizing risk using carnivore-ungulate systems as a case study. Via this process, we documented 244 metrics of risk from 141 studies falling into at least 13 distinct subcategories within three broader categories. Both empirical and theoretical work suggest risk and its effects on prey constitute a complex, multi-dimensional process with expressions varying by spatiotemporal scale. Our survey suggests this multi-scale complexity is reflected in the literature as a whole but often underappreciated in any given study, which complicates comparability among studies and leads to an overemphasis on documenting the presence of risk effects rather than their mechanisms or scale of influence. We suggest risk metrics be placed in a more concrete conceptual framework to clarify inference surrounding risk effects and their cascading effects throughout ecosystems. We recommend studies (i) take a multi-scale approach to characterizing risk; (ii) explicitly consider 'true' predation risk (probability of predation per unit time); and (iii) use risk metrics that facilitate comparison among studies and the evaluation of multiple competing hypotheses. Addressing the pressing questions in risk effects research, including how, to what extent and on what scale they occur, requires leveraging the advantages of the many methods available to characterize risk while minimizing the confusion caused by variability in their application.The NSF Graduate Research Fellowship Program (RJM), the Michigan State University MasterCard Foundation Scholars Program (ABM), CNPq-Brasil (LA), and the University of Montana Boone and Crockett Program (JJM).http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-26562018-07-30cs2017Centre for Wildlife Managemen

Patient-doctor continuity and diagnosis of cancer:electronic medical records study in general practice

BACKGROUND: Continuity of care may affect the diagnostic process in cancer but there is little research. AIM: To estimate associations between patient–doctor continuity and time to diagnosis and referral of three common cancers. DESIGN AND SETTING: Retrospective cohort study in general practices in England. METHOD: This study used data from the General Practice Research Database for patients aged ≥40 years with a diagnosis of breast, colorectal, or lung cancer. Relevant cancer symptoms or signs were identified up to 12 months before diagnosis. Patient–doctor continuity (fraction-of-care index adjusted for number of consultations) was calculated up to 24 months before diagnosis. Time ratios (TRs) were estimated using accelerated failure time regression models. RESULTS: Patient–doctor continuity in the 24 months before diagnosis was associated with a slightly later diagnosis of colorectal (time ratio [TR] 1.01, 95% confidence interval [CI] =1.01 to 1.02) but not breast (TR = 1.00, 0.99 to 1.01) or lung cancer (TR = 1.00, 0.99 to 1.00). Secondary analyses suggested that for colorectal and lung cancer, continuity of doctor before the index consultation was associated with a later diagnosis but continuity after the index consultation was associated with an earlier diagnosis, with no such effects for breast cancer. For all three cancers, most of the delay to diagnosis occurred after referral. CONCLUSION: Any effect for patient–doctor continuity appears to be small. Future studies should compare investigations, referrals, and diagnoses in patients with and without cancer who present with possible cancer symptoms or signs; and focus on ‘difficult to diagnose’ types of cancer

Cis and Trans Effects of Human Genomic Variants on Gene Expression

This work was funded by the Louis-Jeantet Foundation (http://www.jeantet.ch/), the European Research Council (Grant ID: 260927 http://erc.europa.eu/), the Swiss National Foundation (Grant ID: 130342 http://www.snf.ch), NCCR Frontiers In Genetics (http://www.frontiers-in-genetics.org), the UK Medical Research Council (http://www.mrc.ac.uk) and the Wellcome Trust (Grant ID: 092731).

Isolation and Characterization of Multipotent CD24+ Cells From the Renal Papilla of Swine

Over 100,000 patients in the United States are currently waiting for a kidney transplant. With just over 10,000 cadaveric kidneys transplanted annually, it is of the utmost importance to optimize kidney viability upon transplantation. One exciting avenue may be xenotransplantation, which has rejuvenated interest after advanced gene editing techniques have been successfully used in swine. Simultaneously, acute kidney injury (AKI) is associated with high morbidity and mortality and currently lacks effective treatment. Animal models have been used extensively to address both of these issues, with recent emphasis on renal progenitor cells (RPCs). Due to anatomical similarities to humans we aimed to examine progenitor cells from the renal papillae of swine kidneys. To do this, RPCs were dissected from the renal papillae of healthy swine. Cell surface marker expression, proliferation, and differentiation of the RPCs were tested in vitro. Additionally, a mixed lymphocyte reaction was performed to examine immunomodulatory properties. RPCs displayed spindle shaped morphology with limited self-renewing capacity. Isolated RPCs were positive for CD24 and CD133 at early passages, but lost expression with subsequent passaging. Similarly, RPCs displayed myogenic, osteogenic, and adipogenic differentiation capacities at passage 2, but largely lost this by passage 6. Lastly, direct contact of RPCs with human lymphocytes increased release of IL6 and IL8. Taken together, RPCs from the papilla of porcine kidneys display transient stem cell properties that are lost with passaging, and either represent multiple types of progenitor cells, or a multipotent progenitor population. In instances of ischemic insult, augmentation of/with RPCs may potentiate regenerative properties of the kidney. While the use of swine for transplantation and ischemia studies confers obvious advantages, the populations of different progenitor cell populations within pig kidneys warrants further investigation. Ultimately, while gene editing techniques enhance the potential for xenotransplantation of organs or cells, the ultimate success of this strategy may be determined by the (dis)similarities of RPCs from different species

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.

It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution