Averaged Lagrangians and the mean dynamical effects of fluctuations in continuum mechanics

We begin by placing the Generalized Lagrangian Mean (GLM) equations for a compressible adiabatic fluid into the Euler-Poincar\'e (EP) variational framework of fluid dynamics, for an averaged Lagrangian. We then derive a set of approximate small amplitude GLM equations (glm) that express the linear and nonlinear back-reaction effects on the Eulerian mean fluid quantities by the fluctuating displacements of the Lagrangian trajectories in terms of their Eulerian second moments. The new glm EP motion equations for compressible and incompressible ideal fluids are compared with the Euler-alpha turbulence closure equations. An alpha model is a GLM (or glm) fluid theory with a Taylor hypothesis closure (THC). The glm equations lead to generalizations of the Euler-alpha models to include compressibility and magnetic fields.Comment: 95 pages, no figures, submitted to Physica

Diffuse Alveolar Hemorrhage

This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Diffuse alveolar hemorrhage[DAH] is a serious condition that can be life threatening. It can be caused by a constellation of disorders which presents with hemoptysis, anemia, and diffuse alveolar infiltrates. Respiratory failure from DAH can be so severe that it has been called an ARDS mimic/imitator. Early recognition is crucial because prompt diagnosis and treatment are required for survival. DAH should be distinguished from other causes of pulmonary hemorrhage caused by localized pulmonary abnormalities and the bronchial circulation. Early bronchoscopy with bronchoalveolar lavage (BAL) is generally required to confirm the diagnosis of DAH and rule out infection. Progressively bloody bronchoalveolar lavage samples can distinguish DAH. Systemic vasculitis is one of the most common causes of DAH and can be pathologically defined by the presence of cellular inflammation, vessel destruction, tissue necrosis, and eventually, organ dysfunction. Corticosteroids and immunosuppressive agents remain the gold standard for the treatment. The following case illustrates a patient who was dependent on dialysis, then presented with hemoptysis. Bronchoscopy demonstrated progressively bloody bronchoalveolar lavage samples consistent with diffuse alveolar hemorrhage. Serologic testing was consistent with microscopic polyangiitis. The patient experienced a clinical remission with cyclophosphamide and corticosteroids

Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes1,2 and molecular mechanisms that are often specific to cell type3,4. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P &lt; 5 × 10-8) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores5 in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.</p

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Concurrent Sessions C: Fish Screening At Water Diversions I - Design of Large Cylindrical Fish Screen for the USBR Lower Yellowstone Project

The Lower Yellowstone Irrigation District diverts up to 1400 cfs into its main canal system on the lower Yellowstone River in Northeastern Montana. In late 2010, as part of a pallid sturgeon recovery program, the USBR and USACE began construction of a new state-of-the-art screened canal head works structure. After over 100 years of unscreened operations, the new fish screened facility was opened in spring 2012. The head works will be integrated into a major river gradient fish passage facility being proposed for construction soon. When completed, the new passage and protection facilities will reduce fish entrainment and open an additional 165 miles of river habitat for the endangered and native fishes. The new headwork facility’s fish protection system consists of twelve, 6.5-foot diameter and 25 feet long cylindrical fish protection screens. Each screen is designed to seal over the intake’s submerged sluice gates spaced along the 350-foot long riverbank facility. An integrated and flush-mounted track system was built into the vertical concrete walls to raise the screens in the non-irrigation season for protection from the significant ice and flood flows common on the river. When the 71-mile long irrigation canal is operational, each screen is lowered into position and an automatic brush cleaning system is used to keep the 1.75 mm wedge wire slots from clogging. The new intake facility was physically modeled at the USBR Hydraulics Lab along with several river fish passage options. The on-river screen design keeps the fish and debris in the river as opposed to traditional off-river screen designs with fish bypass facilities. The cylindrical design also reduced the facility footprint and allows diversions to occur over the river’s wide-ranging water surface fluctuations. This presentation will focus on the design, construction, and hydraulics of the intake screen facility, as well as the initial season’s operational experiences

(Table T1) Geochemistry of calcium carbonate veins from ODP Holes 206-1256C and 206-1256D

Drilling a complete deep crustal section has been a primary yet elusive goal since the inception of scientific ocean drilling. In situ ocean crustal sections would contribute enormously to our understanding of the formation and subsequent evolution of the ocean crust, in particular the interplay between magmatic, hydrothermal, and tectonic processes. Ocean Drilling Program (ODP) Leg 206 was the first of a multileg project to drill an in situ crustal section that penetrated the gabbroic rocks of the Cocos plate (6°44.2'N, 91°56.1'W), which formed ~15 m.y. ago on the East Pacific Rise during a period of superfast spreading (>200 mm/yr) (Wilson, Teagle, Acton, et al., 2003, doi:10.2973/odp.proc.ir.206.2003). During Leg 206, the upper 500 m of basement was cored in Holes 1256C and 1256D with moderate to high recovery rates. The igneous rocks recovered are predominantly thin (10 cm to 3 m) basalt flows separated by chilled margins. There are also several massive flows (>3 m thick), although their abundance decreases with depth in Hole 1256D, as well as minor pillow basalts, hyaloclastites, and rare dikes. The lavas have been slightly (<10%) altered by low-temperature hydrothermal fluids, which resulted in pervasive dark gray background alteration and precipitation of saponite, pyrite, silica, celadonite, and calcium carbonate veins. Here we present a geochemical analysis of the CaCO3 recovered from cores. The compositions of ridge flank fluids within superfast spreading crust will be determined from these data, following the approach of Hart et al. (1994, doi:10.1029/93JB02035), Yatabe et al. (2000, doi:10.2973/odp.proc.sr.168.003.2000), and Coggon et al. (2004, doi:10.1016/S0012-821X(03)00697-6)

Community Engagement and Psychometric Methods in Aboriginal and Torres Strait Islander Patient-Reported Outcome Measures and Surveys&mdash;A Scoping Review and Critical Analysis

(1) Background: In healthcare settings, patient-reported outcome measures (PROMs) and surveys are accepted, patient-centered measures that provide qualitative information on dimensions of health and wellbeing. The level of psychometric assessment and engagement with end users for their design can vary significantly. This scoping review describes the psychometric and community engagement processes for PROMs and surveys developed for Aboriginal and Torres Strait Islander communities. (2) Methods: The PRISMA ScR guidelines for scoping reviews were followed, aimed at those PROMs and surveys that underwent psychometric assessment. The Aboriginal and Torres Strait Islander Quality Appraisal Tool and a narrative synthesis approach were used. (3) Results: Of 1080 articles, 14 were eligible for review. Most articles focused on a validity assessment of PROMs and surveys, with reliability being less common. Face validity with Aboriginal and Torres Strait Islander communities was reported in most studies, with construct validity through exploratory factor analyses. Methodological design risks were identified in the majority of studies, notably the absence of explicit Indigenous knowledges. Variability existed in the development of PROMs and surveys for Aboriginal and Torres Strait Islander communities. (4) Conclusions: Improvement in inclusion of Indigenous knowledges and research approaches is needed to ensure relevance and appropriate PROM structures. We provide suggestions for research teams to assist in future design