Urban Scale Modeling of Atmospheric Carbon Dioxide and Validation of Emission Inventories

There exists a pressing need for high resolution emissions inventories for cities. For greenhouse gases, cities and regions need a careful analysis of their carbon footprint to design effective policies to control and mitigate emissions. High resolution emissions inventories can be used in conjunction with meteorology models and atmospheric measurements to place top-down constraints on emissions. High resolution emissions inventories for criteria pollutants like NOx, CO, and O3 enable urban-scale air pollution modeling down to the neighborhood level. For example, the Vulcan project estimates CO2 using county-scale vehicle miles traveled (VMT) from the National Mobile Inventory Model (NMIM) County Database (NCD). The Hestia Project similarly allocates CO2 from Vulcan’s county-level inventory down to the building scale using eQUEST and building footprints. On-road transport is the most important sector for anthropogenic CO2, 38% in Portland, 32% nationally. Here we show a new model of CO2 emissions for the Portland, OR metropolitan region. The backbone is traffic counter recordings made by the Portland Bureau of Transportation at 9,352 sites over 21 years (1986-2006), augmented with PORTAL (The Portland Regional Transportation Archive Listing) freeway data. We constructed a regression model to fill in traffic network gaps using GIS data such as road class and population density. EPA MOVES was used to estimate transportation CO2 emissions. Our transportation emissions served as input into WRF meteorological modeling to simulate atmospheric CO2 at sites where frequent CO2 measurements are made. We show preliminary model results

Zoogeomorphological behaviours in fish and the potential impact of benthic feeding on bed material mobility in fluvial landscapes

Foraging by benthivorous fish can affect bed material mobility and sediment flux. This paper collates evidence of benthic feeding effects at local scales and evaluates the possibility that large numbers of foraging fish, each of which accomplishes a small amount of geomorphic work when feeding, may have a cumulative effect across river systems. A first synthesis of research from several disciplines provides a deeper understanding of how fish disturb and condition bed materials with implications for sediment mobility. To evaluate the spatial extent of benthic feeding and therefore the potential for it to have a large-scale effect, the distribution of benthivorous fish is established across a large river network. After quality control, the dataset yields a comprehensive set of fish community information based on over 61,000 individuals and 30 species at 176 sites. The factors that are likely to mediate foraging and its geomorphological effectiveness are considered. A novel scoring system that incorporates three key controls (fish feeding behaviour, fish abundance and fish body size) is then applied across the river network to provide the first prediction of where geomorphologically effective benthic feeding is feasible and its possible relative magnitude. Our results demonstrate that the potential for zoogeomorphic impacts is widespread but variable in space as a function of community composition and the abundance of key benthivores. A preliminary calibration against measured field impacts suggests that benthic feeding may cause measurable geomorphological disturbance at more than 90% of sites. Together, previous work and this unique analysis suggest that benthic feeding is sufficiently effective and extensive to warrant additional research. Investigating the role of benthivorous fish in fluvial geomorphology is important because it may yield results that challenge the assumption that biota are irrelevant sources of energy in geomorphological systems. Key research questions and a roadmap to facilitate progress are identified

Complete replication of hepatitis C virus in cell culture.

Many aspects of the hepatitis C virus (HCV) life cycle have not been reproduced in cell culture, which has slowed research progress on this important human pathogen. Here, we describe a full-length HCV genome that replicates and produces virus particles that are infectious in cell culture (HCVcc). Replication of HCVcc was robust, producing nearly 10(5) infectious units per milliliter within 48 hours. Virus particles were filterable and neutralized with a monoclonal antibody against the viral glycoprotein E2. Viral entry was dependent on cellular expression of a putative HCV receptor, CD81. HCVcc replication was inhibited by interferon-alpha and by several HCV-specific antiviral compounds, suggesting that this in vitro system will aid in the search for improved antivirals

Resolving Gas Dynamics in the Circumnuclear Region of a Disk Galaxy in a Cosmological Simulation

Using a hydrodynamic adaptive mesh refinement code, we simulate the growth and evolution of a galaxy, which could potentially host a supermassive black hole, within a cosmological volume. Reaching a dynamical range in excess of 10 million, the simulation follows the evolution of the gas structure from super-galactic scales all the way down to the outer edge of the accretion disk. Here, we focus on global instabilities in the self-gravitating, cold, turbulence-supported, molecular gas disk at the center of the model galaxy, which provide a natural mechanism for angular momentum transport down to sub-pc scales. The gas density profile follows a power-law scaling as r^-8/3, consistent with an analytic description of turbulence in a quasi-stationary circumnuclear disk. We analyze the properties of the disk which contribute to the instabilities, and investigate the significance of instability for the galaxy's evolution and the growth of a supermassive black hole at the center.Comment: 16 pages (includes appendix), submitted to ApJ. Figures here are at low resolution; for higher resolution version, download http://casa.colorado.edu/~levinerd/ms.pd

Interferon-stimulated gene (ISG)-expression screening reveals the specific antibunyaviral activity of ISG20

Bunyaviruses pose a significant threat to human health, prosperity and food security. In response to viral infections, interferons (IFNs) upregulate the expression of hundreds of interferon stimulated genes (ISGs) whose cumulative action can potently inhibit the replication of bunyaviruses. We used a flow cytometry-based method to screen the ability of ∼500 unique ISGs from humans and rhesus macaques to inhibit the replication of Bunyamwera orthobunyavirus (BUNV), the prototype of both the Peribunyaviridae family and Bunyavirales order. Candidates possessing antibunyaviral activity were further examined using a panel of divergent bunyaviruses. Interestingly, one candidate, ISG20, exhibited potent antibunyaviral activity against most viruses examined from the Peribunyaviridae, Hantaviridae and Nairoviridae families, whereas phleboviruses (Phenuiviridae) largely escaped inhibition. Similar to other viruses known to be targeted by ISG20, the antibunyaviral activity of ISG20 is dependent upon its functional ribonuclease activity. Through use of an infectious VLP assay (based on the BUNV minigenome system), we confirmed that gene expression from all 3 viral segments is strongly inhibited by ISG20. Using in vitro evolution, we generated a substantially ISG20-resistant BUNV and mapped the determinants of ISG20 sensitivity/resistance. Taken together, we report that ISG20 is a broad and potent antibunyaviral factor yet some bunyaviruses are remarkably ISG20 resistant. Thus, ISG20 sensitivity/resistance could influence the pathogenesis of bunyaviruses, many of which are emerging viruses of clinical or veterinary significance

Eleven neurology-related proteins measured in serum are positively correlated to the severity of diabetic neuropathy

About 20% of patients with diabetes suffer from chronic pain with neuropathic characteristics. We investigated the multivariate associations between 92 neurology-related proteins measured in serum from 190 patients with painful and painless diabetic neuropathy. Participants were recruited from the Pain in Neuropathy Study, an observational cross-sectional multicentre study in which participants underwent deep phenotyping. In the exploration cohort, two groups were defined by hierarchical cluster analyses of protein data. The proportion of painless vs painful neuropathy did not differ between the two groups, but one group had a significantly higher grade of neuropathy as measured by the Toronto Clinical Scoring System (TCSS). This finding was replicated in the replication cohort. Analyzing both groups together, we found that a group of 11 inter-correlated proteins (TNFRSF12A, SCARB2, N2DL-2, SKR3, EFNA4, LAYN, CLM-1, CD38, UNC5C, GFR-alpha-1, and JAM-B) were positively associated with TCSS values. Notably, EFNA4 and UNC5C are known to be part of axon guidance pathways. To conclude, although cluster analysis of 92 neurology-related proteins did not distinguish painful from painless diabetic neuropathy, we identified 11 proteins which positively correlated to neuropathy severity and warrant further investigation as potential biomarkers

Structure of population activity in primary motor cortex for single finger flexion and extension

Copyright © 2020 the authors How is the primary motor cortex (M1) organized to control fine finger movements? We investigated the population activity in M1 for single finger flexion and extension, using 7T functional magnetic resonance imaging (fMRI) in female and male human participants and compared these results to the neural spiking patterns recorded in two male monkeys performing the identical task. fMRI activity patterns were distinct for movements of different fingers, but were quite similar for flexion and extension of the same finger. In contrast, spiking patterns in monkeys were quite distinct for both fingers and directions, which is similar to what was found for muscular activity patterns. The discrepancy between fMRI and electrophysiological measurements can be explained by two (non-mutually exclusive) characteristics of the organization of finger flexion and extension movements. Given that fMRI reflects predominantly input and recurrent activity, the results can be explained by an architecture in which neural populations that control flexion or extension of the same finger produce distinct outputs, but interact tightly with each other and receive similar inputs. Additionally, neurons tuned to different movement directions for the same finger (or combination of fingers) may cluster closely together, while neurons that control different finger combinations may be more spatially separated. When measuring this organization with fMRI at a coarse spatial scale, the activity patterns for flexion and extension of the same finger would appear very similar. Overall, we suggest that the discrepancy between fMRI and electrophysiological measurements provides new insights into the general organization of fine finger movements in M1