khmer: Working with Big Data in Bioinformatics

We introduce design and optimization considerations for the 'khmer' package.Comment: Invited chapter for forthcoming book on Performance of Open Source Application

Cool Core Bias in Sunyaev-Zel'dovich Galaxy Cluster Surveys

Sunyaev-Zeldovich (SZ) surveys find massive clusters of galaxies by measuring the inverse Compton scattering of cosmic microwave background off of intra-cluster gas. The cluster selection function from such surveys is expected to be nearly independent of redshift and cluster astrophysics. In this work, we estimate the effect on the observed SZ signal of centrally-peaked gas density profiles (cool cores) and radio emission from the brightest cluster galaxy (BCG) by creating mock observations of a sample of clusters that span the observed range of classical cooling rates and radio luminosities. For each cluster, we make simulated SZ observations by the South Pole Telescope and characterize the cluster selection function, but note that our results are broadly applicable to other SZ surveys. We find that the inclusion of a cool core can cause a change in the measured SPT significance of a cluster between 0.01% - 10% at z > 0.3, increasing with cuspiness of the cool core and angular size on the sky of the cluster (i.e., decreasing redshift, increasing mass). We provide quantitative estimates of the bias in the SZ signal as a function of a gas density cuspiness parameter, redshift, mass, and the 1.4 GHz radio luminosity of the central AGN. Based on this work, we estimate that, for the Phoenix cluster (one of the strongest cool cores known), the presence of a cool core is biasing the SZ significance high by ~ 6%. The ubiquity of radio galaxies at the centers of cool core clusters will offset the cool core bias to varying degrees.Comment: 8 pages, 4 figures, accepted to Ap

Rapid changes in shape and number of MHC class II expressing cells in rat airways after Mycoplasma pulmonis infection

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.Mycoplasma pulmonis infection in rodents causes a chronic inflammatory airway disease with a strong immunological component, leading to mucosal remodeling and angiogenesis. We sought to determine the effect of this infection on the shape and number of dendritic cells and other major histocompatibility complex (MHC) class II expressing cells in the airway mucosa of Wistar rats. Changes in the shape of subepithelial OX6 (anti-MHC class II)-immunoreactive cells were evident in the tracheal mucosa 2 days after intranasal inoculation with M. pulmonis. By 1 week, the shape of the cells had changed from stellate to rounded (mean shape index increased from 0.42 to 0.77). The number of OX6-positive cells was increased 6-fold at 1 week and 16-fold at 4 weeks. Coincident with these changes, many columnar epithelial cells developed OX6 immunoreactivity, which was still present at 4 weeks. We conclude that M. pulmonis infection creates a potent immunologic stimulus that augments and transforms the OX6-immunoreactive cell population in the airways by changing the functional state of airway dendritic cells, initiating an influx of MHC class II expressing cells, and activating expression of MHC class II molecules by airway epithelial cells

Building Energy Efficiency Assessment of Renewable and Cogeneration Energy Efficiency Technologies for the Canadian High Arctic

Arctic communities, challenged by the harsh climate and a lack of local energy resources, are often confronted with finding more sustainable solutions for power and energy. Due to their isolated nature, reductions in energy or fuel use can have important implications for operating costs, security, and energy independence. While high performance buildings have received significant attention in more populated areas, there has been less work done on the opportunities and challenges for these buildings in the Canadian High Arctic. Providing cost-effective logistical support for researchers in the high Arctic, the Polar Continental Shelf Program has operated a field logistics support hub in Resolute, Nunavut since 1958. With increased demand for logistical support and training over the past decade, the Resolute facility has undergone two significant recent expansions. The facility now contains over 7,400 metres squares of living and working space including the Martin Bergmann Complex (provides accommodations for over 237 people), the Operations Centre (warehouse storage, mechanical shops and offices) and the Dr. Roy “Fritz†Koerner Laboratory. With the increased operational requirements, the facility has seen a significant increase in energy use, greenhouse gas emissions and ultimately utility costs. As such, there is a strong desire to reduce energy use and provide for more sustainable facility operations. As the Polar Continental Shelf Program Resolute facility is fairly energy efficient (1.0 GJ/m²) and well maintained, to achieve deep energy savings it is necessary to examine the impact of more innovative strategies, including the integration of cogeneration and heat pump systems. This paper will present an analysis of different energy efficient technologies and strategies for high performance buildings in the Canadian High Arctic. Thus, a comprehensive energy efficiency analysis is performed using the TRNSYS energy simulation tool. First, detailed energy models of the current facilities are developed and calibrated using monitored data. These energy models then form the base for an analysis of innovative energy efficiency strategies including the integration of onsite cogeneration, cold climate heat pumps, and solar integrated technologies. Each strategy is then examined within a techno-economic framework to determine potential utility cost savings, GHG reductions, and simple payback periods. These results provide an important base for the discussion of future high performance buildings in the Canadian High Arctic

Housing and Mobility Toolkit for San Mateo County

Since the end of the Great Recession, San Mateo County has attracted new workers at a record rate without building anywhere near enough housing. This jobs-housing imbalance drives the cost of housing up and forces many moderate and lower-income employees and their families out of the County. A lack of access to quality affordable housing in the County and the entire Bay Area along with limited transportation options means that an increased number of employees drive in and out of the County every workday. The resultant congestion, gridlock, and long commutes along with other negative environmental, social, and economic impacts create a major concern for communities in the County and beyond. Clearly, this problem has two distinct but interrelated dimensions: housing development and transportation planning. A select group of Mineta Transportation Institute (MTI) Research Associates worked closely with representatives from the San Mateo County Home for All initiative to help address this challenge by developing a toolkit of successful case studies with a holistic approach to housing development and transportation planning

Extent of Fermi-surface reconstruction in the high-temperature superconductor HgBa2_2CuO4+δ_{4+\delta}

High magnetic fields have revealed a surprisingly small Fermi-surface in underdoped cuprates, possibly resulting from Fermi-surface reconstruction due to an order parameter that breaks translational symmetry of the crystal lattice. A crucial issue concerns the doping extent of this state and its relationship to the principal pseudogap and superconducting phases. We employ pulsed magnetic field measurements on the cuprate HgBa$_2$CuO$_{4+\delta}$ to identify signatures of Fermi surface reconstruction from a sign change of the Hall effect and a peak in the temperature-dependent planar resistivity. We trace the termination of Fermi-surface reconstruction to two hole concentrations where the superconducting upper critical fields are found to be enhanced. One of these points is associated with the pseudogap end-point near optimal doping. These results connect the Fermi-surface reconstruction to both superconductivity and the pseudogap phenomena.Comment: 5 pages. 3 Figures. PNAS (2020

Development and Testing of a Virtual Flow Meter for Use in Ongoing Commissioning of Commercial and Institutional Buildings

Ongoing commissioning of commercial and institutional buildings relies on the available trend data from a building automation systems (BAS) to be able to monitor the buildings energy performance using developed tools. However, it is often that the BAS has no information of the chilled and condenser water flow rates that pass through the evaporator and condenser, respectively, of a chiller. This thesis proposes a virtual flow meter (VFM) to estimate the chilled and condenser water mass flow rates. The virtual flow meter uses a thermodynamic analysis of a chiller under six different scenarios of available sensors from a BAS with some manufacturer data to fill the gaps left by the missing sensors. This thesis presents the use of the VFM in three case studies to estimate the chilled and condenser water mass flow rates. The evaluation of the accuracy of the VFM model is performed using an uncertainty analysis, statistical indices (CV-RMSE, NMBE) and a paired difference statistical hypothesis test to provide insight into the limits of CV-RMSE and NMBE that determine an acceptable model. Then, the estimates from the VFM are used to estimate the virtual coefficient of performance of the chiller and the cooling plant for use with developed ongoing commissioning methods of cooling plants. This thesis presents the development of a graphical user interface for the VFM model and the sensitivity of the virtual flow meter to it inputs is discussed to aid the user in achieving accurate results

Alluvial sediment or playas: What is the dominant source of sand and silt in desert soil vesicular A horizons, southwest USA

Vesicular A (Av) soil horizons form beneath desert pavements from the accretion of aeolian sediment (dust) commonly thought to be derived primarily from desiccating pluvial lakes and playas, with contributions from ephemeral washes and alluvial fans. Particle size distributions of Av horizons are typically bimodal with primary modes of very fine silt and fine sand, suggesting that the horizon matrix is derived from multiple sources. Here we conduct detailed chemical and physical analysis of both Av horizon soil samples and potential sources of aeolian sediment to better constrain the relative contributions of dust associated with the development of Av horizons. Geochemical data from both sand (125–250 µm) and silt (2–32 µm) fractions in Av horizons and potential dust sources in the eastern Mojave Desert and western Sonora Desert, USA, point to large contributions from nearby sources including distal alluvial fans and washes, and comparably lower contributions from regional sources such as playas. The silt mode is derived from suspension transport of dust, and the fine sand mode is derived from saltating sand. The desiccation of pluvial lakes in the Mojave Desert is commonly believed to have driven episodes of aeolian activity, contributing to sand dunes and Av horizon formation. We propose that alluvial fans and washes are underappreciated as desert dust sources and that pulses of dust from late Pleistocene and Holocene alluvial fans dwarfed pulses of dust from desiccating pluvial lakes in the eastern Mojave Desert