Publications by authors named "Joseph Lancaster"

6 Publications

  • Page 1 of 1

Marsh bird occupancy of wetlands managed for waterfowl in the Midwestern USA.

PLoS One 2020 21;15(2):e0228980. Epub 2020 Feb 21.

Stephen A. Forbes Biological Station, Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Havana, Illinois, United States of America.

Marsh birds (rallids, bitterns, and grebes) depend on emergent wetlands, and habitat loss and degradation are the primary suspected causes for population declines among many marsh bird species. We evaluated the effect of natural wetland characteristics, wetland management practices, and surrounding landscape characteristics on marsh bird occupancy in Illinois during late spring and early summer 2015-2017. We conducted call-back surveys following the North American Standardized Marsh Bird Survey Protocol three times annually at all sites (2015 n = 49, 2016 n = 57, 2017 n = 55). Across all species and groups, detection probability declined 7.1% ± 2.1 each week during the marsh bird survey period. Wetlands managed for waterfowl (ducks, geese, and swans) had greater occupancy than reference wetlands. Marsh bird occupancy increased with greater wetland complexity, intermediate levels of waterfowl management intensity, greater proportions of surface water inundation, and greater proportions of persistent emergent vegetation cover. Wetland management practices that retain surface water during the growing season, encourage perennial emergent plants (e.g., Typha sp.), and increase wetland complexity could be used to provide habitat suitable for waterfowl and marsh birds.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228980PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7034909PMC
May 2020

Acceleration of Ungapped Extension in Mercury BLAST.

Microprocess Microsyst 2009 Jun;33(4):281-289

Department of Computer Science and Engineering, Washington University in St. Louis, E-mail:

The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data efficiently is becoming an increasingly difficult task. There are many available software tools that molecular biologists use for comparing genomic data. This paper focuses on accelerating the most widely used such tool, BLAST. Mercury BLAST takes a streaming approach to the BLAST computation by off loading the performance-critical sections to specialized hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone.This paper presents the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and runs at 100 MHz on available FPGAs, making it an effective and powerful component for accelerating biosequence comparisons. The performance of this stage is 25× that of the standard software distribution, yielding close to 50× performance improvement on the complete BLAST application. The sensitivity is essentially equivalent to that of the standard distribution.
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http://dx.doi.org/10.1016/j.micpro.2009.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771927PMC
June 2009

Mercury BLASTP: Accelerating Protein Sequence Alignment.

ACM Trans Reconfigurable Technol Syst 2008 Jun;1(2)

Dept. of Computer Science and Engineering, Washington University in St. Louis.

Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this paper, we describe the architecture of the portions of the application that are accelerated in the FPGA, and we also describe the integration of these FPGA-accelerated portions with the existing BLASTP software. We have implemented Mercury BLASTP on a commodity workstation with two Xilinx Virtex-II 6000 FPGAs. We show that the new design runs 11-15 times faster than software BLASTP on a modern CPU while delivering close to 99% identical results.
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http://dx.doi.org/10.1145/1371579.1371581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615407PMC
June 2008

Biosequence Similarity Search on the Mercury System.

J VLSI Signal Process Syst Signal Image Video Technol 2007 ;49(1):101-121

Department of Computer Science and Engineering Washington University in St. Louis.

Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2564817PMC
http://dx.doi.org/10.1007/s11265-007-0087-0DOI Listing
January 2007

Analysis of noise in quorum sensing.

OMICS 2003 ;7(3):317-34

Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, USA.

Noise may play a pivotal role in gene circuit functionality, as demonstrated for the genetic switch in the bacterial phage lambda. Like the lambda switch, bacterial quorum sensing (QS) systems operate within a population and contain a bistable switching element, making it likely that noise plays a functional role in QS circuit operation. Therefore, a detailed analysis of the noise behavior of QS systems is needed. We have developed a set of tools generally applicable to the analysis of gene circuits, with an emphasis on investigations in the frequency domain (FD), that we apply here to the QS system in the marine bacterium Vibrio fischeri. We demonstrate that a tight coupling between exact stochastic simulation and FD analysis provides insights into the structure/function relationships in the QS circuit. Furthermore, we argue that a noise analysis is incomplete without consideration of the power spectral densities (PSDs) of the important molecular output signals. As an example we consider reversible reactions in the QS circuit, and show through analysis and exact stochastic simulation that these circuits make significant and dynamic modifications to the noise spectra. In particular, we demonstrate a "whitening" effect, which occurs as the noise is processed through these reversible reactions.
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http://dx.doi.org/10.1089/153623103322452422DOI Listing
May 2004

Laser ablation construction of on-column reagent addition devices for capillary electrophoresis.

Anal Chem 2002 Apr;74(7):1572-7

Department of Chemistry, University of Tennessee, Knoxville 37996-1600, USA.

A simple and reproducible technique for constructing perfectly aligned gaps in fused-silica capillaries has been developed for postcolumn reagent addition with capillary electrophoresis. This technique uses laser ablation with the second harmonic of a Nd:YAG laser (532 nm) at 13.5 mJ/pulse and a repetition rate of 15 Hz to create these gaps. A capillary is glued to a microscope slide and positioned at the focal point of a cylindrical lens using the focused beam from a laser pointer as a reference. Gaps of 14.0 +/- 2.2 microm (n = 33) at the bore of the capillary are produced with a success rate of 94% by ablation with 400 pulses. This simple method of gap construction requires no micromanipulation under a microscope, hydrofluoric acid etching, or use of column fittings. These structures have been used for reagent addition for postcolumn derivatization with laser-induced fluorescence detection and have been tested for the separation of proteins and amino acids. Detection limits of 6 x 10(-7) and 1 x 10(-8) M have been obtained for glycine and tranferrin, respectively. Separation efficiencies obtained using these gap reactors range from 38,000 to 213,000 theoretical plates.
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http://dx.doi.org/10.1021/ac015693wDOI Listing
April 2002
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