The Effect of Supplementary Yeast Culture in Diets for Pigs on the Bioavailability of Dietary Phosphorus

Twenty-four crossbred barrow pigs were used in four replications of six treatments to study the effect of supplementary yeast culture in improving the bioavailability of dietary phosphorus. Pigs were fed corn/soybean diets containing 0.5, 0.4, or 0.3% total phosphorus with or without 0.5% yeast culture. The pigs were fed at 5% of body weight daily in two equal feedings for a seven-day preliminary period followed by a seven-day collection period. The percent apparent dry matter digested, percent apparent absorbed phosphorus, and percent apparent absorbed nitrogen only varied according to the amount of phosphorus in the diet. Yeast culture had no effect on any of these measurements. Serum phosphorus levels in all pigs decreased from beginning to termination of the study with the larger decreases in those pigs receiving less phosphorus in their diet. Supplementing pig diets with yeast culture did not improve bioavailability of dietary phosphorus in this stud

Experimental Air-Broadened Line Parameters in the nu2 Band of CH3D

In this study we report the first experimental measurements of air-broadening and air-induced pressure-shift coefficients for approximately 378 transitions in the nu2 fundamental band of CH3D. These results were obtained from analysis of 17 room temperature laboratory absorption spectra recorded at 0.0056 cm(exp -1) resolution using the McMath-Pierce Fourier transform spectrometer located on Kitt Peak, Arizona. Three absorption cells with path lengths of 10.2, 25 and 150 cm were used to record the spectra. The total sample pressures ranged from 0.129x10(exp -2) to 52.855x10(exp -2) atm with CH3D volume mixing ratios of approximately 0.0109 in air. The spectra were analyzed using a multispectrum non-linear least-squares fitting technique. We report measurements for air pressure-broadening coefficients for transitions with quantum numbers as high as J" = 20 and K = 15, where K" = K' equivalent to K (for a parallel band). The measured air broadening coefficients range from 0.0205 to 0.0835 cm(exp -1) atm(exp -1) at 296 K. All the measured pressure-shift coefficients are negative and are found to vary from about -0.0005 to -0.0080 cm(exp -1) atm(exp -1) at the temperature of the spectra. We have examined the dependence of the measured broadening and shift parameters on the J" and K quantum numbers and also developed empirical expressions to describe the broadening coefficients in terms of m (m = -J", J" and J" + 1 in the (sup Q)P- (sup Q)Q-, and (sup Q)R-branch, respectively) and K. On average, the empirical expressions reproduce the measured broadening coefficients to within 4.4%

Inferring Population Continuity Versus Replacement with aDNA: A Cautionary Tale from the Aleutian Islands

In The Aleutian and Commander Islands and Their Inhabitants (Philadelphia: Wistar Institute of Anatomy and Biology, 1945), Hrdlička proposed a population replacement event in the Aleutian Islands approximately 1,000 years ago based on a perceived temporal shift in cranial morphology. However, the archaeological record indicates cultural, and presumed population, continuity for more than 4,000 years. We use mtDNA haplogroup data in the series of prehistoric eastern Aleutian samples (n = 86) studied craniometrically by Hrdlička to test alternative hypotheses regarding population continuity or replacement in the region. This molecular characterization, in conjunction with direct dating of individual specimens, provided increased resolution for hypothesis testing. Results indicate an apparent shift in mtDNA haplogroup frequencies in the eastern Aleutians approximately 1,000 years ago, in concert with changes in mortuary practices and isotopic signatures reflecting resource acquisition strategies. The earliest Aleut populations were characterized by a high frequency of haplogroup A, as are most modern populations of the North American arctic. Later prehistoric peoples in the Aleutians were characterized by a high frequency of haplogroup D and a correspondingly lower frequency of haplogroup A, a pattern typified by modern Aleut populations

Applying Machine Learning to Neutron-Gamma Ray Discrimination from Scintillator Readout Using Wavelength Shifting Fibers

Advances in machine learning have found wide applications including radiation detection. In this work, machine learning is applied to neutron-gamma ray discrimination of an organic liquid scintillator (OLS) readout using wavelength shifting (WLS) fibers. The objective of using WLS fiber is to enable the transfer of the light signal from the scintillation medium, with almost any active volume geometry, to a low-profile photomultiplier. This is a common practice in high-energy physics research and has proven to be very effective for such applications. The drawback of this approach is the light pulses carried to the photomultiplier through the WLS fibers do not perfectly replicate the original OLS light pulses’ intensities or timing. This drawback causes traditional pulse shape discrimination algorithms applied to the degraded light pulses to fail to discriminate between neutron and gamma ray events. However, differences in the degraded light pulses for neutrons and gamma rays still exist and various machine learning algorithms can be applied to identify these differences. An experimental system was constructed to simultaneously capture part of the scintillation medium signal and the corresponding signal through the WLS fibers. Using the known neutron-gamma ray discrimination characteristics directly measured in the scintillation medium to provide the ground truth, supervised machine learning algorithms were applied to the corresponding light pulses carried to the photomultiplier through the WLS fibers. The results indicate that this approach will enable enhanced recovery of neutron-gamma ray discrimination information. This research effort will focus on two aspects of the OLS-WLS system: 1) developing an experimental system to create machine learning training data and 2) applying and evaluating various machine learning algorithms

BFAST: An Alignment Tool for Large Scale Genome Resequencing

BACKGROUND:The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation. METHODOLOGY:We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. CONCLUSIONS:We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net)

Decontamination Strategy for Large Area and/or Equipment Contaminated with Chemical and Biological Agents using a High Energy Arc Lamp (HEAL)

A strategy for the decontamination of large areas and or equipment contaminated with Biological Warfare Agents (BWAs) and Chemical Warfare Agents (CWAs) was demonstrated using a High Energy Arc Lamp (HEAL) photolysis system. This strategy offers an alternative that is potentially quicker, less hazardous, generates far less waste, and is easier to deploy than those currently fielded by the Department of Defense (DoD). For example, for large frame aircraft the United States Air Force still relies on the combination of weathering (stand alone in environment), air washing (fly aircraft) and finally washing the aircraft with Hot Soapy Water (HSW) in an attempt to remove any remaining contamination. This method is laborious, time consuming (upwards of 12+ hours not including decontamination site preparation), and requires large amounts of water (e.g., 1,600+ gallons for a single large frame aircraft), and generates large amounts of hazardous waste requiring disposal. The efficacy of the HEAL system was demonstrated using diisopropyl methyl phosphonate (DIMP) a G series CWA simulant, and Bacillus globigii (BG) a simulant of Bacillus anthracis. Experiments were designed to simulate the energy flux of a field deployable lamp system that could stand-off 17 meters from a 12m2 target area and uniformly expose a surface at 1360 W/m2. The HEAL system in the absence of a catalyst reduced the amount of B. globigii by five orders of magnitude at a starting concentration of 1.63 x 107 spores. In the case of CWA simulants, the HEAL system in the presence of the catalyst TiO2 effectively degraded DIMP sprayed onto a 100mm diameter Petri dish in 5 minutes

Simultaneous noninvasive recording of skin sympathetic nerve activity and electrocardiogram

BACKGROUND: Sympathetic nerve activity is important to cardiac arrhythmogenesis. OBJECTIVE: The purpose of this study was to develop a method for simultaneous noninvasive recording of skin sympathetic nerve activity (SKNA) and electrocardiogram (ECG) using conventional ECG electrodes. This method (neuECG) can be used to adequately estimate sympathetic tone. METHODS: We recorded neuECG signals from the skin of 56 human subjects. The signals were low-pass filtered to show the ECG and high-pass filtered to show nerve activity. Protocol 1 included 12 healthy volunteers who underwent cold water pressor test and Valsalva maneuver. Protocol 2 included 19 inpatients with epilepsy but without known heart diseases monitored for 24 hours. Protocol 3 included 22 patients admitted with electrical storm and monitored for 39.0 ± 28.2 hours. Protocol 4 included 3 patients who underwent bilateral stellate ganglion blockade with lidocaine injection. RESULTS: In patients without heart diseases, spontaneous nerve discharges were frequently observed at baseline and were associated with heart rate acceleration. SKNA recorded from chest leads (V1-V6) during cold water pressor test and Valsalva maneuver (protocol 1) was invariably higher than during baseline and recovery periods (P < .001). In protocol 2, the average SKNA correlated with heart rate acceleration (r = 0.73 ± 0.14, P < .05) and shortening of QT interval (P < .001). Among 146 spontaneous ventricular tachycardia episodes recorded in 9 patients of protocol 3, 106 episodes (73%) were preceded by SKNA within 30 seconds of onset. Protocol 4 showed that bilateral stellate ganglia blockade by lidocaine inhibited SKNA. CONCLUSION: SKNA is detectable using conventional ECG electrodes in humans and may be useful in estimating sympathetic tone

Discovery of a Novel Compound with Anti-Venezuelan Equine Encephalitis Virus Activity That Targets the Nonstructural Protein 2

Abstract Alphaviruses present serious health threats as emerging and re-emerging viruses. Venezuelan equine encephalitis virus (VEEV), a New World alphavirus, can cause encephalitis in humans and horses, but there are no therapeutics for treatment. To date, compounds reported as anti-VEEV or anti-alphavirus inhibitors have shown moderate activity. To discover new classes of anti-VEEV inhibitors with novel viral targets, we used a high-throughput screen based on the measurement of cell protection from live VEEV TC-83-induced cytopathic effect to screen a 340,000 compound library. Of those, we identified five novel anti-VEEV compounds and chose a quinazolinone compound, CID15997213 (IC50 = 0.84 µM), for further characterization. The antiviral effect of CID15997213 was alphavirus-specific, inhibiting VEEV and Western equine encephalitis virus, but not Eastern equine encephalitis virus. In vitro assays confirmed inhibition of viral RNA, protein, and progeny synthesis. No antiviral activity was detected against a select group of RNA viruses. We found mutations conferring the resistance to the compound in the N-terminal domain of nsP2 and confirmed the target residues using a reverse genetic approach. Time of addition studies showed that the compound inhibits the middle stage of replication when viral genome replication is most active. In mice, the compound showed complete protection from lethal VEEV disease at 50 mg/kg/day. Collectively, these results reveal a potent anti-VEEV compound that uniquely targets the viral nsP2 N-terminal domain. While the function of nsP2 has yet to be characterized, our studies suggest that the protein might play a critical role in viral replication, and further, may represent an innovative opportunity to develop therapeutic interventions for alphavirus infection. Author Summary Alphaviruses occur worldwide, causing significant diseases such as encephalitis or arthritis in humans and animals. In addition, some alphaviruses, such as VEEV, pose a biothreat due to their high infectivity and lack of available treatments. To discover small molecule inhibitors with lead development potential, we used a cell-based assay to screen 348,140 compounds for inhibition of a VEEV-induced cytopathic effect. The screen revealed a scaffold with high inhibitory VEEV cellular potency and low cytotoxicity liability. While most previously reported anti-alphavirus compounds inhibit host proteins, evidence supported that this scaffold targeted the VEEV nsP2 protein, and that inhibition was associated with viral replication. Interestingly, compound resistance studies with VEEV mapped activity to the N-terminal domain of nsP2, to which no known function has been attributed. Ultimately, this discovery has delivered a small molecule-derived class of potent VEEV inhibitors whose activity is coupled to the nsP2 viral protein, a novel target with a previously unestablished biological role that is now implicated in viral replication.This research was supported by the following funding sources: NIH R03MH087448-01A1, University of Louisville Internal Research Initiate grant to DHC, USAMRAA W81XWH-10-2-0064 and W81XWH-08-2-0024 to CBJ. Screening was provided by the Southern Research Specialized Screening Center (U54HG005034-0) and chemistry through the University of Kansas Specialized Chemistry Center (U54HG005031). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Search for gravitational wave bursts in LIGO's third science run

We report on a search for gravitational wave bursts in data from the three LIGO interferometric detectors during their third science run. The search targets subsecond bursts in the frequency range 100-1100 Hz for which no waveform model is assumed, and has a sensitivity in terms of the root-sum-square (rss) strain amplitude of hrss ~ 10^{-20} / sqrt(Hz). No gravitational wave signals were detected in the 8 days of analyzed data.Comment: 12 pages, 6 figures. Amaldi-6 conference proceedings to be published in Classical and Quantum Gravit