Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society

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Vortex Shedding in a Tandem Circular Cylinder System With a Yawed Downstream Cylinder,”

This investigation examines the flow produced by a tandem cylinder system with the downstream cylinder yawed to the mean flow direction. The yaw angle was varied from a ¼ 90 deg (two parallel tandem cylinders) to a ¼ 60 deg; this has the effect of varying the local spacing ratio between the cylinders. Fluctuating pressure and hot-wire measurements were used to determine the vortex-shedding frequencies and flow regimes produced by this previously uninvestigated flow. The results showed that the frequency and magnitude of the vortex shedding varies along the cylinder span depending on the local spacing ratio between the cylinders. In all cases the vortex-shedding frequency observed on the front cylinder had the same shedding frequency as the rear cylinder. In general, at small local spacing ratios the cylinders behaved as a single large body with the shear layers separating from the upstream cylinder and attaching on the downstream cylinder, this caused a correspondingly large, low frequency wake. At other positions where the local span of the tandem cylinder system was larger, small-scale vortices began to form in the gap between the cylinders, which in turn increased the vortex-shedding frequency. At the largest spacings, classical vortex shedding persisted in the gap formed between the cylinders, and both cylinders shed vortices as separate bodies with shedding frequencies typical of single cylinders. At certain local spacing ratios two distinct vortex-shedding frequencies occurred indicating that there was some overlap in these flow regimes

Emerging Use of Gene Expression Microarrays in Plant Physiology

Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry

The melanoma-specific graded prognostic assessment does not adequately discriminate prognosis in a modern population with brain metastases from malignant melanoma

The melanoma-specific graded prognostic assessment (msGPA) assigns patients with brain metastases from malignant melanoma to 1 of 4 prognostic groups. It was largely derived using clinical data from patients treated in the era that preceded the development of newer therapies such as BRAF, MEK and immune checkpoint inhibitors. Therefore, its current relevance to patients diagnosed with brain metastases from malignant melanoma is unclear. This study is an external validation of the msGPA in two temporally distinct British populations.Performance of the msGPA was assessed in Cohort I (1997-2008, n=231) and Cohort II (2008-2013, n=162) using Kaplan-Meier methods and Harrell's c-index of concordance. Cox regression was used to explore additional factors that may have prognostic relevance.The msGPA does not perform well as a prognostic score outside of the derivation cohort, with suboptimal statistical calibration and discrimination, particularly in those patients with an intermediate prognosis. Extra-cerebral metastases, leptomeningeal disease, age and potential use of novel targeted agents after brain metastases are diagnosed, should be incorporated into future prognostic models.An improved prognostic score is required to underpin high-quality randomised controlled trials in an area with a wide disparity in clinical care

Return-to-Play and Competitive Outcomes After Ulnar Collateral Ligament Reconstruction Among Baseball Players: A Systematic Review

Background: Ulnar collateral ligament (UCL) reconstruction (UCLR) is very common in baseball. However, no review has compared the return-to-play (RTP) and in-game performance statistics of pitchers after primary and revision UCLR as well as of position players after UCLR. Purpose: To review, synthesize, and evaluate the published literature on outcomes after UCLR in baseball players to determine RTP and competitive outcomes among various populations of baseball players. Study Design: Systematic review; Level of evidence, 4. Methods: A literature search including studies between 1980 and November 4, 2019, was conducted for articles that included the following terms: ulnar collateral ligament, elbow, medial collateral ligament, Tommy John surgery, throwing athletes, baseball pitchers, biomechanics, and performance. To be included, studies must have evaluated baseball players at any level who underwent UCLR (primary or revision) and assessed RTP and/or competitive outcomes. Results: A total of 29 studies with relatively high methodological quality met the inclusion criteria. After primary UCLR, Major League Baseball (MLB) pitchers returned to play in 80% to 97% of cases in approximately 12 months; however, return to the same level of play (RTSP) was less frequent and took longer, with 67% to 87% of MLB pitchers returning in about 15 months. RTP rates for MLB pitchers after revision UCLR were slightly lower, ranging from 77% to 85%, while RTSP rates ranged from 55% to 78%. RTP rates for catchers (59%-80%) were generally lower than RTP rates for infielders (76%) and outfielders (89%). All studies found a decrease in pitching workloads after UCLR. Fastball usage may also decrease after UCLR. Changes in earned run average and walks plus hits per inning pitched were inconclusive. Conclusion: Pitchers returned to play after UCLR in approximately 12 months and generally took longer to return to their same level of play. Pitchers also returned to play less frequently after revision UCLR. After both primary and revision UCLR, professional pitchers experienced decreased workloads and potentially decreased fastball usage as well. Catchers may RTP after UCLR less frequently than pitchers, infielders, and outfielders possibly because of the frequency of throwing in the position. These results will help guide clinical decision making and patient education when treating UCL tears in baseball players

Observing the host galaxies of high-redshift quasars with JWST: predictions from the BLUETIDES simulation

The bright emission from high-redshift quasars completely conceals their host galaxies in the rest-frame ultraviolet/optical, with detection of the hosts in these wavelengths eluding even the Hubble Space Telescope (HST) using detailed point spread function (PSF) modelling techniques. In this study, we produce mock images of a sample of z = 7 quasars extracted from the BLUETIDES simulation, and apply Markov chain Monte Carlo-based PSF modelling to determine the detectability of their host galaxies with the James Webb Space Telescope (JWST). While no statistically significant detections are made with HST, we predict that at the same wavelengths and exposure times JWST NIRCam imaging will detect ∼ 50 per cent of quasar host galaxies. We investigate various observational strategies, and find that NIRCam wide-band imaging in the long-wavelength filters results in the highest fraction of successful quasar host detections, detecting > 80 per cent of the hosts of bright quasars in exposure times of 5 ks. Exposure times of > 5 ks are required to detect the majority of host galaxies in the NIRCam wide-band filters, however, even 10 ks exposures with MIRI result in < 30 per cent successful host detections. We find no significant trends between galaxy properties and their detectability. The PSF modelling can accurately recover the host magnitudes, radii, and spatial distribution of the larger scale emission, when accounting for the central core being contaminated by residual quasar flux. Care should be made when interpreting the host properties measured using PSF modelling

Autonomous Microbial Sampler (AMS), a device for the uncontaminated collection of multiple microbial samples from submarine hydrothermal vents and other aquatic environments

Author Posting. © Elsevier B.V., 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part I: Oceanographic Research Papers 53 (2006): 894-916, doi:10.1016/j.dsr.2006.01.009.An Autonomous Microbial Sampler (AMS) is described that will obtain uncontaminated and exogenous DNA-free microbial samples from most marine, fresh water and hydrothermal ecosystems. Sampling with the AMS may be conducted using manned submersibles, Remotely Operated Vehicles (ROVs), Autonomous Underwater Vehicles (AUVs), or when tethered to a hydrowire during hydrocast operations on research vessels. The modular device consists of a titanium nozzle for sampling in potentially hot environments (>350°C) and fluid-handling components for the collection of six independent filtered or unfiltered samples. An onboard microcomputer permits sampling to be controlled by the investigator, by external devices (e.g., AUV computer), or by internal programming. Temperature, volume pumped and other parameters are recorded during sampling. Complete protection of samples from microbial contamination was observed in tests simulating deployment of the AMS in coastal seawater, where the sampling nozzle was exposed to seawater containing 1x106 cells ml-1 of a red pigmented tracer organism, Serratia marinorubra. Field testing of the AMS at a hydrothermal vent field was successfully undertaken in 2000. Results of DNA destruction studies have revealed that exposure of samples of the Eukaryote Euglena and the bacterium S. marinorubra to 0.5 N sulfuric acid at 23°C for 1 hour was sufficient to remove Polymerase Chain Reaction (PCR) amplifiable DNA. Studies assessing the suitability of hydrogen peroxide as a sterilizing and DNA-destroying agent showed that 20 or 30% hydrogen peroxide sterilized samples of Serratia in 1 hr and destroyed the DNA of Serratia, in 3 hrs, but not 1 or 2 hrs. DNA AWAY™ killed Serratia and destroyed the DNA of both Serratia and the vent microbe (GB-D) of the genus Pyrococcus in 1 hour.This work was supported by a DOC/NOAA Small Business Innovative Research Award, Contract No. 50-DKNA-9-90116 awarded to McLane Research Laboratories, Inc. and (via subcontract) to the Woods Hole Oceanographic Institution. Some of the microbial testing work was also supported by the National Science Foundation, Grant No. IBN-0131557 and the Woods Hole Oceanographic Inst. Deep Ocean Exploration Institute Grant No. 25051131

Development of a biomarker for Geobacter activity and strain composition: Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)

Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes

Using [Ne V]/[Ne III] to Understand the Nature of Extreme-Ionization Galaxies

Spectroscopic studies of extreme-ionization galaxies (EIGs) are critical to our understanding of exotic systems throughout cosmic time. These EIGs exhibit spectral features requiring >54.42 eV photons: the energy needed to fully ionize helium into He2+ and emit He II recombination lines. They are likely key contributors to reionization, and they can also probe exotic stellar populations or accretion onto massive black holes. To facilitate the use of EIGs as probes of high ionization, we focus on ratios constructed from strong rest-frame UV/optical emission lines, specifically [O III] 5008, H-beta, [Ne III] 3870, [O II] 3727,3729, and [Ne V] 3427. These lines probe the relative intensity at energies of 35.12, 13.62, 40.96, 13.62 eV, and 97.12, respectively, covering a wider range of ionization than traced by other common rest-frame UV/optical techniques. We use ratios of these lines ([Ne V]/[Ne III] = Ne53 and [Ne III]/[O II]), which are closely separated in wavelength, and mitigates effects of dust attenuation and uncertainties in flux calibration. We make predictions from photoionization models constructed from Cloudy that use a broad range of stellar populations and black hole accretion models to explore the sensitivity of these line ratios to changes in the ionizing spectrum. We compare our models to observations from the Hubble Space Telescope and James Webb Space Telescope of galaxies with strong high-ionization emission lines at z ~ 0, z ~ 2, and z ~ 7. We show that the Ne53 ratio can separate galaxies with ionization from 'normal' stellar populations from those with AGN and even 'exotic' Population III models. We introduce new selection methods to identify galaxies with photoionization driven by Population III stars or intermediate-mass black hole accretion disks that could be identified in upcoming high-redshift spectroscopic surveys.Comment: 16 pages, 5 figures, 1 table. Accepted in Ap