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Search Results: 1 - 10 of 152253 matches for " Joe H. Harrison "
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Comparison of Raw Dairy Manure Slurry and Anaerobically Digested Slurry as N Sources for Grass Forage Production
Olivia E. Saunders,Ann-Marie Fortuna,Joe H. Harrison,Elizabeth Whitefield,Craig G. Cogger,Ann C. Kennedy,Andy I. Bary
International Journal of Agronomy , 2012, DOI: 10.1155/2012/101074
Abstract: We conducted a 3-year field study to determine how raw dairy slurry and anaerobically digested slurry (dairy slurry and food waste) applied via broadcast and subsurface deposition to reed canarygrass (Phalaris arundinacea) affected forage biomass, N uptake, apparent nitrogen recovery (ANR), and soil nitrate concentrations relative to urea. Annual N applications ranged from 600?kg?N?ha?1 in 2009 to 300?kg?N?ha?1 in 2011. Forage yield and N uptake were similar across slurry treatments. Soil nitrate concentrations were greatest at the beginning of the fall leaching season, and did not differ among slurry treatments or application methods. Urea-fertilized plots had the highest soil nitrate concentrations but did not consistently have greatest forage biomass. ANR for the slurry treatments ranged from 35 to 70% when calculations were based on ammonium-N concentration, compared with 31 to 65% for urea. Slurry ANR calculated on a total N basis was lower (15 to 40%) due to lower availability of the organic N in the slurries. No consistent differences in soil microbial biomass or other biological indicators were observed. Anaerobically digested slurry supported equal forage production and similar N use efficiency when compared to raw dairy slurry. 1. Introduction There is a need for a set of best management practices that addresses how to utilize the growing quantity of reactive nitrogen (N) produced by livestock operations. Animal agriculture in the United States has become more specialized with farms consolidating and growing in size [1]. The number of dairy farms has decreased by 94% since 1960, but the number of animals has remained constant [2]. Animal consolidation has created challenges with respect to on-farm N surplus, waste management and nutrient loading in the environment [3, 4]. Annually in the United States, more than 5800?Mg of manure N is produced [5]. One approach to ameliorate negative environmental impacts associated with animal manures is through adoption of anaerobic digestion technologies to treat farm-generated manures and food processing wastes [6–9]. Digestion of wastes can provide a stable and consistent source of nutrients comparable to inorganic fertilizers such as urea. Anaerobic digestion converts organic carbon into methane used to generate electricity, and it also converts organic N to plant available ammonium ( ), increasing the ratio of /total N in the effluent [10]. Carbon is removed during both the methane production and fiber removal processes, resulting in a smaller C?:?N ratio of the effluent [11]. Therefore, digested
ChIP-Seq and RNA-Seq Reveal an AmrZ-Mediated Mechanism for Cyclic di-GMP Synthesis and Biofilm Development by Pseudomonas aeruginosa
Christopher J. Jones,David Newsom,Benjamin Kelly,Yasuhiko Irie,Laura K. Jennings,Binjie Xu,Dominique H. Limoli,Joe J. Harrison,Matthew R. Parsek,Peter White,Daniel J. Wozniak
PLOS Pathogens , 2014, DOI: doi/10.1371/journal.ppat.1003984
Abstract: The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression of gene(s) encoding a DGC. In support of this, we observed elevated c-di-GMP in the ΔamrZ mutant compared to the wild type strain. Consistent with other strains that accumulate c-di-GMP, when grown as a biofilm, the ΔamrZ mutant formed larger microcolonies than the wild-type strain. This enhanced biofilm formation was abrogated by expression of a PDE. To identify potential target DGCs, a ChIP-Seq was performed and identified regions of the genome that are bound by AmrZ. RNA-Seq experiments revealed the entire AmrZ regulon, and characterized AmrZ as an activator or repressor at each binding site. We identified an AmrZ-repressed DGC-encoding gene (PA4843) from this cohort, which we named AmrZ dependent cyclase A (adcA). PAO1 overexpressing adcA accumulates 29-fold more c-di-GMP than the wild type strain, confirming the cyclase activity of AdcA. In biofilm reactors, a ΔamrZ ΔadcA double mutant formed smaller microcolonies than the single ΔamrZ mutant, indicating adcA is responsible for the hyper biofilm phenotype of the ΔamrZ mutant. This study combined the techniques of ChIP-Seq and RNA-Seq to define the comprehensive regulon of a bifunctional transcriptional regulator. Moreover, we identified a c-di-GMP mediated mechanism for AmrZ regulation of biofilm formation and chronicity.
High-throughput metal susceptibility testing of microbial biofilms
Joe J Harrison, Raymond J Turner, Howard Ceri
BMC Microbiology , 2005, DOI: 10.1186/1471-2180-5-53
Abstract: This high-throughput method generated 96-statistically equivalent biofilms in a single device and thus allowed for comparative and combinatorial experiments of media, microbial strains, exposure times and metals. By adjusting growth conditions, it was possible to examine biofilms of different microorganisms that had similar cell densities. In one example, Pseudomonas aeruginosa ATCC 27853 was up to 80 times more resistant to heavy metalloid oxyanions than Escherichia coli TG1. Further, biofilms were up to 133 times more tolerant to tellurite (TeO32-) than corresponding planktonic cultures. Regardless of the growth medium, the tolerance of biofilm and planktonic cell E. coli JM109 to metals was time-dependent.This method results in accurate, easily reproducible comparisons between the susceptibility of planktonic cells and biofilms to metals. Further, it was possible to make direct comparisons of the ability of different microbial strains to withstand metal toxicity. The data presented here also indicate that exposure time is an important variable in metal susceptibility testing of bacteria.Determination of the minimum inhibitory concentration (MIC), based on antimicrobial activity against planktonic organisms, is the standard assay for susceptibility testing. Biofilms, which present with distinct physiology compared to planktonic cells, are infamous for their ability to withstand a wide range of antimicrobials, including metals [1-4]. Despite the ubiquitous distribution of metals and the predominance of microbial biofilms in the environment and in device-associated infections, very few studies have comparatively examined biofilm susceptibility to metals relative to planktonic cells. The scarcity of data in this regard may be attributable to the existing methods used to grow biofilms, which typically include contamination prone flow systems. Metal susceptibility testing also entails challenges not encountered with antibiotics. This includes complexation of metals wit
Solutions To Lipschitz Variational Problems With Cohomological Spanning Conditions
J. Harrison,H. Pugh
Mathematics , 2015,
Abstract: We prove existence and regularity of minimizers for Lipschitz integrands over general surfaces of arbitrary dimension and codimension in \( \R^n \), satisfying a cohomological boundary condition. Our result specializes to a version of Plateau's problem in the case of a constant integrand. We generalize and extend methods of Reifenberg, Besicovitch, and Adams; in particular, we prove an asymptotic monotonicity result (density exists in the absence of true monotonicity,) we generalize a type of minimizing sequence used by Reifenberg (whose limits have nice properties, including lower bounds on lower density and finite Hausdorff measure,) and develop cohomological spanning conditions.
Pelvic Mass 21 Years after Total Hip Arthroplasty
Joe Miller,Thomas H. Tarter
Case Reports in Urology , 2013, DOI: 10.1155/2013/424319
Abstract: Background. Long-term urologic complications after total hip arthroplasty are rare, and reports in the urologic literature are scant. We present a recent case and review the relevant literature. Case. A 77-year-old man was referred to the urology clinic for a single episode of gross painless hematuria, abnormal urine cytology, and pelvic mass. He had a significant smoking history. Surgical history included right total hip arthroplasty 21 years prior. Results. Pelvic ultrasound revealed a large mass abutting the right bladder wall. Subsequent computed tomography indicated that the mass was extrinsic to the bladder. Results of computed tomography-guided biopsy of the mass were consistent with foreign body granuloma. Surveillance imaging confirmed no growth or progression, and intervention was deferred. Conclusion. Long-term complications of total hip arthroplasty may present with signs and symptoms of urologic disease. Reports in the urologic literature are rare. 1. Introduction Urinary retention and urinary tract infection are common postoperative complications after total hip arthroplasty (THA) but long-term urologic complications are rare. We report a case of a patient with a history of THA referred for hematuria, abnormal urine cytology, and a pelvic mass and present a review of the relevant literature. 2. Case Report A 77-year-old man was referred to the urology clinic for evaluation of a single episode of gross painless hematuria, abnormal urine cytology, and pelvic mass. The patient had a previous 30 pack-year smoking history but had quit 12 years prior. His past medical history was significant for hypertension, hyperlipidemia, and gout. His past surgical history included right THA 21 years prior, with revision 10 years prior to referral. On presentation, he denied abdominal or pelvic pain, dysuria, or further episodes of gross hematuria. Physical exam was normal. Repeat voided urine cytology was negative for malignant cells. Pelvic ultrasound showed an extrinsic mass adjacent to the right bladder wall (Figure 1). Review of the subsequent computed tomography (CT) of the abdomen and pelvis revealed a 5.7 × 4.6?cm mass in the right pelvis causing mass-effect distortion of the bladder. No invasion of the bladder wall was evident (Figure 2). A CT-guided biopsy of the mass produced only acellular material. Cystoscopic examination revealed no evidence of urothelial tumor or lesion or foreign body intrusion. A follow-up CT performed at an interval of 3 months showed no change in the size or character of the mass, and observation was discontinued, with
Rate-optimal posterior contraction for sparse PCA
Chao Gao,Harrison H. Zhou
Statistics , 2013, DOI: 10.1214/14-AOS1268
Abstract: Principal component analysis (PCA) is possibly one of the most widely used statistical tools to recover a low-rank structure of the data. In the high-dimensional settings, the leading eigenvector of the sample covariance can be nearly orthogonal to the true eigenvector. A sparse structure is then commonly assumed along with a low rank structure. Recently, minimax estimation rates of sparse PCA were established under various interesting settings. On the other side, Bayesian methods are becoming more and more popular in high-dimensional estimation, but there is little work to connect frequentist properties and Bayesian methodologies for high-dimensional data analysis. In this paper, we propose a prior for the sparse PCA problem and analyze its theoretical properties. The prior adapts to both sparsity and rank. The posterior distribution is shown to contract to the truth at optimal minimax rates. In addition, a computationally efficient strategy for the rank-one case is discussed.
Discussion: Latent variable graphical model selection via convex optimization
Zhao Ren,Harrison H. Zhou
Statistics , 2012, DOI: 10.1214/12-AOS985
Abstract: Discussion of "Latent variable graphical model selection via convex optimization" by Venkat Chandrasekaran, Pablo A. Parrilo and Alan S. Willsky [arXiv:1008.1290].
Rate exact Bayesian adaptation with modified block priors
Chao Gao,Harrison H. Zhou
Statistics , 2013,
Abstract: A novel block prior is proposed for adaptive Bayesian estimation. The prior does not depend on the smoothness of the function or the sample size. It puts sufficient prior mass near the true signal and automatically concentrates on its effective dimension. A rate-optimal posterior contraction is obtained in a general framework, which includes density estimation, white noise model, Gaussian sequence model, Gaussian regression and spectral density estimation.
Bernstein-von Mises Theorems for Functionals of Covariance Matrix
Chao Gao,Harrison H. Zhou
Statistics , 2014,
Abstract: We provide a general theoretical framework to derive Bernstein-von Mises theorems for matrix functionals. The conditions on functionals and priors are explicit and easy to check. Results are obtained for various functionals including entries of covariance matrix, entries of precision matrix, quadratic forms, log-determinant, eigenvalues in the Bayesian Gaussian covariance/precision matrix estimation setting, as well as for Bayesian linear and quadratic discriminant analysis.
Bis[(3-chlorobenzyl)ammonium] 2-phenylpropanedioate dihydrate
Jerry Joe Ebow Kingsley Harrison,Robert Kingsford-Adaboh,Kazuma Gotoh,Hiroyuki Ishida
Acta Crystallographica Section E , 2010, DOI: 10.1107/s1600536810029764
Abstract: In the asymmetric unit of the title compound, 2C7H9ClN+·C9H6O42 ·2H2O, there are two crystallographically independent cations, one dianion and two water molecules. The dihedral angle between the two carboxylate groups of the dianion is 78.1 (2)°. In the crystal, the components are held together by N—H...O, O—H...O and C—H...O hydrogen bonds, forming a layer parallel to the bc plane, with the hydrophilic and hydrophobic groups located in the inner and outer regions of the layers, respectively.
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