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Bioengineering

Paul D. Cotter
2012 Bioengineered  
Figure 3 . 3 Dr paul Cotter.  ...  About Dr Paul Cotter Dr Paul Cotter (Fig. 3) , "self-cloning" means the removal of nucleic acid from a cell or organism, followed by the re-insertion of all or part of that nucleic acid-with or without  ... 
doi:10.4161/bioe.21601 pmid:22922299 pmcid:PMC3489705 fatcat:voelxwvywvddhibpp47jcatspe

Ensemble Transport Adaptive Importance Sampling [article]

Colin Cotter, Simon Cotter, Paul Russell
2019 arXiv   pre-print
Markov chain Monte Carlo methods are a powerful and commonly used family of numerical methods for sampling from complex probability distributions. As applications of these methods increase in size and complexity, the need for efficient methods increases. In this paper, we present a particle ensemble algorithm. At each iteration, an importance sampling proposal distribution is formed using an ensemble of particles. A stratified sample is taken from this distribution and weighted under the
more » ... or, a state-of-the-art ensemble transport resampling method is then used to create an evenly weighted sample ready for the next iteration. We demonstrate that this ensemble transport adaptive importance sampling (ETAIS) method outperforms MCMC methods with equivalent proposal distributions for low dimensional problems, and in fact shows better than linear improvements in convergence rates with respect to the number of ensemble members. We also introduce a new resampling strategy, multinomial transformation (MT), which while not as accurate as the ensemble transport resampler, is substantially less costly for large ensemble sizes, and can then be used in conjunction with ETAIS for complex problems. We also focus on how algorithmic parameters regarding the mixture proposal can be quickly tuned to optimise performance. In particular, we demonstrate this methodology's superior sampling for multimodal problems, such as those arising from inference for mixture models, and for problems with expensive likelihoods requiring the solution of a differential equation, for which speed-ups of orders of magnitude are demonstrated. Likelihood evaluations of the ensemble could be computed in a distributed manner, suggesting that this methodology is a good candidate for parallel Bayesian computations.
arXiv:1508.01132v4 fatcat:ptdlgxfuvrcypllamzwdaakcwe

Bioengineering of the model lantibiotic nisin

Des Field, Paul D Cotter, R Paul Ross, Colin Hill
2015 Bioengineered  
doi:10.1080/21655979.2015.1049781 pmid:25970137 pmcid:PMC4601270 fatcat:arkwcymyufev5fnyyjxzdwpr7a

Lantibiotic Resistance

Lorraine A. Draper, Paul D. Cotter, Colin Hill, R. Paul Ross
2015 Microbiology and Molecular Biology Reviews  
doi:10.1128/mmbr.00051-14 pmid:25787977 pmcid:PMC4394878 fatcat:kojtqeulerddfap7ryyxmhoxqm

Hours of Labor.Lazare TeperShorter Hours: A Study of the Movement Since the Civil War.Marion Cotter Cahill

Paul H. Douglas
1933 American Journal of Sociology  
By Marion Cotter CAHILL. New York: Columbia University Press, 1932. Pp. 300. $4.50. These two workman-like studies of the movement toward shorter hours admirably complement each other. Dr.  ... 
doi:10.1086/216461 fatcat:w2tjsqo55fendm4fijtnpu37ue

Beneficial modulation of the gut microbiota

Calum J. Walsh, Caitriona M. Guinane, Paul W. O'Toole, Paul D. Cotter
2014 FEBS Letters  
this 376 damage has recently become more evident through the application of high throughput DNA-based 377 sequencing technologies to assess the composition of gut microbial populations (for review see Cotter  ... 
doi:10.1016/j.febslet.2014.03.035 pmid:24681100 fatcat:zgssv2i23rg6hb56hptrpdfzy4

Bacteriocin Production: a Probiotic Trait?

Alleson Dobson, Paul D. Cotter, R. Paul Ross, Colin Hill
2011 Applied and Environmental Microbiology  
ABSTRACTBacteriocins are an abundant and diverse group of ribosomally synthesized antimicrobial peptides produced by bacteria and archaea. Traditionally, bacteriocin production has been considered an important trait in the selection of probiotic strains, but until recently, few studies have definitively demonstrated the impact of bacteriocin production on the ability of a strain to compete within complex microbial communities and/or positively influence the health of the host. Although research
more » ... in this area is still in its infancy, there is intriguing evidence to suggest that bacteriocins may function in a number of ways within the gastrointestinal tract. Bacteriocins may facilitate the introduction of a producer into an established niche, directly inhibit the invasion of competing strains or pathogens, or modulate the composition of the microbiota and influence the host immune system. Here we review the role of bacteriocin production in complex microbial communities and their potential to enhance human health.
doi:10.1128/aem.05576-11 pmid:22038602 pmcid:PMC3255625 fatcat:jz7jp2h5dzdv7d27nft76buimq

Surfing the Digital Wave [chapter]

Barry Smyth, Paul Cotter
1999 Lecture Notes in Computer Science  
In the future digital TV will offer an unprecedented level of programme choice. We are told that this will lead to dramatic increases in viewer satisfaction as all viewing tastes are catered for all of the time. However, the reality may be somewhat different. We have not yet developed the tools to deal with this increased level of choice (for example, conventional TV guides will be virtually useless), and viewers will face a significant and frustrating information overload problem. This paper
more » ... scribes a solution in the form of the PTV system. PTV employs user profiling and information filtering techniques to generate web-based TV viewing guides that are personalised for the viewing preferences of individual users. The paper explains how PTV constructs graded user profiles to drive a hybrid recommendation technique, combining case-based and collaborative information filtering methods. The results of an extensive empirical study to evaluate the quality of PTV's casebased and collaborative filtering strategies are also described.
doi:10.1007/3-540-48508-2_41 fatcat:km3asy5yzveyvdehffo7bkya3u

Bacteriocin production: a relatively unharnessed probiotic trait?

James W. Hegarty, Caitriona M. Guinane, R. Paul Ross, Colin Hill, Paul D. Cotter
2016 F1000Research  
Cotter PD, Ross RP, Hill C: Bacteriocins -a viable alternative to antibiotics? Nat Rev Microbiol. 2013; 11(2): 95-105. PubMed Abstract | Publisher Full Text 7.  ...  Murphy EF, Cotter PD, Hogan A, et al.: Divergent metabolic outcomes arising from targeted manipulation of the gut microbiota in diet-induced obesity. Gut. 2013; 62(2): 220-6.  ... 
doi:10.12688/f1000research.9615.1 pmid:27853525 pmcid:PMC5089130 fatcat:iyjfvvcjz5ht5lzg54krhqxgbi

Atypical hemograms of the commercial duck

Paul F. Cotter
2021 Poultry Science  
HV and eosinophils were scarce in this study (Cotter, personal observation) so that descriptions will be reserved to occasions when they are more frequent. (Cotter and Bakst, 2017) .  ...  Atypical cells of all classes were detected in commercial hens (Cotter, 2015a, b) and specific pathogen free chicks (Cotter and Heller, 2016) whose H/L ratios were at non-stress levels with normal  ... 
doi:10.1016/j.psj.2021.101248 pmid:34225201 fatcat:7rdllgp2ivh6paem5myufimo2y

Composition of the early intestinal microbiota

Fiona Fouhy, R. Paul Ross, Gerald F. Fitzgerald, Catherine Stanton, Paul D. Cotter
2012 Gut microbes  
doi:10.4161/gmic.20169 pmid:22572829 pmcid:PMC3427213 fatcat:7u7xqjafvnecpefzsqw5iboaqq

Metabolic phenotyping of the human microbiome

Wiley Barton, Orla O'Sullivan, Paul D. Cotter
2019 F1000Research  
Huseyin CE, O'Toole PW, Cotter PD, et al.: Forgotten fungi-the gut mycobiome in human health and disease. FEMS Microbiol Rev. 2017; 41(4): 479-511.  ... 
doi:10.12688/f1000research.19481.1 pmid:31824656 pmcid:PMC6880276 fatcat:t5tx5ong3ja2zgc4rebr5pcqy4

Antimicrobials

Eileen F. Murphy, Siobhan F. Clarke, Tatiana M. Marques, Colin Hill, Catherine Stanton, R. Paul Ross, Robert M. O'Doherty, Fergus Shanahan, Paul D. Cotter
2013 Gut microbes  
Paul Ross, 2, 3 Robert M. O'Doherty, 4 Fergus Shanahan 2,6, * and Paul D.  ...  Cotter 1 and has been repeatedly shown to be associated with a higher risk of mortality. 2 The relatively recent discovery that the composition and metabolic activity of the gut microbiota may affect  ... 
doi:10.4161/gmic.22328 pmid:23018760 pmcid:PMC3555886 fatcat:uv5xhxxaprfm5h7epohz5mxc4q

The potential for emerging therapeutic options forClostridium difficileinfection

Harsh Mathur, Mary C Rea, Paul D Cotter, R Paul Ross, Colin Hill
2014 Gut microbes  
doi:10.4161/19490976.2014.983768 pmid:25564777 pmcid:PMC4615897 fatcat:uap5xvhjtjbfjedwra7kisixry

Plasmacyte Heterogeneity of Lame Ducklings

Paul F. Cotter
2022 Journal of Immunological Sciences  
The aim is to describe the array of plasmacytes (PC), cells known as the source of antibody, occurring in the bone marrow (BM) of lame ducklings. The method is by a light microscopic examination of touch preparation slides made from femur samples and stained with Wright-Giemsa. Samples were obtained on site at commercial farms where slide preparations were made; reducing the possibility that observations are technical artifacts. The results: indicate that PC occur in a multitude of sizes,
more » ... , nuclear/cytoplasmic (N/C) ratios, ploidy, and nuclear and cytoplasmic conditions. Normal PC are illustrated first, followed by atypical forms. Some PC are presented in the context of neighboring BM cells of the granulocyte, erythrocyte, and reticulum cell (histiocyte) series. More than 100 Mott-type PC were measured in a single sample from a 13-day lame duck; and several distinct forms were identified. Size, as measured by their longest axis, varied from 6.1 to 28 μm and it appears to be normally distributed. Moreover, N/C ratios were distributed across a three-fold range (0.3 – 0.9) indicating Mott phenotypes can occur at multiple developmental stages. Motts differed in Russell Body (RB) size, and nuclear condition. A novel Mott type, "orb" form, with partially lysed nuclei is also described. PC were often found in association with giant granulated histiocytes (ggh) and non-granulated giant histiocytes (gh). Other atypical forms are "hand-mirror" PC, trinucleate and binucleate PC resembling cells seen in multiple myeloma (MM) and lymphomas. Collectively these PC variants constitute "reactive plasmatosis" (RP) likely arising as a consequence of the presence of various bacteria including Streptococcus and E. coli. The conclusions: It is demonstrated that RP as occurs in lame ducklings suffering from bacterial infections, provides a unique theater for the study of PC variability. Atypical PC, some resembling neoplastic types, were common in RP BM. The significance of the study relates to the importance of PC in disease and immunity; therefore, these observations should interest those who specialize in these areas. They expand the knowledge of avian plasmacyte morphology.
doi:10.29245/2578-3009/2022/1.1225 fatcat:so6gdosibvbhtc3quj6pqhe4ly
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