Ernest Haskell (1876-1925): A Retrospective Exhibition: A Portfolio of Selected Work

Composition and printing by The Anthoensen Press, Portland, Maine.https://digitalcommons.bowdoin.edu/art-museum-exhibition-catalogs/1045/thumbnail.jp

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with arXiv:1103.434

Secular trends in pediatric antiretroviral treatment programs in rural and urban Zambia: a retrospective cohort study

<p>Abstract</p> <p>Background</p> <p>Since 2003 pediatric antiretroviral treatment (ART) programs have scaled-up in sub-Saharan Africa and should be evaluated to assess progress and identify areas for improvement. We evaluated secular trends in the characteristics and treatment outcomes of children in three pediatric ART clinics in urban and rural areas in Zambia.</p> <p>Methods</p> <p>Routinely collected data were analyzed from three ART programs in rural (Macha and Mukinge) and urban (Lusaka) Zambia between program implementation and July 2008. Data were obtained from electronic medical record systems and medical record abstraction, and were categorized by year of program implementation. Characteristics of all HIV-infected and exposed children enrolled in the programs and all children initiating treatment were compared by year of implementation.</p> <p>Results</p> <p>Age decreased and immunologic characteristics improved in all groups over time in both urban and rural clinics, with greater improvement observed in the rural clinics. Among children both eligible and ineligible for ART at clinic enrollment, the majority started treatment within a year. A high proportion of children, particularly those ineligible for ART at clinic enrollment, were lost to follow-up prior to initiating ART. Among children initiating ART, clinical and immunologic outcomes after six months of treatment improved in both urban and rural clinics. In the urban clinics, mortality after six months of treatment declined with program duration, and in the rural clinics, the proportion of children defaulting by six months increased with program duration.</p> <p>Conclusions</p> <p>Treatment programs are showing signs of progress in the care of HIV-infected children, particularly in the rural clinics where scale-up increased rapidly over the first three years of program implementation. However, continued efforts to optimize care are needed as many children continue to enroll in ART programs at a late stage of disease and thus are not receiving the full benefits of treatment.</p

Crop Updates 2005 Oilseeds

This session covers fifteen papers from different authors: 1. ACKNOWLEDGEMENTS, Douglas Hamilton, FARMING SYSTEMS DEVELOPMENT OFFICER CROP AGRONOMY AND NUTRITION 2. Canola workshop at Crop Updates 2005, Oilseeds WA, John Duff, EXECUTIVE OFFICER OILSEEDS WA 3. Comparison of IT and TT canola varieties in geographic zones of WA, 2003-4, Graham Walton and Hasan Zaheer, Department of Agriculture 4. Farmer scale canola variety trials in WA, 2004, Graham Walton, John Duff, Neil Harris and Heather Cosgriff, Oilseeds WA 5. Oilseed crops for industrial uses, Margaret C. Campbell, Centre for Legumes in Mediterranean Agriculture (CLIMA), Graham Walton,Department of Agriculture 6. Weed control opportunities with GM canola, Bill Crabtree, Independent Consultant, Northam 7. Soil and tissue tests for the sulfur requirements of canola, R.F. Brennan and M.D.A. Bolland, Department of Agriculture 8. Tests to predict the potassium requirements of canola, R.F. Brennan and M.D.A. Bolland, Department of Agriculture 9. Genotypic variation in potassium efficiency of canola, P.M. Damon and Z. Rengel, Faculty of Natural and Agricultural Sciences, UWA 10. Atrazine contamination of groundwater in the agricultural region of Western Australia, Russell Speed1, Neil Rothnie2, John Simons1, Ted Spadek2 and John Moore1;1Department of Agriculture, 2Chemistry Centre (WA) PESTS AND DISEASES 11. Controlling aphids and Beet western yellows virus in canola using imidacloprid seed dressing, Brenda Coutts and Roger Jones; Department of Agriculture 12. Managing sclerotinia in canola, Neil Harris, Dovuro Seeds Western Australia 13. Slugs, the trail of destruction in canola, Neil Harris, Dovuro Seeds Western Australia 14. Blackleg risk assessment and strategies for risk management in canola during 2005 and beyond, Moin Salam, Ravjit Khanguraand Art Diggle, Department of Agriculture 15. Modelling: BRAT – Blackleg Risk Appraisal Tool, Moin Salam, Ravjit KhanguraDepartment of Agricultur

MFA15 (MFA 2015)

Catalogue of a culminating student exhibition held at the Mildred Lane Kemper Art Museum, May 1 - August 2, 2015 . Introduction / Heather Corcoran and Patricia Olynyk -- Diana Casanova / Emily J. Hanson -- Andrea M. Coates : in the operating theater / Stephanie Dering -- Margaux Crump -- Brandon Daniels -- Addoley Dzegede : do you prefer answers or truth? / Aaron Coleman -- Vita Eruhimovitz -- Carling Hale -- Amanda Helman -- Mike Helms / Ming Ying Hong -- Ming Ying Hong / Emily J. Hanson -- Sea A Joung / Ervin Malakaj -- Stephanie Kang / Jeremy Shipley -- Dayna Jean Kriz / Andrew Johnson -- Thomas Moore : you should move to the city / Nathaniel Rosenthalis -- Jacob Muldowney -- Laurel Panella / Garrett Clough -- Caitlin Penny -- On the bridge, between Juarez and El Paso / Eric Lyle Schultz -- Jeremy Shipley -- Emmeline Solomon -- Kellie Spano / Margaux Crump -- Michael Aaron Williams -- Austin R. Wolf : monumental labor / Adam Turl.https://openscholarship.wustl.edu/books/1015/thumbnail.jp

Crop Updates 2009 - Weeds

This session covers twenty three papers from different authors: Herbicides 1. New pre-seeding grass selective herbicides – How well do they work in zero or no-till systems? Dr Catherine Borgerand Dr Abul Hashem, Department of Agriculture and Food 2. Velocity®—An alternate mode of action for the control of wild radish in cereals, Mike Clarke, Bayer Cropscience Pty Ltd, Dr Aik Cheam, Department of Agriculture and Food, Dr Michael Walsh, WAHRI, University of Western Australia 3. Herbicide tolerance of new barley varieties, Harmohinder Dhammu, Vince Lambert, Chris Roberts and Russell Quartermaine, Department of Agriculture and Food 4. Herbicide tolerance of Desi chickpea – influence of seeding depth and rainfall, Harmohinder Dhammu, and David Nicholson, Department of Agriculture and Food 5. Herbicide tolerance of new wheat varieties, Harmohinder Dhammu, and David Nicholson, Department of Agriculture and Food 6. PARAGON plus Bromicide 200: a triple mode-of-action approach to combating wild radish, Raphanus raphanistrum, Mike Jackson and Bill Campbell, Nufarm Australia Limited 7. Interaction of glyphosate dose, annual ryegrass growth stage and environmental conditions on the performance of glyphosate for control of annual ryegrass, John Moore, Abul Hashem, Mario D’Antuono, Paul Matson and Dave Nicholson, Department of Agriculture and Food 8. Metribuzin pre-sowing of lupins, Peter Newman, Department of Agriculture and Food 9. Wild radish herbicides - you get what you pay for, Peter Newman, Department of Agriculture and Food 10. Glyphosate-the consequences of cutting rates, Sally Peltzer and Dave Minkey, Department of Agriculture and Food, and Australian Herbicide Resistance Initiative 11. Reasons to use only the full label herbicide rate, Stephen B Powles, Qin Yu, Mechelle Owen, Roberto Busi and Sudheesh Manalil, WA Herbicide Resistance Initiative, School of Plant Biology, University of Western Australia 12. Mandelup has reasonable tolerance to atrazine, Leigh Smith and Peter White, Department of Agriculture and Food Herbicide resistance 13. Risk of glyphosate resistance in wide-row lupin cropping systems, Fiona Evans, Abul Hashem and Art Diggle, Department of Agriculture and Food 14. More glyphosate-resistant annual ryegrass populations within Western Australia, Dr Abul Hashem and Dr Catherine Borger, Department of Agriculture and Food 15. Western Australian farmers are sowing herbicide-resistant weed seed into their cropping paddocks! Mechelle Owen1, Pippa Michael2and Stephen Powles1, 1WA Herbicide Resistance Initiative, School of Plant Biology, University of Western Australia, 2Muresk Institute, Curtin University of Technology Integrated Weed Management 16. Inversion ploughing: Effects of long-term deep burial on weed seed reserves, Aik Cheam and Siew Lee, Department of Agriculture and Food 17. How long cam wild radish seeds survive in the soil? Aik Cheam and Siew Lee, Department of Agriculture and Food 18. An economic comparison of IWM tools, Rob Grima, Department of Agriculture and Food 19. Emerging weeds in changing farming systems, Dr Abul Hashem, Department of Agriculture and Food 20. Eight years of IWM smashes ryegrass seed banks by 98 per cent over 31 focus paddocks, Peter Newman, Glenn Adam and Trevor Bell, Department of Agriculture and Food 21. Mouldboard plough - the answer to all the problems with sandplain farming! Peter Newman and Steve Davies, Department of Agriculture and Food 22. Flaxleaf fleabane - coming to a property near you! Sally Peltzer, Department of Agriculture and Food, 23. Trimming weed seed heads and crop-topping reduce seed bank of wild radish, Glen Riethmuller and Abul Hashem, Department of Agriculture and Foo

12-month mortality and loss-to-program in antiretroviral-treated children: The IeDEA pediatric West African Database to evaluate AIDS (pWADA), 2000-2008

<p>Abstract</p> <p>Background</p> <p>The IeDEA West Africa Pediatric Working Group (pWADA) was established in January 2007 to study the care and treatment of HIV-infected children in this region. We describe here the characteristics at antiretroviral treatment (ART) initiation and study the 12-month mortality and loss-to-program of HIV-infected children followed in ART programs in West Africa.</p> <p>Methods</p> <p>Standardized data from HIV-infected children followed-up in ART programs were included. Nine clinical centers from six countries contributed to the dataset (Benin, Côte d'Ivoire, Gambia, Ghana, Mali and Senegal). Inclusion criteria were the followings: age 0-15 years and initiated triple antiretroviral drug regimens. Baseline time was the date of ART initiation. WHO criteria was used to define severe immunosuppression based on CD4 count by age or CD4 percent < 15%. We estimated the 12-month Kaplan-Meier probabilities of mortality and loss-to-program (death or loss to follow-up > 6 months) after ART initiation and factors associated with these two outcomes.</p> <p>Results</p> <p>Between June 2000 and December 2007, 2170 children were included. Characteristics at ART initiation were the following: median age of 5 years (Interquartile range (IQR: 2-9) and median CD4 percentage of 13% (IQR: 7-19). The most frequent drug regimen consisted of two nucleoside reverse transcriptase inhibitors and one non-nucleoside reverse transcriptase inhibitors (62%). During the first 12 months, 169 (7.8%) children died and 461(21.2%) were lost-to-program. Overall, in HIV-infected children on ART, the 12-month probability of death was 8.3% (95% Confidence Interval (CI): 7.2-9.6%), and of loss-to-program was 23.1% (95% CI: 21.3-25.0%). Both mortality and loss-to program were associated with advanced clinical stage, CD4 percentage < 15% at ART initiation and year (> 2005) of ART initiation.</p> <p>Conclusion</p> <p>Innovative and sustainable approaches are needed to better document causes of death and increase retention in HIV pediatric clinics in West Africa.</p

Accuracy and precision in quantitative fluorescence microscopy

The light microscope has long been used to document the localization of fluorescent molecules in cell biology research. With advances in digital cameras and the discovery and development of genetically encoded fluorophores, there has been a huge increase in the use of fluorescence microscopy to quantify spatial and temporal measurements of fluorescent molecules in biological specimens. Whether simply comparing the relative intensities of two fluorescent specimens, or using advanced techniques like Förster resonance energy transfer (FRET) or fluorescence recovery after photobleaching (FRAP), quantitation of fluorescence requires a thorough understanding of the limitations of and proper use of the different components of the imaging system. Here, I focus on the parameters of digital image acquisition that affect the accuracy and precision of quantitative fluorescence microscopy measurements

Factors associated with paradoxical immune response to antiretroviral therapy in HIV infected patients: a case control study

<p>Abstract</p> <p>Background</p> <p>A paradoxical immunologic response (PIR) to Highly Active Antiretroviral Therapy (HAART), defined as viral suppression without CD4 cell-count improvement, has been reported in the literature as 8 to 42%, around 15% in most instances. The present study aims to determine, in a cohort of HIV infected patients in Brazil, what factors were independently associated with such a discordant response to HAART.</p> <p>Methods</p> <p>A case-control study (1:4) matched by gender was conducted among 934 HIV infected patients on HAART in Brazil. Cases: patients with PIR, defined as CD4 < 350 cells/mm³(hazard ratio for AIDS or death of at least 8.5) and undetectable HIV viral load on HAART for at least one year. Controls: similar to cases, but with CD4 counts ≥ 350 cells/mm³. Eligibility criteria were applied. Data were collected from medical records using a standardized form. Variables were introduced in a hierarchical logistic regression model if a p-value < 0.1 was determined in a bivariate analysis.</p> <p>Results</p> <p>Among 934 patients, 39 cases and 160 controls were consecutively selected. Factors associated with PIR in the logistic regression model were: total time in use of HAART (OR 0.981; CI 95%: 0.96-0.99), nadir CD4-count (OR 0.985; CI 95%: 0.97-0.99), and time of undetectable HIV viral load (OR 0.969; CI 95%: 0.94-0.99).</p> <p>Conclusions</p> <p>PIR seems to be related to a delay in the management of immunodeficient patients, as shown by its negative association with nadir CD4-count. Strategies should be implemented to avoid such a delay and improve the adherence to HAART as a way to implement concordant responses.</p