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Compositional principal component analysis generates gut microbiota profiles that associate with children's diet and body composition
- Claudia Leong, Jillian J. Haszard, Anne-Louise M. Heath, Gerald W. Tannock, Blair Lawley, Sonya L. Cameron, Ewa A. Szymlek-Gay, Andrew R. Gray, Barry J. Taylor, Barbara C. Galland, Julie A. Lawrence, Anna Otal, Alan Hughes, Rachael W Taylor
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- Journal:
- Proceedings of the Nutrition Society / Volume 79 / Issue OCE2 / 2020
- Published online by Cambridge University Press:
- 10 June 2020, E284
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Gut microbiota data obtained by DNA sequencing are not only complex because of the number of taxa that may be detected within human cohorts, but also compositional because characteristics of the microbiota are described in relative terms (e.g., “relative abundance” of particular bacterial taxa expressed as a proportion of the total abundance of taxa). Nutrition researchers often use standard principal component analysis (PCA) to derive dietary patterns from complex food data, enabling each participant's diet to be described in terms of the extent to which it fits their cohort's dietary patterns. However, compositional PCA methods are not commonly used to describe patterns of microbiota in the way that dietary patterns are used to describe diets. This approach would be useful for identifying microbiota patterns that are associated with diet and body composition. The aim of this study is to use compositional PCA to describe gut microbiota profiles in 5 year old children and explore associations between microbiota profiles, diet, body mass index (BMI) z-score, and fat mass index (FMI) z-score. This study uses a cross-sectional data for 319 children who provided a faecal sample at 5 year of age. Their primary caregiver completed a 123-item quantitative food frequency questionnaire validated for foods of relevance to the gut microbiota. Body composition was determined using dual-energy x-ray absorptiometry, and BMI and FMI z-scores calculated. Compositional PCA identified and described gut microbiota profiles at the genus level, and profiles were examined in relation to diet and body size. Three gut microbiota profiles were found. Profile 1 (positive loadings on Blautia and Bifidobacterium; negative loadings on Bacteroides) was not related to diet or body size. Profile 2 (positive loadings on Bacteroides; negative loadings on uncultured Christensenellaceae and Ruminococcaceae) was associated with a lower BMI z-score (r = -0.16, P = 0.003). Profile 3 (positive loadings on Faecalibacterium, Eubacterium and Roseburia) was associated with higher intakes of fibre (r = 0.15, P = 0.007); total (r = 0.15, P = 0.009), and insoluble (r = 0.13, P = 0.021) non-starch polysaccharides; protein (r = 0.12, P = 0.036); meat (r = 0.15, P = 0.010); and nuts, seeds and legumes (r = 0.11, P = 0.047). Further regression analyses found that profile 2 and profile 3 were independently associated with BMI z-score and diet respectively. We encourage fellow researchers to use compositional PCA as a method for identifying further links between the gut, diet and obesity, and for developing the next generation of research in which the impact on body composition of dietary interventions that modify the gut microbiota is determined.
A National Spinal Muscular Atrophy Registry for Real-World Evidence
- Victoria L. Hodgkinson, Maryam Oskoui, Joshua Lounsberry, Saïd M’Dahoma, Emily Butler, Craig Campbell, Alex MacKenzie, Hugh J. McMillan, Louise Simard, Jiri Vajsar, Bernard Brais, Kristine M. Chapman, Nicolas Chrestian, Meghan Crone, Peter Dobrowolski, Susan Dojeiji, James J. Dowling, Nicolas Dupré, Angela Genge, Hernan Gonorazky, Simona Hasal, Aaron Izenberg, Wendy Johnston, Edward Leung, Hanns Lochmüller, Jean K. Mah, Alier Marerro, Rami Massie, Laura McAdam, Anna McCormick, Michel Melanson, Michelle M. Mezei, Cam-Tu E. Nguyen, Colleen O’Connell, Erin K. O’Ferrall, Gerald Pfeffer, Cecile Phan, Stephanie Plamondon, Chantal Poulin, Xavier Rodrigue, Kerri L. Schellenberg, Kathy Selby, Jordan Sheriko, Christen Shoesmith, Garth Smith, Monique Taillon, Sean Taylor, Jodi Warman Chardon, Scott Worley, Lawrence Korngut
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- Journal:
- Canadian Journal of Neurological Sciences / Volume 47 / Issue 6 / November 2020
- Published online by Cambridge University Press:
- 04 June 2020, pp. 810-815
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Background:
Spinal muscular atrophy (SMA) is a devastating rare disease that affects individuals regardless of ethnicity, gender, and age. The first-approved disease-modifying therapy for SMA, nusinursen, was approved by Health Canada, as well as by American and European regulatory agencies following positive clinical trial outcomes. The trials were conducted in a narrow pediatric population defined by age, severity, and genotype. Broad approval of therapy necessitates close follow-up of potential rare adverse events and effectiveness in the larger real-world population.
Methods:The Canadian Neuromuscular Disease Registry (CNDR) undertook an iterative multi-stakeholder process to expand the existing SMA dataset to capture items relevant to patient outcomes in a post-marketing environment. The CNDR SMA expanded registry is a longitudinal, prospective, observational study of patients with SMA in Canada designed to evaluate the safety and effectiveness of novel therapies and provide practical information unattainable in trials.
Results:The consensus expanded dataset includes items that address therapy effectiveness and safety and is collected in a multicenter, prospective, observational study, including SMA patients regardless of therapeutic status. The expanded dataset is aligned with global datasets to facilitate collaboration. Additionally, consensus dataset development aimed to standardize appropriate outcome measures across the network and broader Canadian community. Prospective outcome studies, data use, and analyses are independent of the funding partner.
Conclusion:Prospective outcome data collected will provide results on safety and effectiveness in a post-therapy approval era. These data are essential to inform improvements in care and access to therapy for all SMA patients.
Microbial Preparations (Probiotics) for the Prevention of Clostridium difficile Infection in Adults and Children: An Individual Patient Data Meta-analysis of 6,851 Participants
- Bradley C. Johnston, Lyubov Lytvyn, Calvin Ka-Fung Lo, Stephen J. Allen, Duolao Wang, Hania Szajewska, Mark Miller, Stephan Ehrhardt, John Sampalis, Deniz G. Duman, Pietro Pozzoni, Agostino Colli, Elisabet Lönnermark, Christian P. Selinger, Samford Wong, Susan Plummer, Mary Hickson, Ruzha Pancheva, Sandra Hirsch, Bengt Klarin, Joshua Z Goldenberg, Li Wang, Lawrence Mbuagbaw, Gary Foster, Anna Maw, Behnam Sadeghirad, Lehana Thabane, Dominik Mertz
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 39 / Issue 7 / July 2018
- Published online by Cambridge University Press:
- 26 April 2018, pp. 771-781
- Print publication:
- July 2018
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OBJECTIVE
To determine whether probiotic prophylaxes reduce the odds of Clostridium difficile infection (CDI) in adults and children.
DESIGNIndividual participant data (IPD) meta-analysis of randomized controlled trials (RCTs), adjusting for risk factors.
METHODSWe searched 6 databases and 11 grey literature sources from inception to April 2016. We identified 32 RCTs (n=8,713); among them, 18 RCTs provided IPD (n=6,851 participants) comparing probiotic prophylaxis to placebo or no treatment (standard care). One reviewer prepared the IPD, and 2 reviewers extracted data, rated study quality, and graded evidence quality.
RESULTSProbiotics reduced CDI odds in the unadjusted model (n=6,645; odds ratio [OR] 0.37; 95% confidence interval [CI], 0.25–0.55) and the adjusted model (n=5,074; OR, 0.35; 95% CI, 0.23–0.55). Using 2 or more antibiotics increased the odds of CDI (OR, 2.20; 95% CI, 1.11–4.37), whereas age, sex, hospitalization status, and high-risk antibiotic exposure did not. Adjusted subgroup analyses suggested that, compared to no probiotics, multispecies probiotics were more beneficial than single-species probiotics, as was using probiotics in clinical settings where the CDI risk is ≥5%. Of 18 studies, 14 reported adverse events. In 11 of these 14 studies, the adverse events were retained in the adjusted model. Odds for serious adverse events were similar for both groups in the unadjusted analyses (n=4,990; OR, 1.06; 95% CI, 0.89–1.26) and adjusted analyses (n=4,718; OR, 1.06; 95% CI, 0.89–1.28). Missing outcome data for CDI ranged from 0% to 25.8%. Our analyses were robust to a sensitivity analysis for missingness.
CONCLUSIONSModerate quality (ie, certainty) evidence suggests that probiotic prophylaxis may be a useful and safe CDI prevention strategy, particularly among participants taking 2 or more antibiotics and in hospital settings where the risk of CDI is ≥5%.
TRIAL REGISTRATIONPROSPERO 2015 identifier: CRD42015015701
Infect Control Hosp Epidemiol 2018;771–781
Notes on contributors
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- By Margaret Bent, Anna Maria Busse Berger, Lawrence F. Bernstein, Bonnie J. Blackburn, M. Jennifer Bloxam, Philippe Canguilhem, Julie E. Cumming, Anthony M. Cummings, David Fallows, David Fiala, Alison K. Frazier, James Hankins, Leofranc Holford-Strevens, Deborah Howard, Andrew Kirkman, Michael Long, Laurenz Lütteken, Evan A. MacCarthy, Patrick Macey, Honey Meconi, John Milsom, Klaus Pietschmann, Alejandro Enrique Planchart, Yolanda Plumley, Keith Polk, Anne Walters Robertson, Jesse Rodin, David J. Rothenberg, Thomas Schmidt-Beste, Peter Schubert, Nicole Schwindt, Richard Sherr, Pamela F. Starr, Anne Stone, Reinhard Strohm, Richard Taruskin, Blake Wilson, Emily Zazulia
- Edited by Anna Maria Busse Berger, University of California, Davis, Jesse Rodin, Stanford University, California
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- The Cambridge History of Fifteenth-Century Music
- Published online:
- 05 July 2015
- Print publication:
- 16 July 2015, pp xix-xxvi
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Faunal and Environmental Change in the Late Miocene Siwaliks of Northern Pakistan
- John C. Barry, Michèle E. Morgan, Lawrence J. Flynn, David Pilbeam, Anna K. Behrensmeyer, S. Mahmood Raza, Imran A. Khan, Catherine Badgley, Jason Hicks, Jay Kelley
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- Journal:
- Paleobiology / Volume 28 / Issue S2 / Spring 2002
- Published online by Cambridge University Press:
- 14 July 2015, pp. 1-71
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The Siwalik formations of northern Pakistan consist of deposits of ancient rivers that existed throughout the early Miocene through the late Pliocene. The formations are highly fossiliferous with a diverse array of terrestrial and freshwater vertebrates, which in combination with exceptional lateral exposure and good chronostratigraphic control allows a more detailed and temporally resolved study of the sediments and faunas than is typical in terrestrial deposits. Consequently the Siwaliks provide an opportunity to document temporal differences in species richness, turnover, and ecological structure in a terrestrial setting, and to investigate how such differences are related to changes in the fluvial system, vegetation, and climate. Here we focus on the interval between 10.7 and 5.7 Ma, a time of significant local tectonic and global climatic change. It is also the interval with the best temporal calibration of Siwalik faunas and most comprehensive data on species occurrences. A methodological focus of this paper is on controlling sampling biases that confound biological and ecological signals. Such biases include uneven sampling through time, differential preservation of larger animals and more durable skeletal elements, errors in age-dating imposed by uncertainties in correlation and paleomagnetic timescale calibrations, and uneven taxonomic treatment across groups. We attempt to control for them primarily by using a relative-abundance model to estimate limits for the first and last appearances from the occurrence data. This model also incorporates uncertainties in age estimates. Because of sampling limitations inherent in the terrestrial fossil record, our 100-Kyr temporal resolution may approach the finest possible level of resolution for studies of vertebrate faunal changes over periods of millions of years.
Approximately 40,000 specimens from surface and screenwash collections made at 555 localities form the basis of our study. Sixty percent of the localities have maximum and minimum age estimates differing by 100 Kyr or less, 82% by 200 Kyr or less. The fossils represent 115 mammalian species or lineages of ten orders: Insectivora, Scandentia, Primates, Tubulidentata, Proboscidea, Pholidota, Lagomorpha, Perissodactyla, Artiodactyla, and Rodentia. Important taxa omitted from this study include Carnivora, Elephantoidea, and Rhinocerotidae. Because different collecting methods were used for large and small species, they are treated separately in analyses. Small species include insectivores, tree shrews, rodents, lagomorphs, and small primates. They generally weigh less than 5 kg.
The sediments of the study interval were deposited by coexisting fluvial systems, with the larger emergent Nagri system being displaced between 10.1 and 9.0 Ma by an interfan Dhok Pathan system. In comparison to Nagri floodplains, Dhok Pathan floodplains were less well drained, with smaller rivers having more seasonally variable flow and more frequent avulsions. Paleosol sequences indicate reorganization of topography and drainage accompanying a transition to a more seasonal climate. A few paleosols may have formed under waterlogged, grassy woodlands, but most formed under drier conditions and more closed vegetation.
The oxygen isotopic record also indicates significant change in the patterns of precipitation beginning at 9.2 Ma, in what may have been a shift to a drier and more seasonal climate. The carbon isotope record demonstrates that after 8.1 Ma significant amounts of C4 grasses began to appear and that by 6.8 Ma floodplain habitats included extensive C4 grasslands. Plant communities with predominantly C3 plants were greatly diminished after 7.0 Ma, and those with predominantly C4 plants, which would have been open woodlands or grassy woodlands, appeared as early as 7.4 Ma.
Inferred first and last appearances show a constant, low level of faunal turnover throughout the interval 10.7–5.7-Ma, with three short periods of elevated turnover at 10.3, 7.8, and 7.3–7.0 Ma. The three pulses account for nearly 44% of all turnover. Throughout the late Miocene, species richness declined steadily, and diversity and richness indices together with data on body size imply that community ecological structure changed abruptly just after 10 Ma, and then again at 7.8 Ma. Between 10 and 7.8 Ma the large-mammal assemblages were strongly dominated by equids, with more balanced faunas before and after. The pattern of appearance and disappearance is selective with respect to inferred habits of the animals. Species appearing after 9.0 Ma are grazers or typical of more open habitats, whereas many species that disappear can be linked to more closed vegetation. We presume exceptions to this pattern were animals of the mixed C3/C4 communities or the wetter parts of the floodplain that did not persist into the latest Miocene. The pace of extinction accelerates once there is C4 vegetation on the floodplain.
The 10.3 Ma event primarily comprises disappearance of taxa that were both common and of long duration. The event does not correlate to any obvious local environmental or climatic event, and the pattern of species disappearance and appearance suggests that biotic interactions may have been more important than environmental change.
The 7.8 Ma event is characterized solely by appearances, and that at 7.3 Ma by a combination of appearances and disappearances. These two latest Miocene events include more taxa that were shorter ranging and less common, a difference of mode that developed between approximately 9.0 and 8.5 Ma when many short-ranging and rare species began to make appearances. Both events also show a close temporal correlation to changes in floodplain deposition and vegetation. The 7.8 Ma event follows the widespread appearance of C4 vegetation and is coincident with the shift from equid-dominated to more evenly balanced large-mammal assemblages. The 7.3 to 7.0 Ma event starts with the first occurrence of C4-dominated floras and ends with the last occurrence of C3-dominated vegetation. Absence of a consistent relationship between depositional facies and the composition of faunal assemblages leads us to reject fluvial system dynamics as a major cause of faunal change. The close correlation of latest Miocene species turnover and ecological change to expansion of C4 plants on the floodplain, in association with oxygen isotopic and sedimentological evidence for increasingly drier and more seasonal climates, causes us to favor explanations based on climatic change for both latest Miocene pulses.
The Siwalik record supports neither “coordinated stasis” nor “turnover pulse” evolutionary models. The brief, irregularly spaced pulses of high turnover are characteristic of both the stasis and pulse models, but the high level of background turnover that eliminates 65–70% of the initial species shows there is no stasis in the Siwalik record. In addition, the steadily declining species richness and abrupt, uncoordinated changes in diversity do not fit either model.
The CNDR: Collaborating to Translate New Therapies for Canadians
- Lawrence Korngut, Craig Campbell, Megan Johnston, Timothy Benstead, Angela Genge, Alex MacKenzie, Anna McCormick, Douglas Biggar, Pierre Bourque, Hannah Briemberg, Colleen O'Connell, Suzan Dojeiji, Joseph Dooley, Ian Grant, Gillian Hogan, Wendy Johnston, Sanjay Kalra, Hans D. Katzberg, Jean K. Mah, Laura McAdam, Hugh J. McMillan, Michel Melanson, Kathryn Selby, Christen Shoesmith, Garth Smith, Shannon L. Venance, Joy Wee,
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- Journal:
- Canadian Journal of Neurological Sciences / Volume 40 / Issue 5 / September 2013
- Published online by Cambridge University Press:
- 23 September 2014, pp. 698-704
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Background:
Patient registries represent an important method of organizing “real world” patient information for clinical and research purposes. Registries can facilitate clinical trial planning and recruitment and are particularly useful in this regard for uncommon and rare diseases. Neuromuscular diseases (NMDs) are individually rare but in aggregate have a significant prevalence. In Canada, information on NMDs is lacking. Barriers to performing Canadian multicentre NMD research exist which can be overcome by a comprehensive and collaborative NMD registry.
Methods:We describe the objectives, design, feasibility and initial recruitment results for the Canadian Neuromuscular Disease Registry (CNDR).
Results:The CNDR is a clinic-based registry which launched nationally in June 2011, incorporates paediatric and adult neuromuscular clinics in British Columbia, Alberta, Ontario, Quebec, New Brunswick and Nova Scotia and, as of December 2012, has recruited 1161 patients from 12 provinces and territories. Complete medical datasets have been captured on 460 “index disease” patients. Another 618 “non-index” patients have been recruited with capture of physician-confirmed diagnosis and contact information. We have demonstrated the feasibility of blended clinic and central office-based recruitment. “Index disease” patients recruited at the time of writing include 253 with Duchenne and Becker muscular dystrophy, 161 with myotonic dystrophy, and 71 with ALS.
Conclusions:The CNDR is a new nationwide registry of patients with NMDs that represents an important advance in Canadian neuromuscular disease research capacity. It provides an innovative platform for organizing patient information to facilitate clinical research and to expedite translation of recent laboratory findings into human studies.
Contributors
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- By Blair C. Armstrong, David A. Balota, Lawrence W. Barsalou, Jos J. A. Van Berkum, Lera Boroditsky, Gregory A. Bryant, Cristina Cacciari, Joana Cholin, Morten H. Christiansen, Stella Christie, Eve V. Clark, Herbert H. Clark, Eliana Colunga, John F. Connolly, Michael J. Cortese, Seana Coulson, George S. Cree, Christopher M. Crew, Gary S. Dell, Kevin Diependaele, Judit Druks, Thomas A. Farmer, Anne Fernald, Kelly Forbes, Carol A. Fowler, Michael Frank, Stephen J. Frost, Dedre Gentner, Raymond W. Gibbs, Monica Gonzalez-Marquez, Arthur C. Graesser, Jonathan Grainger, Zenzi M. Griffin, Mary Hare, Harlan D. Harris, Marc F. Joanisse, Leonard Katz, Albert Kim, Gina R. Kuperberg, Nicole Landi, Birte Loenneker-Rodman, Danielle S. MacNamara, James S. Magnuson, Ken McRae, W. Einar Mencl, Daniel Mirman, Jennifer B. Misyak, Srini Narayanan, Kate Nation, Randy L. Newman, Lee Osterhout, Roberto Padovani, Karalyn Patterson, Kenneth R. Pugh, Terry Regier, Douglas Roland, Jay G. Rueckl, Vasile Rus, Jenny R. Saffran, Sarah D. Sahni, Arthur G. Samuel, Rebecca Sandak, Dominiek Sandra, Sophie Scott, Mark S. Seidenberg, Linda B. Smith, Michael J. Spivey, Meghan Sumner, Daniel Tranel, Gabriella Vigliocco, Nicole L. Wilson, Anna Woollams
- Edited by Michael Spivey, Ken McRae, University of Western Ontario, Marc Joanisse, University of Western Ontario
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- Book:
- The Cambridge Handbook of Psycholinguistics
- Published online:
- 05 November 2012
- Print publication:
- 20 August 2012, pp xi-xiv
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Winter sky brightness and cloud cover at Dome A, Antarctica
- Anna M. Moore, Yi Yang, Jianning Fu, Michael C. B. Ashley, Xiangqun Cui, Long Long Feng, Xuefei Gong, Zhongwen Hu, Jon S. Lawrence, Daniel M. Luong-Van, Reed Riddle, Zhaohui Shang, Geoff Sims, John W. V. Storey, Nicholas F. H. Tothill, Tony Travouillon, Lifan Wang, Huigen Yang, Ji Yang, Xu Zhou, Zhenxi Zhu
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- Journal:
- Proceedings of the International Astronomical Union / Volume 8 / Issue S288 / August 2012
- Published online by Cambridge University Press:
- 30 January 2013, pp. 34-37
- Print publication:
- August 2012
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At the summit of the Antarctic plateau, Dome A offers an intriguing location for future large scale optical astronomical observatories. The Gattini Dome A project was created to measure the optical sky brightness and large area cloud cover of the winter-time sky above this high altitude Antarctic site. The wide field camera and multi-filter system was installed on the PLATO instrument module as part of the Chinese-led traverse to Dome A in January 2008. This automated wide field camera consists of an Apogee U4000 interline CCD coupled to a Nikon fisheye lens enclosed in a heated container with glass window. The system contains a filter mechanism providing a suite of standard astronomical photometric filters (Bessell B, V, R) and a long-pass red filter for the detection and monitoring of airglow emission. The system operated continuously throughout the 2009, and 2011 winter seasons and part-way through the 2010 season, recording long exposure images sequentially for each filter. We have in hand one complete winter-time dataset (2009) returned via a manned traverse. We present here the first measurements of sky brightness in the photometric V band, cloud cover statistics measured so far and an estimate of the extinction.
Airglow and Aurorae from Dome A, Antarctica
- Geoff Sims, Michael C. B. Ashley, Xiangqun Cui, Jon R. Everett, LongLong Feng, Xuefei Gong, Shane Hengst, Zhongwen Hu, Jon S. Lawrence, Daniel M. Luong-Van, Anna M. Moore, Reed Riddle, Zhaohui Shang, John W. V. Storey, Nick Tothill, Tony Travouillon, Lifan Wang, Huigen Yang, Ji Yang, Xu Zhou, Zhenxi Zhu
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- Journal:
- Proceedings of the International Astronomical Union / Volume 8 / Issue S288 / August 2012
- Published online by Cambridge University Press:
- 30 January 2013, pp. 302-303
- Print publication:
- August 2012
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Despite the absence of artificial light pollution at Antarctic plateau sites such as Dome A, other factors such as airglow, aurorae and extended periods of twilight have the potential to adversely affect optical observations. We present a statistical analysis of the airglow and aurorae at Dome A using spectroscopic data from Nigel, an optical/near-IR spectrometer operating in the 300–850 nm range. The median auroral contribution to the B, V and R photometric bands is found to be 22.9, 23.4 and 23.0 mag arcsec−2 respectively. We are also able to quantify the amount of annual dark time available as a function of wavelength; on average twilight ends when the Sun reaches a zenith distance of 102.6°.
Contributors
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- By Rose Teteki Abbey, K. C. Abraham, David Tuesday Adamo, LeRoy H. Aden, Efrain Agosto, Victor Aguilan, Gillian T. W. Ahlgren, Charanjit Kaur AjitSingh, Dorothy B E A Akoto, Giuseppe Alberigo, Daniel E. Albrecht, Ruth Albrecht, Daniel O. Aleshire, Urs Altermatt, Anand Amaladass, Michael Amaladoss, James N. Amanze, Lesley G. Anderson, Thomas C. Anderson, Victor Anderson, Hope S. Antone, María Pilar Aquino, Paula Arai, Victorio Araya Guillén, S. Wesley Ariarajah, Ellen T. Armour, Brett Gregory Armstrong, Atsuhiro Asano, Naim Stifan Ateek, Mahmoud Ayoub, John Alembillah Azumah, Mercedes L. García Bachmann, Irena Backus, J. Wayne Baker, Mieke Bal, Lewis V. Baldwin, William Barbieri, António Barbosa da Silva, David Basinger, Bolaji Olukemi Bateye, Oswald Bayer, Daniel H. Bays, Rosalie Beck, Nancy Elizabeth Bedford, Guy-Thomas Bedouelle, Chorbishop Seely Beggiani, Wolfgang Behringer, Christopher M. Bellitto, Byard Bennett, Harold V. Bennett, Teresa Berger, Miguel A. Bernad, Henley Bernard, Alan E. Bernstein, Jon L. Berquist, Johannes Beutler, Ana María Bidegain, Matthew P. Binkewicz, Jennifer Bird, Joseph Blenkinsopp, Dmytro Bondarenko, Paulo Bonfatti, Riet en Pim Bons-Storm, Jessica A. Boon, Marcus J. Borg, Mark Bosco, Peter C. Bouteneff, François Bovon, William D. Bowman, Paul S. Boyer, David Brakke, Richard E. Brantley, Marcus Braybrooke, Ian Breward, Ênio José da Costa Brito, Jewel Spears Brooker, Johannes Brosseder, Nicholas Canfield Read Brown, Robert F. Brown, Pamela K. Brubaker, Walter Brueggemann, Bishop Colin O. Buchanan, Stanley M. Burgess, Amy Nelson Burnett, J. Patout Burns, David B. Burrell, David Buttrick, James P. Byrd, Lavinia Byrne, Gerado Caetano, Marcos Caldas, Alkiviadis Calivas, William J. Callahan, Salvatore Calomino, Euan K. Cameron, William S. Campbell, Marcelo Ayres Camurça, Daniel F. Caner, Paul E. Capetz, Carlos F. Cardoza-Orlandi, Patrick W. Carey, Barbara Carvill, Hal Cauthron, Subhadra Mitra Channa, Mark D. Chapman, James H. Charlesworth, Kenneth R. Chase, Chen Zemin, Luciano Chianeque, Philip Chia Phin Yin, Francisca H. Chimhanda, Daniel Chiquete, John T. Chirban, Soobin Choi, Robert Choquette, Mita Choudhury, Gerald Christianson, John Chryssavgis, Sejong Chun, Esther Chung-Kim, Charles M. A. Clark, Elizabeth A. Clark, Sathianathan Clarke, Fred Cloud, John B. Cobb, W. Owen Cole, John A Coleman, John J. Collins, Sylvia Collins-Mayo, Paul K. Conkin, Beth A. Conklin, Sean Connolly, Demetrios J. Constantelos, Michael A. Conway, Paula M. Cooey, Austin Cooper, Michael L. Cooper-White, Pamela Cooper-White, L. William Countryman, Sérgio Coutinho, Pamela Couture, Shannon Craigo-Snell, James L. Crenshaw, David Crowner, Humberto Horacio Cucchetti, Lawrence S. Cunningham, Elizabeth Mason Currier, Emmanuel Cutrone, Mary L. Daniel, David D. Daniels, Robert Darden, Rolf Darge, Isaiah Dau, Jeffry C. Davis, Jane Dawson, Valentin Dedji, John W. de Gruchy, Paul DeHart, Wendy J. Deichmann Edwards, Miguel A. De La Torre, George E. Demacopoulos, Thomas de Mayo, Leah DeVun, Beatriz de Vasconcellos Dias, Dennis C. Dickerson, John M. Dillon, Luis Miguel Donatello, Igor Dorfmann-Lazarev, Susanna Drake, Jonathan A. Draper, N. Dreher Martin, Otto Dreydoppel, Angelyn Dries, A. J. Droge, Francis X. D'Sa, Marilyn Dunn, Nicole Wilkinson Duran, Rifaat Ebied, Mark J. Edwards, William H. Edwards, Leonard H. Ehrlich, Nancy L. Eiesland, Martin Elbel, J. Harold Ellens, Stephen Ellingson, Marvin M. Ellison, Robert Ellsberg, Jean Bethke Elshtain, Eldon Jay Epp, Peter C. Erb, Tassilo Erhardt, Maria Erling, Noel Leo Erskine, Gillian R. Evans, Virginia Fabella, Michael A. Fahey, Edward Farley, Margaret A. Farley, Wendy Farley, Robert Fastiggi, Seena Fazel, Duncan S. Ferguson, Helwar Figueroa, Paul Corby Finney, Kyriaki Karidoyanes FitzGerald, Thomas E. FitzGerald, John R. Fitzmier, Marie Therese Flanagan, Sabina Flanagan, Claude Flipo, Ronald B. Flowers, Carole Fontaine, David Ford, Mary Ford, Stephanie A. Ford, Jim Forest, William Franke, Robert M. Franklin, Ruth Franzén, Edward H. Friedman, Samuel Frouisou, Lorelei F. Fuchs, Jojo M. Fung, Inger Furseth, Richard R. Gaillardetz, Brandon Gallaher, China Galland, Mark Galli, Ismael García, Tharscisse Gatwa, Jean-Marie Gaudeul, Luis María Gavilanes del Castillo, Pavel L. Gavrilyuk, Volney P. Gay, Metropolitan Athanasios Geevargis, Kondothra M. George, Mary Gerhart, Simon Gikandi, Maurice Gilbert, Michael J. Gillgannon, Verónica Giménez Beliveau, Terryl Givens, Beth Glazier-McDonald, Philip Gleason, Menghun Goh, Brian Golding, Bishop Hilario M. Gomez, Michelle A. Gonzalez, Donald K. Gorrell, Roy Gottfried, Tamara Grdzelidze, Joel B. Green, Niels Henrik Gregersen, Cristina Grenholm, Herbert Griffiths, Eric W. Gritsch, Erich S. Gruen, Christoffer H. Grundmann, Paul H. Gundani, Jon P. Gunnemann, Petre Guran, Vidar L. Haanes, Jeremiah M. Hackett, Getatchew Haile, Douglas John Hall, Nicholas Hammond, Daphne Hampson, Jehu J. Hanciles, Barry Hankins, Jennifer Haraguchi, Stanley S. Harakas, Anthony John Harding, Conrad L. Harkins, J. William Harmless, Marjory Harper, Amir Harrak, Joel F. Harrington, Mark W. Harris, Susan Ashbrook Harvey, Van A. Harvey, R. Chris Hassel, Jione Havea, Daniel Hawk, Diana L. Hayes, Leslie Hayes, Priscilla Hayner, S. Mark Heim, Simo Heininen, Richard P. Heitzenrater, Eila Helander, David Hempton, Scott H. Hendrix, Jan-Olav Henriksen, Gina Hens-Piazza, Carter Heyward, Nicholas J. Higham, David Hilliard, Norman A. Hjelm, Peter C. Hodgson, Arthur Holder, M. Jan Holton, Dwight N. Hopkins, Ronnie Po-chia Hsia, Po-Ho Huang, James Hudnut-Beumler, Jennifer S. Hughes, Leonard M. Hummel, Mary E. Hunt, Laennec Hurbon, Mark Hutchinson, Susan E. Hylen, Mary Beth Ingham, H. Larry Ingle, Dale T. Irvin, Jon Isaak, Paul John Isaak, Ada María Isasi-Díaz, Hans Raun Iversen, Margaret C. Jacob, Arthur James, Maria Jansdotter-Samuelsson, David Jasper, Werner G. Jeanrond, Renée Jeffery, David Lyle Jeffrey, Theodore W. Jennings, David H. Jensen, Robin Margaret Jensen, David Jobling, Dale A. Johnson, Elizabeth A. Johnson, Maxwell E. Johnson, Sarah Johnson, Mark D. Johnston, F. Stanley Jones, James William Jones, John R. Jones, Alissa Jones Nelson, Inge Jonsson, Jan Joosten, Elizabeth Judd, Mulambya Peggy Kabonde, Robert Kaggwa, Sylvester Kahakwa, Isaac Kalimi, Ogbu U. Kalu, Eunice Kamaara, Wayne C. Kannaday, Musimbi Kanyoro, Veli-Matti Kärkkäinen, Frank Kaufmann, Léon Nguapitshi Kayongo, Richard Kearney, Alice A. Keefe, Ralph Keen, Catherine Keller, Anthony J. Kelly, Karen Kennelly, Kathi Lynn Kern, Fergus Kerr, Edward Kessler, George Kilcourse, Heup Young Kim, Kim Sung-Hae, Kim Yong-Bock, Kim Yung Suk, Richard King, Thomas M. King, Robert M. Kingdon, Ross Kinsler, Hans G. Kippenberg, Cheryl A. Kirk-Duggan, Clifton Kirkpatrick, Leonid Kishkovsky, Nadieszda Kizenko, Jeffrey Klaiber, Hans-Josef Klauck, Sidney Knight, Samuel Kobia, Robert Kolb, Karla Ann Koll, Heikki Kotila, Donald Kraybill, Philip D. W. Krey, Yves Krumenacker, Jeffrey Kah-Jin Kuan, Simanga R. Kumalo, Peter Kuzmic, Simon Shui-Man Kwan, Kwok Pui-lan, André LaCocque, Stephen E. Lahey, John Tsz Pang Lai, Emiel Lamberts, Armando Lampe, Craig Lampe, Beverly J. Lanzetta, Eve LaPlante, Lizette Larson-Miller, Ariel Bybee Laughton, Leonard Lawlor, Bentley Layton, Robin A. Leaver, Karen Lebacqz, Archie Chi Chung Lee, Marilyn J. Legge, Hervé LeGrand, D. L. LeMahieu, Raymond Lemieux, Bill J. Leonard, Ellen M. Leonard, Outi Leppä, Jean Lesaulnier, Nantawan Boonprasat Lewis, Henrietta Leyser, Alexei Lidov, Bernard Lightman, Paul Chang-Ha Lim, Carter Lindberg, Mark R. Lindsay, James R. Linville, James C. Livingston, Ann Loades, David Loades, Jean-Claude Loba-Mkole, Lo Lung Kwong, Wati Longchar, Eleazar López, David W. Lotz, Andrew Louth, Robin W. Lovin, William Luis, Frank D. Macchia, Diarmaid N. J. MacCulloch, Kirk R. MacGregor, Marjory A. MacLean, Donald MacLeod, Tomas S. Maddela, Inge Mager, Laurenti Magesa, David G. Maillu, Fortunato Mallimaci, Philip Mamalakis, Kä Mana, Ukachukwu Chris Manus, Herbert Robinson Marbury, Reuel Norman Marigza, Jacqueline Mariña, Antti Marjanen, Luiz C. L. Marques, Madipoane Masenya (ngwan'a Mphahlele), Caleb J. D. Maskell, Steve Mason, Thomas Massaro, Fernando Matamoros Ponce, András Máté-Tóth, Odair Pedroso Mateus, Dinis Matsolo, Fumitaka Matsuoka, John D'Arcy May, Yelena Mazour-Matusevich, Theodore Mbazumutima, John S. McClure, Christian McConnell, Lee Martin McDonald, Gary B. McGee, Thomas McGowan, Alister E. McGrath, Richard J. McGregor, John A. McGuckin, Maud Burnett McInerney, Elsie Anne McKee, Mary B. McKinley, James F. McMillan, Ernan McMullin, Kathleen E. McVey, M. 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Yee, Viktor Yelensky, Yeo Khiok-Khng, Gustav K. K. Yeung, Angela Yiu, Amos Yong, Yong Ting Jin, You Bin, Youhanna Nessim Youssef, Eliana Yunes, Robert Michael Zaller, Valarie H. Ziegler, Barbara Brown Zikmund, Joyce Ann Zimmerman, Aurora Zlotnik, Zhuo Xinping
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Index
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Frontmatter
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Acknowledgements
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1 - Introduction: learning from experiences of participatory biodiversity assessment
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Summary
Introduction
A few years ago, curious to find out how individuals can bring about change in environmental policy, I arranged to meet volunteers who collect data about species distributions. My first interview was with a lively, successful group of volunteers in the south of England, who had developed a new approach for monitoring hedgerows. Ancient hedgerows are important for conservation in Britain, helping to maintain diversity of habitat, and connect up patches of otherwise isolated woodland. As a result of systematic surveys, some of them by volunteers, the British Government had changed the law and introduced incentives for farmers to replant them (in 1992), and regulations to protect them (in 1994).
Certainly the volunteers were enthusiastic about their successes and policy impact. But what they mostly wanted to talk about was the beauty of hedgerows, the pleasure they found in observing the variety in a line of trees, and the feeling that without the excuse of collecting data, they were being a little self-indulgent by spending time in nature. As one said, ‘It's nice, but as long as you do it with a purpose in mind and at the end of it you feel you've done something really quite good’.
Thousands of miles away, other people were collecting data about species, but these data had a more immediate effect on their lives. They were villagers in Karnataka, in southern India, who shared management of their forests with the state Forest Department.
List of contributors
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12 - The personal and political of volunteers' data: towards a national biodiversity database for the UK
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Britain has an exceptional tradition of natural history societies and amateur naturalists who collect data about species distributions, frequency and behaviour (Bell et al., this volume). This chapter examines an attempt to harness the data for a wider range of purposes, and the ways in which different actors have perceived and responded to this. Many of the volunteers have a strong personal attachment to their data, and to the ways in which they hope that it will be used. When powerful organizations become involved in managing the data, the volunteers can perceive threats and opportunities for the value of their data. The chapter considers the need to balance these emotional and political aspects in developing an effective national data management system. It is based on a cross-cutting analysis of research into the processes behind biodiversity action plans and biological recording, conducted over several years in the UK (Gillett and Lawrence, 2003; Lawrence, 2005; Lawrence, 2006; Lawrence and Molteno in press; Lawrence and Turnhout, 2005). The chapter draws on interviews with volunteers and professionals involved in the complex organizational landscape that has evolved around biological data collection and sharing, descriptions of the process on websites and in reports, and on presentations made at the annual National Biodiversity Network conferences.
The supply side: growth of biological recording
Biological recording, or the collection of data about the distribution and abundance of species, has a long history in Britain, going back to the leisure time of country vicars in the eighteenth century (Moss, 2004).
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- Participatory Biodiversity Assessment for Policy, Planning and Practice
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In a world of increasing demands for biodiversity information, participatory biodiversity assessment and monitoring is becoming more significant. Whilst other books have focused on methods, or links to conservation or development, this book is written particularly for policy makers and planners. Introductory chapters analyze the challenges of the approach, the global legislation context, and the significance of the Millennium Ecosystem Assessment. Specially commissioned case studies provide evidence from 17 countries, by 50 authors with expertise in both biological and social sciences. Ranging from community conservation projects in developing countries to amateur birdwatching in the UK, they describe the context, objectives, stakeholders and processes, and reflect on the success of outcomes. Rather than advocating any particular approach, the book takes a constructively critical look at the motives, experiences and outcomes of such approaches, with cross-cutting lessons to inform planning and interpretation of future participatory projects and their contribution to policy objectives.
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Regenerating Agriculture: Policies and Practice for Sustainability and Self Reliance. By Jules N. Pretty. London: Earthscan (1995), pp. 320, paperback £12.95, ISBN 1-85383-198-0, hardback £29.95, ISBN 1-85383-227-8.
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36 - HSV: persistence in the population: epidemiology, transmission
- from Part III - Pathogenesis, clinical disease, host response, and epidemiology: HSV-1 and HSV-2
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- By Anna Wald, University of Washington, USA, Lawrence Corey, University of Washington, Fred Hutchinson Cancer Research Center, WA, USA
- Edited by Ann Arvin, Stanford University, California, Gabriella Campadelli-Fiume, Università degli Studi, Bologna, Italy, Edward Mocarski, Emory University, Atlanta, Patrick S. Moore, University of Pittsburgh, Bernard Roizman, University of Chicago, Richard Whitley, University of Alabama, Birmingham, Koichi Yamanishi, University of Osaka, Japan
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Epidemiology of HSV-1 and HSV-2
Herpes simplex viruses are among the most ubiquitous of human infections. The frequency of HSV infection has been measured by testing various populations for the presence of antibody, as both virus and the immune response are thought to persist after infection for the life of the host. Worldwide, ∼90% of people have one or both viruses. HSV-1 is the more prevalent virus, with 65% of persons in the United States having antibodies to HSV-1 (Xu et al., 2002). The epidemiology in Europe is similar, with at least half of the population seropositive for HSV-1. In the developing world, HSV-1 is almost universal, and usually acquired from intimate contact with family in early childhood (Whitley et al., 1998). After childhood, the HSV-1 prevalence rates increase minimally with age. Rates of HSV-1 infection are similar for men and women. In the United States, African-Americans and Asians have higher rates of HSV-1 infection than whites. The majority of infections are oral, although most are asymptomatic. Some data suggest that in developed countries, acquisition of HSV-1 is delayed from early childhood to adolescence or young adulthood (Hashido et al., 1999; Mertz et al., 2003).
HSV-2 infections are markedly less frequent than HSV-1 infections, with 15%–80% of people in various populations infected (Corey and Wald, 1999). The rates of infection vary with country as well as levels of sexual activity.