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• Journal article
  Schwind JS, Wolking DJ, Brownstein JS, PREDICT Consortium1, Mazet JAK, Smith WAet al., 2014,

  Evaluation of local media surveillance for improved disease recognition and monitoring in global hotspot regions.

  , PLoS One, Vol: 9

  Digital disease detection tools are technologically sophisticated, but dependent on digital information, which for many areas suffering from high disease burdens is simply not an option. In areas where news is often reported in local media with no digital counterpart, integration of local news information with digital surveillance systems, such as HealthMap (Boston Children's Hospital), is critical. Little research has been published in regards to the specific contribution of local health-related articles to digital surveillance systems. In response, the USAID PREDICT project implemented a local media surveillance (LMS) pilot study in partner countries to monitor disease events reported in print media. This research assessed the potential of LMS to enhance digital surveillance reach in five low- and middle-income countries. Over 16 weeks, select surveillance system attributes of LMS, such as simplicity, flexibility, acceptability, timeliness, and stability were evaluated to identify strengths and weaknesses in the surveillance method. Findings revealed that LMS filled gaps in digital surveillance network coverage by contributing valuable localized information on disease events to the global HealthMap database. A total of 87 health events were reported through the LMS pilot in the 16-week monitoring period, including 71 unique reports not found by the HealthMap digital detection tool. Furthermore, HealthMap identified an additional 236 health events outside of LMS. It was also observed that belief in the importance of the project and proper source selection from the participants was crucial to the success of this method. The timely identification of disease outbreaks near points of emergence and the recognition of risk factors associated with disease occurrence continue to be important components of any comprehensive surveillance system for monitoring disease activity across populations. The LMS method, with its minimal resource commitment, could be one tool used to

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• Book chapter
  Arinaminpathy N, Metcalf CJE, Grenfell BT, 2014,

  Viral Dynamics and Mathematical Models

  , Viral Infections of Humans, Publisher: Springer US, Pages: 81-96, ISBN: 9781489974471
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• Conference paper
  Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pepin J, Posada D, Peeters M, Pybus OG, Lemey Pet al., 2014,

  Establishment and early spread of the AIDS pandemic

  , International Workshop on Antiviral Drug Resistance - Meeting the Global Challenge, Publisher: INT MEDICAL PRESS LTD, Pages: A7-A7, ISSN: 1359-6535
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  • Citations: 1
• Conference paper
  Davidovic S, Galesic M, Katsikopoulos K, Arinaminpathy Net al., 2014,

  Modeling Uncertainty in Banking Networks

  , 11th International Symposium on Distributed Computing and Artificial Intelligence (DCAI), Publisher: SPRINGER-VERLAG BERLIN, Pages: 107-114, ISSN: 2194-5357
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  • Citations: 1
• Book chapter
  Allen T, Murray K, Olival KJ, Daszak Pet al., 2014,

  EIGHT CRITICAL QUESTIONS FOR PANDEMIC PREDICTION

  , INFLUENCE OF GLOBAL ENVIRONMENTAL CHANGE ON INFECTIOUS DISEASE DYNAMICS: WORKSHOP SUMMARY, Publisher: NATL ACADEMIES PRESS, Pages: 182-193
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• Journal article
  Marston M, Newell ML, Crampin A, Lutalo T, Musoke R, Gregson S, Nyamukapa C, Nakiyingi-Miiro J, Urassa M, Isingo R, Zaba Bet al., 2013,

  Is the Risk of HIV Acquisition Increased during and Immediately after Pregnancy? A Secondary Analysis of Pooled HIV Community-Based Studies from the ALPHA Network

  , PLOS ONE, Vol: 8, ISSN: 1932-6203
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  • Citations: 27
• Journal article
  Murray KA, Verde Arregoitia LD, Davidson A, Di Marco M, Di Fonzo MMIet al., 2013,

  Threat to the point: Improving the value of comparative extinction risk analysis for conservation action

  , Global Change Biology, Vol: 20, Pages: 483-494, ISSN: 1354-1013

  Comparative extinction risk analysis is a common approach for assessing the relative plight of biodiversity and making conservation recommendations. However, the usefulness of such analyses for conservation practice has been questioned. One reason for underperformance may be that threats arising from global environmental changes (e.g., habitat loss, invasive species, climate change) are often overlooked, despite being widely regarded as proximal drivers of species' endangerment. We explore this problem by (i) reviewing the use of threats in this field and (ii) quantitatively investigating the effects of threat exclusion on the interpretation and potential application of extinction risk model results. We show that threat variables are routinely (59%) identified as significant predictors of extinction risk, yet while most studies (78%) include extrinsic factors of some kind (e.g., geographic or bioclimatic information), the majority (63%) do not include threats. Despite low overall usage, studies are increasingly employing threats to explain patterns of extinction risk. However, most continue to employ methods developed for the analysis of heritable traits (e.g., body size, fecundity), which may be poorly suited to the treatment of nonheritable predictors including threats. In our global mammal and continental amphibian extinction risk case studies, omitting threats reduced model predictive performance, but more importantly (i) reduced mechanistic information relevant to management; (ii) resulted in considerable disagreement in species classifications (12% and 5% for amphibians and mammals, respectively, translating to dozens and hundreds of species); and (iii) caused even greater disagreement (20-60%) in a downstream conservation application (species ranking). We conclude that the use of threats in comparative extinction risk analysis is important and increasing but currently in the early stages of development. Priorities for future studies include improving uptake

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• Journal article
  Otete EH, Ahankari AS, Jones H, Bolton KJ, Jordan CW, Boswell TC, Wilcox MH, Ferguson NM, Beck CR, Puleston RLet al., 2013,

  Parameters for the Mathematical Modelling of <i>Clostridium difficile</i> Acquisition and Transmission: A Systematic Review

  , PLOS ONE, Vol: 8, ISSN: 1932-6203
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  • Citations: 11
• Journal article
  Koukounari A, Donnelly CA, Moustaki I, Tukahebwa EM, Kabatereine NB, Wilson S, Webster JP, Deelder AM, Vennervald BJ, van Dam GJet al., 2013,

  A Latent Markov Modelling Approach to the Evaluation of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda

  , PLOS Computational Biology, Vol: 9, ISSN: 1553-734X

  Regular treatment with praziquantel (PZQ) is the strategy for human schistosomiasis control aiming to prevent morbidity in later life. With the recent resolution on schistosomiasis elimination by the 65th World Health Assembly, appropriate diagnostic tools to inform interventions are keys to their success. We present a discrete Markov chains modelling framework that deals with the longitudinal study design and the measurement error in the diagnostic methods under study. A longitudinal detailed dataset from Uganda, in which one or two doses of PZQ treatment were provided, was analyzed through Latent Markov Models (LMMs). The aim was to evaluate the diagnostic accuracy of Circulating Cathodic Antigen (CCA) and of double Kato-Katz (KK) faecal slides over three consecutive days for Schistosoma mansoni infection simultaneously by age group at baseline and at two follow-up times post treatment. Diagnostic test sensitivities and specificities and the true underlying infection prevalence over time as well as the probabilities of transitions between infected and uninfected states are provided. The estimated transition probability matrices provide parsimonious yet important insights into the re-infection and cure rates in the two age groups. We show that the CCA diagnostic performance remained constant after PZQ treatment and that this test was overall more sensitive but less specific than single-day double KK for the diagnosis of S. mansoni infection. The probability of clearing infection from baseline to 9 weeks was higher among those who received two PZQ doses compared to one PZQ dose for both age groups, with much higher re-infection rates among children compared to adolescents and adults. We recommend LMMs as a useful methodology for monitoring and evaluation and treatment decision research as well as CCA for mapping surveys of S. mansoni infection, although additional diagnostic tools should be incorporated in schistosomiasis elimination programs.

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• Journal article
  Josefsson L, von Stockenstrom S, Faria NR, Sinclair E, Bacchetti P, Killian M, Epling L, Tan A, Ho T, Lemey P, Shao W, Hunt PW, Somsouk M, Wylie W, Douek DC, Loeb L, Custer J, Hoh R, Poole L, Deeks SG, Hecht F, Palmer Set al., 2013,

  The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time

  , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: E4987-E4996, ISSN: 0027-8424
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  • Citations: 228

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