Constructing computer virus phylogenies

There has been much recent algorithmic work on the problem of reconstructing the evolutionary history of biological species. Computer virus specialists are interested in finding the evolutionary history of computer viruses - a virus is often written using code fragments from one or more other viruses, which are its immediate ancestors. A phylogeny for a collection of computer viruses is a directed acyclic graph whose nodes are the viruses and whose edges map ancestors to descendants and satisfy the property that each code fragment is "invented" only once. To provide a simple explanation for the data, we consider the problem of constructing such a phylogeny with a minimum number of edges. In general this optimization problem is NP-complete; some associated approximation problems are also hard, but others are easy. When tree solutions exist, they can be constructed and randomly sampled in polynomial time

Comparison of osteoporosis pharmacotherapy fracture rates: Analysis of a marketScan® claims database cohort

Background: Several different classes of medications have been shown to be efficacious at preventing fractures in patients with osteoporosis. No study has compared real world efficacy at preventing fractures between all currently approved medications. Objectives: To directly compare the efficacy of all currently available osteoporosis medications by using a large population claims database. Methods: The Truven Health Analytics MarketScan® database from 2008 - 2012 was used to identify all patients who started a new osteoporosis medication. Patients who experienced a fracture after at least 12 months of treatment were identified and risk factors for fracture for all patients were recorded. Logistic regression was used to account for and quantify the contribution of risk factors, and to make direct comparisons between different osteoporosis medications. Results: A total of 51649 patients were included in the cohort, with an average age of 56 years. The overall incidence rate of fracture was 1.55 per 100 person - years of treatment. Orally administered medications had the lowest fracture rates, led by raloxifene and alendronate (1.24 and 1.54 respectively), while parenterally administered medications including teriparatide and zolerdonic acid had the highest rates (3.90 and 1.98 respectively). No statistically significant differences found between oral or parenterally administered bisphosphonate medications. Conclusions: While patients taking orally administered drugs including bisphosphonates had less frequent incident fracture no statistically significant differences were found between most drugs in head - to - head comparisons, even considering the route of administration of bisphosphonates. These findings support previous evidence that minimal differences in efficacy exist between different osteoporosis medications. This is the first study using a large database to compare all currently available osteoporosis treatments and will hopefully be augmented by further study to provide more evidence to make clinical decisions on osteoporosis medication use. © 2017 American Association of Neuropathologists, Inc

Central place foragers and moving stimuli : a hidden-state model to discriminate the processes affecting movement

We thank Orkney Islands Council for access to Eynhallow and Talisman Energy (UK) Ltd for fieldwork and equipment support. Marine Scotland provided access to anonymized VMS data. Handling and tagging of fulmars was conducted under licenses from the British Trust for Ornithology and the UK Home Office. EE was funded by a Marine Alliance for Science and Technology for Scotland/University of Aberdeen College of Life Sciences and Medicine studentship. We are grateful to Jason Matthiopoulos, Thomas Cornulier, Beth Scott, David Lusseau, Julien Martin and Tiago Marques for suggestions on model development, and to the many colleagues who assisted with fieldwork. We thank Emer Rogan and University College Cork for providing desk space to EP. Finally, we thank Editor-in-Chief Ben Sheldon, Associate Editor Luca Borger and three anonymous reviewers for their useful comments on the paper. Data available from the Dryad Digital Repository: https://doi:10.5061/dryad.0d377r6 (Pirotta et al., 2018)Peer reviewedPostprintPostprintPostprintPostprin

Evaluation of Reproductive Function in Turkana Women with Enzyme Immunoassays of Urinary Hormones in the Field

The frequently reported observation that nomadic populations have lower fertility than their settled counterparts is often attributed to what are perceived as harsh, stressful conditions under which the nomads live. But the consequences of the hypothesized stresses for the reproductive biology or demography of these populations have been documented only a little. Traditionally, the Turkana of northwest Kenya are nomadic herders, but increasing numbers have settled on agricultural development schemes. We used an array of hormonal assays along with anthropometric indexes of nutritional status and interviews covering reproductive history, recent menstruation, diet, and health to compare reproductive function in nomadic and settled Turkana women. First morning urine samples were collected for three consecutive days during a series of surveys. Human choriogonadotropin (hCG; a marker for pregnancy), luteinizing hormone (LH; an indicator of ovulation), and pregnanediol glucuronide (PdG; an indicator of postovulatory luteal function) were assessed in the field with commercially available dipstick enzyme immunoassays. These assays along with the interview data allowed us to determine the reproductive status (e.g., pregnant or cycling, and if cycling, which phase of the ovarian cycle) of 166 nomadic and 194 settled Turkana women. The cross-sectional classifications allowed inferences of conception rates and normality of ovarian function. Follow-up surveys provided rates of pregnancy loss. Compared with the settled women, the nomadic women exhibited lower pregnancy rates and cycling nomadic women were less likely to show evidence of ovulation or luteal function. These results suggest that reproductive function of the nomadic women is diminished relative to the settled women. However, the settled women experienced a much higher rate of pregnancy loss, which may mean that their effective fecundability is in fact lower than that of the nomadic women. This study is the first to apply such a wide range of hormonal assays in the field. It demonstrates that field-based assays are feasible and robust and can play an important role in epidemiological and biodemographic studies, even in remote locations under conditions that would ordinarily be considered incompatible with on-site laboratory analysis