Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

Determinants of medication adherence to antihypertensive medications among a Chinese population using Morisky medication adherence scale

<b>Background and objectives</b> Poor adherence to medications is one of the major public health challenges. Only one-third of the population reported successful control of blood pressure, mostly caused by poor drug adherence. However, there are relatively few reports studying the adherence levels and their associated factors among Chinese patients. This study aimed to study the adherence profiles and the factors associated with antihypertensive drug adherence among Chinese patients.<p></p> <b>Methods</b> A cross-sectional study was conducted in an outpatient clinic located in the New Territories Region of Hong Kong. Adult patients who were currently taking at least one antihypertensive drug were invited to complete a self-administered questionnaire, consisting of basic socio-demographic profile, self-perceived health status, and self-reported medication adherence. The outcome measure was the Morisky Medication Adherence Scale (MMAS-8). Good adherence was defined as MMAS scores greater than 6 points (out of a total score of 8 points).<p></p> <b>Results</b> From 1114 patients, 725 (65.1%) had good adherence to antihypertensive agents. Binary logistic regression analysis was conducted. Younger age, shorter duration of antihypertensive agents used, job status being employed, and poor or very poor self-perceived health status were negatively associated with drug adherence.<p></p> <b>Conclusion</b> This study reported a high proportion of poor medication adherence among hypertensive subjects. Patients with factors associated with poor adherence should be more closely monitored to optimize their drug taking behavior

The impact of obesity on time spent with the provider and number of medications managed during office-based physician visits using a cross-sectional, national health survey

<p>Abstract</p> <p>Background</p> <p>Obesity is associated with morbidity, mortality, and increased health care costs. Few studies have examined the impact of obesity on outpatient office visits. The purpose of this study was to determine if outpatient visits by obese persons required more time with the provider and more prescription medication management compared to visits made by non-obese persons.</p> <p>Methods</p> <p>Obesity status was determined for 9,280 patient visits made by persons aged 18 years or older in the 2006 National Ambulatory Medical Care Survey. Multivariate analyses compared obese and non-obese visits, stratified by sex, for duration of the visit and the number of medications mentioned at the visit.</p> <p>Results</p> <p>Average duration of visit was higher among visits with patients determined to be obese. However, these differences were not considered significant after statistical testing. Visits made by obese female patients were significantly more likely to involve more than two prescription medications (OR 1.26, 95% CI 1.05 - 1.51) and visits made by obese male patients were significantly more likely to involve more than two prescription medications (OR 1.46, 95% CI 1.16 - 1.83) as compared to visits made by non-obese patients.</p> <p>Conclusion</p> <p>Time spent with the provider was found to be greater among visits with obese patients, but not significantly different from visits with non-obese patients. The number of medications for each visit was found to be significantly greater for visits where the patient was considered to be obese. Increased time for the visit and increased numbers of medication for each visit translate into increased costs. These findings document the impact of obesity on our health care system and have great implications on medical care cost and planning.</p

Tick-, mosquito-, and rodent-borne parasite sampling designs for the National Ecological Observatory Network

Parasites and pathogens are increasingly recognized as significant drivers of ecological and evolutionary change in natural ecosystems. Concurrently, transmission of infectious agents among human, livestock, and wildlife populations represents a growing threat to veterinary and human health. In light of these trends and the scarcity of long-term time series data on infection rates among vectors and reservoirs, the National Ecological Observatory Network (NEON) will collect measurements and samples of a suite of tick-, mosquito-, and rodent-borne parasites through a continental-scale surveillance program. Here, we describe the sampling designs for these efforts, highlighting sampling priorities, field and analytical methods, and the data as well as archived samples to be made available to the research community. Insights generated by this sampling will advance current understanding of and ability to predict changes in infection and disease dynamics in novel, interdisciplinary, and collaborative ways. (Résumé d'auteur

Tick-, Mosquito-, and Rodent-Borne Parasite Sampling Designs for the National Ecological Observatory Network [Special Feature: NEON Design]

Parasites and pathogens are increasingly recognized as significant drivers of ecological and evolutionary change in natural ecosystems. Concurrently, transmission of infectious agents among human, livestock, and wildlife populations represents a growing threat to veterinary and human health. In light of these trends and the scarcity of long-term time series data on infection rates among vectors and reservoirs, the National Ecological Observatory Network (NEON) will collect measurements and samples of a suite of tick-, mosquito-, and rodent-borne parasites through a continental-scale surveillance program. Here, we describe the sampling designs for these efforts, highlighting sampling priorities, field and analytical methods, and the data as well as archived samples to be made available to the research community. Insights generated by this sampling will advance current understanding of and ability to predict changes in infection and disease dynamics in novel, interdisciplinary, and collaborative ways

The caribbean coastal marine productivity program (CARICOMP)

CARICOMP is a regional scientific program to study land-sea interaction processes in the Caribbean coastal zone. It has been collecting data since 1992, when a Data Management Centre was established at the University of the West Indies in Jamaica. Initially it focuses on documenting the structure and productivity of major coastal communities (mangrove forests, seagrass meadows and coral reefs) at relatively undisturbed sites in diverse physical settings. Second, by regular recording of physical and biological parameters, it monitors for change, seeking to distinguish natural from anthropogenic disturbance. Third, it constitutes a regional network of observers, able to collaborate on studies of region-wide events. Examples are presented of the diverse data sets collected by the Program.Fil: Alcolado, Pedro M.. Instituto de Oceanología; CubaFil: Alleng, Gerard. No especifíca;Fil: Bonair, Kurt. No especifíca;Fil: Bone, David. Universidad Simón Bolívar; VenezuelaFil: Buchan, Kenneth. No especifíca;Fil: Bush, Phillippe G.. Protection and Conservation Unit; Islas CaimánFil: De Meyer, Kalli. No especifíca;Fil: Garcia, Jorge R.. Universidad de Puerto Rico; Puerto RicoFil: Garzón Ferreira, Jaime. Instituto de Investigaciones Marinas y Costeras; ColombiaFil: Gayle, Peter M. H.. Discovery Bay Marine Laboratory; JamaicaFil: Gerace, Donald T.. Bahamian Field Station; BahamasFil: Geraldes, Francisco X.. Universidad Autonoma de Santo Domingo.; República DominicanaFil: Dahlgren, Eric Jordán. Universidad Nacional Autónoma de México; MéxicoFil: Kjferve, Björn. University of South Carolina; Estados UnidosFil: Klein, Eduardo. Universidad Simón Bolívar; VenezuelaFil: Koltes, Karen. Smithsonian Institution; Estados UnidosFil: Laydoo, Richard S.. No especifíca;Fil: Linton, Dulcie M.. University of the West Indies ; JamaicaFil: Ogden, John C.. Florida Institute of Oceanography; Estados UnidosFil: Oxenford, Hazel A.. McGill University; BarbadosFil: Parker, Christoph. McGill University; BarbadosFil: Penchaszadeh, Pablo Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Pors, Leon P. P. J.. Universidad Simón Bolívar; VenezuelaFil: Ramírez Ramírez, Javier. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados. Departamento de Física; MéxicoFil: Ruiz Rentería, Francisco. Universidad Nacional Autónoma de México; MéxicoFil: Ryan, Joseph D.. Centro de Investigación y Documentación de la Costa Atlántica; NicaraguaFil: Smith, Struan R.. Bermuda Biological Station for Research; BermudasFil: Tschirky, John. Latin American and Caribbean Division; Estados UnidosFil: Varela, Ramon. Estación de Investigaciones Marinas de Margarita; VenezuelaFil: Walker, Susan. No especifíca;Fil: Weil, Ernesto. Universidad de Puerto Rico; Puerto RicoFil: Wiebe, William J.. University of Georgia; Estados UnidosFil: Woodley, Jeremy D.. University of the West Indies; JamaicaFil: Zieman, Joseph C.. University of Virginia; Estados Unido

Data-driven sentence simplification: Survey and benchmark

Sentence Simplification (SS) aims to modify a sentence in order to make it easier to read and understand. In order to do so, several rewriting transformations can be performed such as replacement, reordering, and splitting. Executing these transformations while keeping sentences grammatical, preserving their main idea, and generating simpler output, is a challenging and still far from solved problem. In this article, we survey research on SS, focusing on approaches that attempt to learn how to simplify using corpora of aligned original-simplified sentence pairs in English, which is the dominant paradigm nowadays. We also include a benchmark of different approaches on common datasets so as to compare them and highlight their strengths and limitations. We expect that this survey will serve as a starting point for researchers interested in the task and help spark new ideas for future developments