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https://www.readbyqxmd.com/read/29028869/mg-rast-version-4-lessons-learned-from-a-decade-of-low-budget-ultra-high-throughput-metagenome-analysis
#1
Folker Meyer, Saurabh Bagchi, Somali Chaterji, Wolfgang Gerlach, Ananth Grama, Travis Harrison, Tobias Paczian, William L Trimble, Andreas Wilke
As technologies change, MG-RAST is adapting. Newly available software is being included to improve accuracy and performance. As a computational service constantly running large volume scientific workflows, MG-RAST is the right location to perform benchmarking and implement algorithmic or platform improvements, in many cases involving trade-offs between specificity, sensitivity and run-time cost. The work in [Glass EM, Dribinsky Y, Yilmaz P, et al. ISME J 2014;8:1-3] is an example; we use existing well-studied data sets as gold standards representing different environments and different technologies to evaluate any changes to the pipeline...
September 26, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29028838/sequentially-optimized-reconstruction-strategy-a-meta-strategy-for-perimetry-testing
#2
Şerife Seda Kucur, Raphael Sznitman
Perimetry testing is an automated method to measure visual function and is heavily used for diagnosing ophthalmic and neurological conditions. Its working principle is to sequentially query a subject about perceived light using different brightness levels at different visual field locations. At a given location, this query-patient-feedback process is expected to converge at a perceived sensitivity, such that a shown stimulus intensity is observed and reported 50% of the time. Given this inherently time-intensive and noisy process, fast testing strategies are necessary in order to measure existing regions more effectively and reliably...
2017: PloS One
https://www.readbyqxmd.com/read/29027331/when-does-it-pay-to-invest-in-a-patch-the-evolution-of-intentional-niche-construction
#3
Kathryn A Mohlenhoff, Brian F Codding
Humans modify their environments in ways that significantly transform the earth's ecosystems. Recent research suggests that such niche-constructing behaviors are not passive human responses to environmental variation, but instead should be seen as active and intentional management of the environment. Although such research is useful in highlighting the interactive dynamics between humans and their natural world, the niche-construction framework, as currently applied, fails to explain why people would decide to modify their environments in the first place...
September 2017: Evolutionary Anthropology
https://www.readbyqxmd.com/read/29027240/low-dose-ct-reconstruction-using-spatially-encoded-nonlocal-penalty
#4
Kyungsang Kim, Georges El Fakhri, Quanzheng Li
PURPOSE: Computed tomography (CT) is one of the most used imaging modalities for imaging both symptomatic and asymptomatic patients. However, because of the high demand for lower radiation dose during CT scans, the reconstructed image can suffer from noise and artifacts due to the trade-off between the image quality and the radiation dose. The purpose of this paper is to improve the image quality of quarter dose images and to select the best hyperparameters using the regular dose image as ground truth...
October 2017: Medical Physics
https://www.readbyqxmd.com/read/29026880/adaptive-social-strategies-in-a-solitary-carnivore
#5
L Mark Elbroch, Michael Levy, Mark Lubell, Howard Quigley, Anthony Caragiulo
Cost-benefit trade-offs for individuals participating in social behaviors are the basis for current theories on the evolution of social behaviors and societies. However, research on social strategies has largely ignored solitary animals, in which we assume that rare interactions are explained by courtship or territoriality or, in special circumstances, resource distributions or kinship. We used directed network analysis of conspecific tolerance at food sources to provide evidence that a solitary carnivore, the puma (Puma concolor), exhibited adaptive social strategies similar to more social animals...
October 2017: Science Advances
https://www.readbyqxmd.com/read/29024072/structurally-deformed-mos2-for-electrochemically-stable-thermally-resistant-and-highly-efficient-hydrogen-evolution-reaction
#6
Yen-Chang Chen, Ang-Yu Lu, Ping Lu, Xiulin Yang, Chang-Ming Jiang, Marina Mariano, Brian Kaehr, Oliver Lin, André Taylor, Ian D Sharp, Lain-Jong Li, Stanley S Chou, Vincent Tung
The emerging molybdenum disulfide (MoS2 ) offers intriguing possibilities for realizing a transformative new catalyst for driving the hydrogen evolution reaction (HER). However, the trade-off between catalytic activity and long-term stability represents a formidable challenge and has not been extensively addressed. This study reports that metastable and temperature-sensitive chemically exfoliated MoS2 (ce-MoS2 ) can be made into electrochemically stable (5000 cycles), and thermally robust (300 °C) while maintaining synthetic scalability and excellent catalytic activity through physical-transformation into 3D structurally deformed nanostructures...
October 12, 2017: Advanced Materials
https://www.readbyqxmd.com/read/29023482/the-trade-off-between-morphology-and-control-in-the-co-optimized-design-of-robots
#7
Andre Rosendo, Marco von Atzigen, Fumiya Iida
Conventionally, robot morphologies are developed through simulations and calculations, and different control methods are applied afterwards. Assuming that simulations and predictions are simplified representations of our reality, how sure can roboticists be that the chosen morphology is the most adequate for the possible control choices in the real-world? Here we study the influence of the design parameters in the creation of a robot with a Bayesian morphology-control (MC) co-optimization process. A robot autonomously creates child robots from a set of possible design parameters and uses Bayesian Optimization (BO) to infer the best locomotion behavior from real world experiments...
2017: PloS One
https://www.readbyqxmd.com/read/29023381/design-of-a-low-cost-air-levitation-system-for-teaching-control-engineering
#8
Jesus Chacon, Jacobo Saenz, Luis de la Torre, Jose Manuel Diaz, Francisco Esquembre
Air levitation is the process by which an object is lifted without mechanical support in a stable position, by providing an upward force that counteracts the gravitational force exerted on the object. This work presents a low-cost lab implementation of an air levitation system, based on open solutions. The rapid dynamics makes it especially suitable for a control remote lab. Due to the system's nature, the design can be optimized and, with some precision trade-off, kept affordable both in cost and construction effort...
October 12, 2017: Sensors
https://www.readbyqxmd.com/read/29021399/modelling-of-anti-latency-treatment-in-hiv-what-is-the-optimal-duration-of-anti-retroviral-free-hiv-remission
#9
Deborah Cromer, Mykola Pinkevych, Thomas A Rasmussen, Sharon R Lewin, Stephen J Kent, Miles P Davenport
A number of treatment strategies are currently being developed to promote anti-retroviral free HIV cure or remission. While complete elimination of the HIV reservoir would prevent recurrence of infection, it is not clear how different remission lengths would affect viral rebound and transmission. In this work we use a stochastic model to show that a treatment that achieves a one-year average time to viral remission will still lead to nearly a quarter of subjects experiencing viral rebound within the first three months...
October 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29020867/activation-of-the-behavioral-immune-system-putting-the-brakes-on-affiliation
#10
Natsumi Sawada, Emilie Auger, John E Lydon
Evolutionary psychologists propose that humans evolved a first line of defense against pathogens: the behavioral immune system (BIS). The BIS is thought to be functionally flexible such that the likelihood and magnitude of BIS activation depends on the individual's perceived vulnerability to disease (PVD). Because conspecifics are sources of infection, the BIS has implications for affiliation. By priming and measuring chronic levels of PVD, we examined PVD's relation to affiliation in zero-acquaintance situations in the laboratory, online, and during speed-dating events...
October 1, 2017: Personality & Social Psychology Bulletin
https://www.readbyqxmd.com/read/29020131/data-adaptive-estimation-for-double-robust-methods-in-population-based-cancer-epidemiology-risk-differences-for-lung-cancer-mortality-by-emergency-presentation
#11
Miguel Angel Luque-Fernandez, Aurélien Belot, Linda Valeri, Giovanni Ceruli, Camille Maringe, Bernard Rachet
We propose a structural framework for population-based cancer epidemiology and evaluate the performance of double-robust estimators for a binary exposure in cancer mortality. We performed numerical analyses to study the bias and efficiency of these estimators. Furthermore, we compared two different model selection strategies based on 1) the Akaike and Bayesian Information Criteria and 2) machine-learning algorithms, and illustrated double-robust estimators' performance in a real setting. In simulations with correctly specified models and near-positivity violations, all but the naïve estimators presented relatively good performance...
September 11, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29020041/how-will-climate-change-pathways-and-mitigation-options-alter-incidence-of-vector-borne-diseases-a-framework-for-leishmaniasis-in-south-and-meso-america
#12
Bethan V Purse, Dario Masante, Nicholas Golding, David Pigott, John C Day, Sergio Ibañez-Bernal, Melanie Kolb, Laurence Jones
The enormous global burden of vector-borne diseases disproportionately affects poor people in tropical, developing countries. Changes in vector-borne disease impacts are often linked to human modification of ecosystems as well as climate change. For tropical ecosystems, the health impacts of future environmental and developmental policy depend on how vector-borne disease risks trade off against other ecosystem services across heterogeneous landscapes. By linking future socio-economic and climate change pathways to dynamic land use models, this study is amongst the first to analyse and project impacts of both land use and climate change on continental-scale patterns in vector-borne diseases...
2017: PloS One
https://www.readbyqxmd.com/read/29019295/exploring-values-of-health-technology-assessment-agencies-using-reflective-multicriteria-and-rare-disease-case
#13
Mireille M Goetghebeur, Monika Wagner, Dima Samaha, William O'Neil, Danielle Badgley, Hector Castro-Jaramillo, Payam Abrishami, Antonio Sarria-Santamera, Irina Cleemput, Michele Tringali
OBJECTIVES: Tackling ethical dilemmas faced by reimbursement decision makers requires deeper understanding of values on which health technology assessment (HTA) agencies are founded and how trade-offs are made. This was explored in this study including the case of rare disease. METHODS: Representatives from eight HTA explored values on which institutions are founded using a narrative approach and reflective multicriteria (developed from EVIDEM, criteria derived from ethical imperatives of health care)...
October 11, 2017: International Journal of Technology Assessment in Health Care
https://www.readbyqxmd.com/read/29019161/assessing-the-use-of-a-feedback-module-to-model-eq-5d-5l-health-states-values-in-hong-kong
#14
Eliza L Y Wong, Juan Manuel Ramos-Goñi, Annie W L Cheung, Amy Y K Wong, Oliver Rivero-Arias
BACKGROUND: An international valuation protocol exists for obtaining societal values for each of the 3125 health states of the five-level EuroQol-five dimensions (EQ-5D-5L) questionnaire. A feedback module (FM) that can be related to theoretical models used in behavioral economics was recently included in this protocol. OBJECTIVES: Our objective was to assess the impact of using an FM to estimate an EQ-5D-5L value set in Hong Kong. METHODS: EQ-5D-5L health states were elicited using a composite time trade-off (C-TTO) and a discrete-choice (DC) experiment...
October 10, 2017: Patient
https://www.readbyqxmd.com/read/29019023/challenges-associated-with-estimating-utility-in-wet-age-related-macular-degeneration-a-novel-regression-analysis-to-capture-the-bilateral-nature-of-the-disease
#15
Robert Hodgson, Timothy Reason, David Trueman, Rose Wickstead, Jeanette Kusel, Adam Jasilek, Lindsay Claxton, Matthew Taylor, Ruth Pulikottil-Jacob
INTRODUCTION: The estimation of utility values for the economic evaluation of therapies for wet age-related macular degeneration (AMD) is a particular challenge. Previous economic models in wet AMD have been criticized for failing to capture the bilateral nature of wet AMD by modelling visual acuity (VA) and utility values associated with the better-seeing eye only. METHODS: Here we present a de novo regression analysis using generalized estimating equations (GEE) applied to a previous dataset of time trade-off (TTO)-derived utility values from a sample of the UK population that wore contact lenses to simulate visual deterioration in wet AMD...
October 10, 2017: Advances in Therapy
https://www.readbyqxmd.com/read/29018951/the-role-of-the-mating-system-and-intraspecific-brood-parasitism-in-the-costs-of-reproduction-in-a-passerine-bird
#16
Raquel Monclús, Jaime Muriel, Lorenzo Pérez-Rodríguez, Anders P Møller, Diego Gil
Limited resources trigger trade-offs in resource allocation. Reproduction is one of the most demanding activities in terms of energy, and costs related to reproduction can be apparent either as reduced future reproduction or as survival. However, costs are not always detected, because individual heterogeneity in quality and resource acquisition may explain variation in costs among individuals. We conducted a comprehensive study in spotless starlings (Sturnus unicolor) nesting in Central Spain to determine whether costs of reproduction could be detectable in the short and/or long term and whether prenatal or postnatal investment were driving these costs...
October 10, 2017: Oecologia
https://www.readbyqxmd.com/read/29018488/higher-resting-metabolic-rate-in-long-lived-breeding-ansell-s-mole-rats-fukomys-anselli
#17
Charlotte Katharina Maria Schielke, Hynek Burda, Yoshiyuki Henning, Jan Okrouhlík, Sabine Begall
BACKGROUND: Reproduction is an energetically expensive process that supposedly impairs somatic integrity in the long term, because resources are limited and have to be allocated between reproduction and somatic maintenance, as predicted by the life history trade-off model. The consequence of reduced investment in somatic maintenance is a gradual deterioration of function, i.e. senescence. However, this classical trade-off model gets challenged by an increasing number of contradicting studies...
2017: Frontiers in Zoology
https://www.readbyqxmd.com/read/29018197/the-chromosomal-organization-of-horizontal-gene-transfer-in-bacteria
#18
Pedro H Oliveira, Marie Touchon, Jean Cury, Eduardo P C Rocha
Bacterial adaptation is accelerated by the acquisition of novel traits through horizontal gene transfer, but the integration of these genes affects genome organization. We found that transferred genes are concentrated in only ~1% of the chromosomal regions (hotspots) in 80 bacterial species. This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements...
October 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/29017463/subjective-health-expectations-of-patients-with-age-related-macular-degeneration-treated-with-antivegf-drugs
#19
Márta Péntek, Valentin Brodszky, Zsolt Biró, Zsófia Kölkedi, Árpád Dunai, János Németh, Petra Baji, Fanni Rencz, László Gulácsi, Miklós D Resch
BACKGROUND: Subjective expectations regarding future health may influence patients' judgement of current health and treatment effects, as well as adherence to therapies in chronic diseases. We aimed to explore subjective expectations on longevity and future health-related quality of life (HRQOL) of patients with age-related macular degeneration (AMD) treated with antiVEGF injections and analyse the influencing factors. METHODS: Consecutive AMD patients in two ophthalmology centres were included...
October 10, 2017: BMC Geriatrics
https://www.readbyqxmd.com/read/29016633/apparent-survival-and-cost-of-reproduction-for-white-lined-tanager-tachyphonus-rufus-thraupidae-in-the-northern-atlantic-rainforest-brazil
#20
Phoeve Macario, Mauro Pichorim, Paul F Doherty, Guilherme S Toledo-Lima, Tonny M Oliveira-Júnior, Thanyria P F Câmara, Shirley Macjane Melo, João Lucas S Silveira, Juliana C Araújo, Leonardo F França
Understanding latitudinal variation in avian life-history traits has been a focus of many demographic studies around the world. However, we still know little about annual or intra-annual demographic variation within tropical regions or about how factors such as breeding season and precipitation influence demographic rates. In this study, we estimated intra-annual apparent survival of the White-lined Tanager (Tachyphonus rufus) using capture-mark-recapture data from northeastern Brazil. We tested whether survival varied seasonally (breeding vs...
2017: PloS One
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