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https://www.readbyqxmd.com/read/28092570/identifying-epigenetic-biomarkers-using-maximal-relevance-and-minimal-redundancy-based-feature-selection-for-multi-omics-data
#1
Saurav Mallik, Tapas Bhadra, Ujjwal Maulik
Epigenetic Biomarker discovery is an important task in bioinformatics. In this article, we develop a new framework of identifying statistically significant epigenetic biomarkers using maximal-relevance and minimal-redundancy criterion based feature (gene) selection for multi-omics dataset. Firstly, we determine the genes that have both expression as well as methylation values, and follow normal distribution. Similarly, we identify the genes which consist of both expression and methylation values, but do not follow normal distribution...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28091989/hazardous-metal-pollution-in-a-protected-coastal-area-from-northern-patagonia-argentina
#2
C H Marinho, E Giarratano, J L Esteves, M A Narvarte, M N Gil
The San Antonio Bay is a protected natural coastal area of Argentina that has been exposed to mining wastes over the last three decades. Iron and trace metals of potential concern to biota and human health (Cd, Pb, Cu, and Zn) were investigated in the sediments from the bay and in the soils of the Pile (mining wastes). Concentrations of Cd (45 mg kg(-1)), Pb (42,853 mg kg(-1)), Cu (24,505 mg kg(-1)), and Zn (28,686 mg kg(-1)) in the soils Pile exceeded guidelines for agricultural, residential, and industrial land uses...
January 13, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28091764/isolation-of-campylobacter-spp-from-three-species-of-antarctic-penguins-in-different-geographic-locations
#3
F J García-Peña, M T Llorente, T Serrano, M J Ruano, J Belliure, J Benzal, S Herrera-León, V Vidal, V D'Amico, D Pérez-Boto, A Barbosa
The presence of Campylobacter species was studied in three Antarctic penguin species, Adélie (Pygoscelis adeliae), chinstrap (Pygoscelis antarctica) and gentoo (Pygoscelis papua). A total of 390 penguins were captured in 12 different rookeries along the Antarctic Peninsula with differences in the amount of human visitation: six colonies were highly visited [Stranger Point, King George Island (P. papua and P. adeliae); Hannah Point, Livingston Island (P. papua and P. antarctica); Deception Island (P. antarctica); and Paradise Bay, Antarctic Peninsula (P...
January 13, 2017: EcoHealth
https://www.readbyqxmd.com/read/28091595/geological-support-for-the-umbrella-effect-as-a-link-between-geomagnetic-field-and-climate
#4
Ikuko Kitaba, Masayuki Hyodo, Takeshi Nakagawa, Shigehiro Katoh, David L Dettman, Hiroshi Sato
The weakening of the geomagnetic field causes an increase in galactic cosmic ray (GCR) flux. Some researchers argue that enhanced GCR flux might lead to a climatic cooling by increasing low cloud formation, which enhances albedo (umbrella effect). Recent studies have reported geological evidence for a link between weakened geomagnetic field and climatic cooling. However, more work is needed on the mechanism of this link, including whether the umbrella effect is playing a central role. In this research, we present new geological evidence that GCR flux change had a greater impact on continental climate than on oceanic climate...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090334/an-experimental-validation-of-genomic-selection-in-octoploid-strawberry
#5
Salvador A Gezan, Luis F Osorio, Sujeet Verma, Vance M Whitaker
The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013-2014 and 2014-2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28089466/contaminants-of-emerging-concern-in-caspian-tern-compared-to-herring-gull-eggs-from-michigan-colonies-in-the-great-lakes-of-north-america
#6
Guanyong Su, Robert J Letcher, Jeremy N Moore, Lisa L Williams, Keith A Grasman
A broad suite of 87 contaminants of emerging concern (CECs), including 26 polybrominated diphenyl ethers (PBDEs), 23 non-PBDEs halogenated FRs (NPHFRs), 16 organophosphate esters (OPEs), 4 perfluorinated sulfonates (PFSAs), 13 perfluorinated carboxylic acids (PFCAs) and 5 emerging perfluoroalkyl acids (PFAAs) or precursors, were determined in 30 individual Caspian tern (listed as a threatened species in the U.S. State of Michigan) eggs collected in 2013 and 2014 from Michigan nesting sites on Two Tree Island (St, Mary's River), Charity Reef (Saginaw Bay) and Channel-Shelter Island (a Confined Disposal Facility (CDF) in Saginaw Bay)...
January 12, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28089211/toxicity-effects-of-an-environmental-realistic-herbicide-mixture-on-the-seagrass-zostera-noltei
#7
Noël J Diepens, Evelyne Buffan-Dubau, Hélène Budzinski, Jean Kallerhoff, Georges Merlina, Jérome Silvestre, Isabelle Auby, Nathalie Tapie, Arnaud Elger
Worldwide seagrass declines have been observed due to multiple stressors. One of them is the mixture of pesticides used in intensive agriculture and boat antifouling paints in coastal areas. Effects of mixture toxicity are complex and poorly understood. However, consideration of mixture toxicity is more realistic and ecologically relevant for environmental risk assessment (ERA). The first aim of this study was to determine short-term effects of realistic herbicide mixture exposure on physiological endpoints of Zostera noltei...
January 11, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28088848/mercury-bioaccumulation-in-estuarine-fishes-novel-insights-from-sulfur-stable-isotopes
#8
James J Willacker, Collin A Eagles-Smith, Joshua T Ackerman
Estuaries are transitional habitats characterized by complex biogeochemical and ecological gradients that result in substantial variation in fish total mercury concentrations (THg). We leveraged these gradients and used carbon (δ(13)C), nitrogen (δ(15)N), and sulfur (δ(34)S) stable isotopes to examine the ecological and biogeochemical processes underlying THg bioaccumulation in fishes from the San Francisco Bay Estuary. We employed a tiered approach that first examined processes influencing variation in fish THg among wetlands, and subsequently examined the roles of habitat and within-wetland processes in generating larger-scale patterns in fish THg...
January 15, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28088357/joint-genome-wide-prediction-in-several-populations-accounting-for-randomness-of-genotypes-a-hierarchical-bayes-approach-ii-multivariate-spike-and-slab-priors-for-marker-effects-and-derivation-of-approximate-bayes-and-fractional-bayes-factors-for-the-complete
#9
Carlos Alberto Martínez, Kshitij Khare, Arunava Banerjee, Mauricio A Elzo
This study corresponds to the second part of a companion paper devoted to the development of Bayesian multiple regression models accounting for randomness of genotypes in across population genome-wide prediction. This family of models considers heterogeneous and correlated marker effects and allelic frequencies across populations, and has the ability of considering records from non-genotyped individuals and individuals with missing genotypes in any subset of loci without the need for previous imputation, taking into account uncertainty about imputed genotypes...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28087525/capturing-compositional-variation-in-denitrifying-communities-a-multiple-primer-approach-that-includes-autotrophic-denitrifying-epsilonproteobacteria
#10
Sheryl A Murdock, S Kim Juniper
: Denitrifying Epsilonproteobacteria may dominate nitrogen loss processes in marine habitats with intense redox gradients but assessment of their importance is limited by currently available primers for nitrite reductase genes. Nine new primers targeting the nirS gene of denitrifying Epsilonproteobacteria were designed and tested for use in sequencing and quantitative PCR on two microbial mat samples (Vent 2 and Vent 4) from the Calypso hydrothermal vent field, Bay of Plenty, New Zealand...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28081166/comparison-of-criteria-for-choosing-the-number-of-classes-in-bayesian-finite-mixture-models
#11
Kazem Nasserinejad, Joost van Rosmalen, Wim de Kort, Emmanuel Lesaffre
Identifying the number of classes in Bayesian finite mixture models is a challenging problem. Several criteria have been proposed, such as adaptations of the deviance information criterion, marginal likelihoods, Bayes factors, and reversible jump MCMC techniques. It was recently shown that in overfitted mixture models, the overfitted latent classes will asymptotically become empty under specific conditions for the prior of the class proportions. This result may be used to construct a criterion for finding the true number of latent classes, based on the removal of latent classes that have negligible proportions...
2017: PloS One
https://www.readbyqxmd.com/read/28079830/geographic-coverage-of-male-circumcision-in-western-kenya
#12
Adam Akullian, Mathews Onyango, Daniel Klein, Jacob Odhiambo, Anna Bershteyn
Voluntary Medical Male Circumcision (VMMC) for human immunodeficiency virus (HIV) prevention has scaled up rapidly among young men in western Kenya since 2008. Whether the program has successfully reached uncircumcised men evenly across the region is largely unknown. Using data from two cluster randomized surveys from the 2008 and 2014 Kenyan Demographic Health Survey (KDHS), we mapped the continuous spatial distribution of circumcised men by age group across former Nyanza Province to identify geographic areas where local circumcision prevalence is lower than the overall, regional prevalence...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28078815/repeat-measurements-of-uterine-artery-pulsatility-index-mean-arterial-pressure-and-serum-placental-growth-factor-at-12-22-and-32-weeks-in-the-prediction-of-preeclampsia
#13
Silvia Andrietti, Stefania Carlucci, Alan Wright, David Wright, Kypros H Nicolaides
OBJECTIVE: To investigate the potential value of repeat measurements of uterine artery pulsatility index (UTPI), mean arterial pressure (MAP) and serum placental growth factor (PLGF) at 12, 22 and 32 weeks' gestation in the prediction of preeclampsia (PE) after 32 weeks. METHODS: The data were derived from prospective screening for adverse obstetric outcomes in women attending for their routine hospital visit at 11-13, 19-24 and / or 30-34 weeks' gestation in two maternity hospitals in England...
January 12, 2017: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28075331/predictive-modeling-of-respiratory-tumor-motion-for-real-time-prediction-of-baseline-shifts
#14
Arvind Balasubramanian, Rittika Shamsuddin, Balakrishnan Prabhakaran, Amit Sawant
Baseline shifts in respiratory patterns can result in significant spatiotemporal changes in patient anatomy (compared to that captured during simulation), in turn, causing geometric and dosimetric errors in the administration of thoracic and abdominal radiotherapy. We propose predictive modeling of the tumor motion trajectories for predicting a baseline shift ahead of its occurrence. The key idea is to use the features of the tumor motion trajectory over a 1-minute window, and predict the occurrence of a baseline shift in the 5 seconds that immediately follow (lookahead window)...
January 11, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28073760/better-diagnostic-signatures-from-rnaseq-data-through-use-of-auxiliary-co-data
#15
Putri W Novianti, Barbara C Snoek, Saskia M Wilting, Mark A van de Wiel
: Our aim is to improve omics based prediction and feature selection using multiple sources of auxiliary information: co-data. Adaptive group regularized ridge regression (GRridge) was proposed to achieve this by estimating additional group-based penalty parameters through an empirical Bayes method at a low computational cost. We illustrate the GRridge method and software on RNA sequencing data sets. The method boosts the performance of an ordinary ridge regression and outperforms other classifiers...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073756/feature-selection-using-a-one-dimensional-na%C3%A3-ve-bayes-classifier-increases-the-accuracy-of-support-vector-machine-classification-of-cdr3-repertoires
#16
Mattia Cinelli, Yuxin Sun, Katharine Best, James M Heather, Shlomit Reich-Zeliger, Eric Shifrut, Nir Friedman, John Shawe-Taylor, Benny Chain
MOTIVATION: Somatic DNA recombination, the hallmark of vertebrate adaptive immunity, has the potential to generate a vast diversity of antigen receptor sequences. How this diversity captures antigen specificity remains incompletely understood. In this study we use high throughput sequencing to compare the global changes in T cell receptor β chain complementarity determining region 3 (CDR3β) sequences following immunization with ovalbumin administered with complete Freund's adjuvant (CFA) or CFA alone...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073565/heterogeneous-distribution-in-sediments-and-dispersal-in-waters-of-alexandrium-minutum-in-a-semi-enclosed-coastal-ecosystem
#17
Z K Klouch, F Caradec, M Plus, T Hernández-Fariñas, L Pineau-Guillou, A Chapelle, S Schmitt, J Quéré, L Guillou, R Siano
Within the framework of research aimed at using genetic methods to evaluate harmful species distribution and their impact on coastal ecosystems, a portion of the ITS1rDNA of Alexandrium minutum was amplified by real-time PCR from DNA extracts of superficial (1-3cm) sediments of 30 subtidal and intertidal stations of the Bay of Brest (Brittany, France), during the winters of 2013 and 2015. Cell germinations and rDNA amplifications of A. minutum were obtained for sediments of all sampled stations, demonstrating that the whole bay is currently contaminated by this toxic species...
December 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073553/the-effects-of-light-intensity-on-the-growth-of-japanese-gambierdiscus-spp-dinophyceae
#18
Takamichi Yoshimatsu, Chaoyu Tie, Haruo Yamaguchi, Hiroshi Funaki, Chiho Honma, Kouki Tanaka, Masao Adachi
Marine toxic dinoflagellates of the genus Gambierdiscus are the causative agents of ciguatera fish poisoning (CFP), a form of seafood poisoning that is widespread in tropical, subtropical and temperate regions worldwide. The distributions of Gambierdiscus australes, Gambierdiscus scabrosus and two phylotypes of Gambierdiscus spp. type 2 and type 3 have been reported for the waters surrounding the main island of Japan. To explore the bloom dynamics and the vertical distribution of these Japanese species and phylotypes of Gambierdiscus, the effects of light intensity on their growth were tested, using a photoirradiation-culture system...
December 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073525/delineation-of-the-role-of-nutrient-variability-and-dreissenids-mollusca-bivalvia-on-phytoplankton-dynamics-in-the-bay-of-quinte-ontario-canada
#19
Yuko Shimoda, Sue B Watson, Michelle E Palmer, Marten A Koops, Shan Mugalingam, Andrew Morley, George B Arhonditsis
The Bay of Quinte, a Z-shaped embayment at the northeastern end of Lake Ontario, has a long history of eutrophication problems primarily manifested as spatially extensive algal blooms and predominance of toxic cyanobacteria. The purpose of this study was to identify the structural changes of the phytoplankton community induced by two environmental alterations: point-source phosphorus (P) loading reduction in the late 1970s and establishment of dreissenid mussels in the mid-1990s. A combination of statistical techniques was used to draw inference about compositional shifts of the phytoplankton assemblage, the consistency of the seasonal succession patterns along with the mechanisms underlying the algal biovolume variability in the Bay of Quinte over the past three decades...
May 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073507/evidence-of-freshwater-algal-toxins-in-marine-shellfish-implications-for-human-and-aquatic-health
#20
Corinne M Gibble, Melissa B Peacock, Raphael M Kudela
The occurrence of freshwater harmful algal bloom toxins impacting the coastal ocean is an emerging threat, and the potential for invertebrate prey items to concentrate toxin and cause harm to human and wildlife consumers is not yet fully recognized. We examined toxin uptake and release in marine mussels for both particulate and dissolved phases of the hepatotoxin microcystin, produced by the freshwater cyanobacterial genus Microcystis. We also extended our experimental investigation of particulate toxin to include oysters (Crassostrea sp...
November 2016: Harmful Algae
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