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https://www.readbyqxmd.com/read/29451846/link-between-the-adult-and-the-metacercaria-of-clinostomum-heluans-braun-1899-trematoda-clinostomidae-through-dna-sequences-and-its-phylogenetic-position-within-the-genus-clinostomum-leidy-1856
#1
Rosario Briosio-Aguilar, Hudson Alves Pinto, Maria Amparo Rodríguez-Santiago, Karina López-García, Martin Garcia-Varela, Gerardo Perez-Ponce de Leon
The phylogenetic position of Clinostomum heluans Braun, 1899 within the genus Clinostomum Leidy, 1856 is reported in this study based on sequences of the barcoding region of the mitochondrial cytochrome c oxidase subunit 1 gene (COX1). Additionally, molecular data are used to link the adult and the metacercariae of the species. The metacercariae of C. heluans were found encysted infecting the cichlid fish Australoheros sp. in Minas Gerais, Brazil, whereas the adults were obtained from the mouth cavity of the Great White egret Ardea alba, in Campeche, Mexico...
February 16, 2018: Journal of Parasitology
https://www.readbyqxmd.com/read/29451425/biliary-tract-infecting-myxosporeans-from-estuarine-and-reef-stonefish-scorpaeniformes-synanceiidae-off-eastern-australia-with-descriptions-of-sphaeromyxa-horrida-n-sp-and-myxidium-lapipiscis-n-sp-myxosporea-bivalvulida
#2
Terrence Miller, Samantha Barnett, Jamie Seymour, Timothy Jenkins, Marissa McNamara, Robert Douglas Adlard
Two new species of myxosporeans are described from the gall bladders of Estuarine Stonefish, Synanceia horrida, and Reef Stonefish, Synanceia verrucosa, from localities off Cairns, in tropical north Queensland (QLD) and in Moreton Bay in southern QLD, Australia. Sphaeromyxa horrida n. sp. can be distinguished from congeners in the morphologically distinct "balbianii" species group within Sphaeromyxa based on morphometric differences in length and width of mature spores, length and width of polar capsules and unique SSU rDNA sequence composition relative to other taxa...
February 16, 2018: Journal of Parasitology
https://www.readbyqxmd.com/read/29451087/multiple-imputation-with-sequential-penalized-regression
#3
Faisal M Zahid, Christian Heumann
Missing data is a common issue that can cause problems in estimation and inference in biomedical, epidemiological and social research. Multiple imputation is an increasingly popular approach for handling missing data. In case of a large number of covariates with missing data, existing multiple imputation software packages may not work properly and often produce errors. We propose a multiple imputation algorithm called mispr based on sequential penalized regression models. Each variable with missing values is assumed to have a different distributional form and is imputed with its own imputation model using the ridge penalty...
January 1, 2018: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/29450705/modeling-competence-development-in-the-presence-of-selection-bias
#4
Sabine Zinn, Timo Gnambs
A major challenge for representative longitudinal studies is panel attrition, because some respondents refuse to continue participating across all measurement waves. Depending on the nature of this selection process, statistical inferences based on the observed sample can be biased. Therefore, statistical analyses need to consider a missing-data mechanism. Because each missing-data model hinges on frequently untestable assumptions, sensitivity analyses are indispensable to gauging the robustness of statistical inferences...
February 15, 2018: Behavior Research Methods
https://www.readbyqxmd.com/read/29449878/complete-chloroplast-genome-of-the-medicinal-plant-amomum-compactum-gene-organization-comparative-analysis-and-phylogenetic-relationships-within-zingiberales
#5
Ming-Li Wu, Qing Li, Jiang Xu, Xi-Wen Li
Background: Amomum compactum is one of the basic species of the traditional herbal medicine amomi fructus rotundus, with great pharmacology effect. The system position of A. compactum is not clear yet, and the introduction of this plant has been hindered by many plant diseases. However, the correlational molecular studies are relatively scarce. Methods: The total chloroplast (cp) DNA was extracted according to previous studies, and then sequenced by 454 GS FLX Titanium platform...
2018: Chinese Medicine
https://www.readbyqxmd.com/read/29449446/improving-accuracy-of-simultaneously-reconstructed-activity-and-attenuation-maps-using-deep-learning
#6
Donghwi Hwang, Kyeong Yun Kim, Seung Kwan Kang, Seongho Seo, Jin Chul Paeng, Dong Soo Lee, Jae Sung Lee
Simultaneous reconstruction of activity and attenuation using the maximum likelihood reconstruction of activity and attenuation (MLAA) augmented by time-of-flight (TOF) information is a promising method for positron emission tomography (PET) attenuation correction. However, it still suffers from several problems, including crosstalk artifacts, slow convergence speed, and noisy attenuation maps (μ-maps). In this work, we developed deep convolutional neural networks (CNNs) to overcome these MLAA limitations, and we verified their feasibility using a clinical brain PET data set...
February 15, 2018: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/29448075/improving-mass-univariate-analysis-of-neuroimaging-data-by-modelling-important-unknown-covariates-application-to-epigenome-wide-association-studies
#7
Bryan Guillaume, Changqing Wang, Joann Poh, Mo Jun Shen, Mei Lyn Ong, Pei Fang Tan, Neerja Karnani, Michael Meaney, Anqi Qiu
Statistical inference on neuroimaging data is often conducted using a mass-univariate model, equivalent to fitting a linear model at every voxel with a known set of covariates. Due to the large number of linear models, it is challenging to check if the selection of covariates is appropriate and to modify this selection adequately. The use of standard diagnostics, such as residual plotting, is clearly not practical for neuroimaging data. However, the selection of covariates is crucial for linear regression to ensure valid statistical inference...
February 12, 2018: NeuroImage
https://www.readbyqxmd.com/read/29447183/a-mass-density-model-can-account-for-the-size-weight-illusion
#8
Christian Wolf, Wouter M Bergmann Tiest, Knut Drewing
When judging the heaviness of two objects with equal mass, people perceive the smaller and denser of the two as being heavier. Despite the large number of theories, covering bottom-up and top-down approaches, none of them can fully account for all aspects of this size-weight illusion and thus for human heaviness perception. Here we propose a new maximum-likelihood estimation model which describes the illusion as the weighted average of two heaviness estimates with correlated noise: One estimate derived from the object's mass, and the other from the object's density, with estimates' weights based on their relative reliabilities...
2018: PloS One
https://www.readbyqxmd.com/read/29446081/under-the-weather-the-direct-effects-of-climate-warming-on-a-threatened-desert-lizard-are-mediated-by-their-activity-phase-and-burrow-system
#9
Danae Moore, Adam Stow, Michael Ray Kearney
1.For ectotherms such as lizards, the importance of behavioral thermoregulation in avoiding thermal extremes is well established and is increasingly acknowledged in modern studies of climate warming and its impacts. Less appreciated and understood are the buffering roles of retreat sites and activity phase, in part because of logistical challenges of studying below-ground activity. Burrowing and nocturnal activity are key behavioral adaptations that have enabled a diverse range of reptiles to survive extreme environmental temperatures within hot desert regions...
February 15, 2018: Journal of Animal Ecology
https://www.readbyqxmd.com/read/29446071/indistinguishability-tests-in-the-actor-partner-interdependence-model
#10
Fien Gistelinck, Tom Loeys, Mieke Decuyper, Marieke Dewitte
When considering dyadic data, one of the questions is whether the roles of the two dyad members can be considered equal. This question may be answered empirically using indistinguishability tests in the actor-partner interdependence model. In this paper several issues related to such indistinguishability tests are discussed: the difference between maximum likelihood and restricted maximum likelihood based tests for equality in variance parameters; the choice between the structural equation modelling and multilevel modelling framework; and the use of sequential testing rather than one global test for a set of indistinguishability tests...
February 15, 2018: British Journal of Mathematical and Statistical Psychology
https://www.readbyqxmd.com/read/29443502/direct-classification-of-gc-%C3%A3-gc-analyzed-complex-mixtures-using-non-negative-matrix-factorization-based-feature-extraction
#11
Yasuyuki Zushi, Shunji Hashimoto
Complex chemical mixtures need to be evaluated to, for example, aid in medical diagnoses, assess product quality, and assess environmental conditions. Two-dimensional gas chromatography (GC × GC), which is a comprehensive analytical technique, combined with data classification techniques has attracted great interest for assessing mixtures. In this study, a nontarget cross-sample analysis-based unsupervised direct classification method using non-negative matrix factorization was developed for assessing mixtures analyzed by GC × GC...
February 14, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29443086/using-three-color-single-molecule-fret-to-study-the-correlation-of-protein-interactions
#12
Markus Götz, Philipp Wortmann, Sonja Schmid, Thorsten Hugel
Single-molecule Förster resonance energy transfer (smFRET) has become a widely used biophysical technique to study the dynamics of biomolecules. For many molecular machines in a cell proteins have to act together with interaction partners in a functional cycle to fulfill their task. The extension of two-color to multi-color smFRET makes it possible to simultaneously probe more than one interaction or conformational change. This not only adds a new dimension to smFRET experiments but it also offers the unique possibility to directly study the sequence of events and to detect correlated interactions when using an immobilized sample and a total internal reflection fluorescence microscope (TIRFM)...
January 30, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29442279/robust-estimation-in-accelerated-failure-time-models
#13
Sanjoy K Sinha
The accelerated failure time model is widely used for analyzing censored survival times often observed in clinical studies. It is well-known that the ordinary maximum likelihood estimators of the parameters in the accelerated failure time model are generally sensitive to potential outliers or small deviations from the underlying distributional assumptions. In this paper, we propose and explore a robust method for fitting the accelerated failure time model to survival data by bounding the influence of outliers in both the outcome variable and associated covariates...
February 13, 2018: Lifetime Data Analysis
https://www.readbyqxmd.com/read/29441237/comparison-of-complex-networks-and-tree-based-methods-of-phylogenetic-analysis-and-proposal-of-a-bootstrap-method
#14
Aristóteles Góes-Neto, Marcelo V C Diniz, Daniel S Carvalho, Gilberto C Bomfim, Angelo A Duarte, Jerzy A Brzozowski, Thierry C Petit Lobão, Suani T R Pinho, Charbel N El-Hani, Roberto F S Andrade
Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits...
2018: PeerJ
https://www.readbyqxmd.com/read/29438894/novel-edge-treatment-method-for-improving-the-transmission-reconstruction-quality-in-tomographic-gamma-scanning
#15
Miaomiao Han, Zhirong Guo, Haifeng Liu, Qinghua Li
Tomographic Gamma Scanning (TGS) is a method used for the nondestructive assay of radioactive wastes. In TGS, the actual irregular edge voxels are regarded as regular cubic voxels in the traditional treatment method. In this study, in order to improve the performance of TGS, a novel edge treatment method is proposed that considers the actual shapes of these voxels. The two different edge voxel treatment methods were compared by computing the pixel-level relative errors and normalized mean square errors (NMSEs) between the reconstructed transmission images and the ideal images...
February 6, 2018: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/29438538/testing-the-role-of-the-red-queen-and-court-jester-as-drivers-of-the-macroevolution-of-apollo-butterflies
#16
Fabien L Condamine, Jonathan Rolland, Sebastian Höhna, Felix A H Sperling, Isabel Sanmartín
In macroevolution, the Red Queen (RQ) model posits that biodiversity dynamics depend mainly on species-intrinsic biotic factors such as interactions among species or life-history traits, while the Court Jester (CJ) model states that extrinsic environmental abiotic factors have a stronger role. Until recently, a lack of relevant methodological approaches has prevented the unraveling of contributions from these two types of factors to the evolutionary history of a lineage. Here we take advantage of the rapid development of new macroevolution models that tie diversification rates to changes in paleoenvironmental (extrinsic) and/or biotic (intrinsic) factors...
February 9, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29438519/convergent-evolution-of-human-isolated-h7n9-avian-influenza-a-viruses
#17
Dan Xiang, Xuejuan Shen, Zhiqing Pu, David M Irwin, Ming Liao, Yongyi Shen
Background: Avian influenza A virus (AIV) H7N9 has caused five epidemic waves of human infections in China since 2013. AIVs may face strong selection to adapt to novel conditions when establishing themselves in humans. In this study, we sought to determine whether adaptive evolution had occurred in human-isolated H7N9 viruses. Methods: We evaluated all available genomes of H7N9 AIVs. Maximum likelihood trees were separately reconstructed for all eight genes. Signals of positive selection and convergent evolution were then detected on branches that lead to changes in host tropism (from avian to human)...
February 9, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29438407/the-complete-mitochondrial-genome-of-somanniathelphusa-boyangensis-and-phylogenetic-analysis-of-genus-somanniathelphusa-crustacea-decapoda-parathelphusidae
#18
Xin-Nan Jia, Shu-Xin Xu, Jun Bai, Yi-Fan Wang, Zong-Heng Nie, Chun-Chao Zhu, Yan Wang, Yi-Xiong Cai, Jie-Xin Zou, Xian-Min Zhou
In this study, the authors first obtained the mitochondrial genome of Somanniathelphusa boyangensis. The results showed that the mitochondrial genome is 17,032bp in length, included 13 protein-coding genes, 2 rRNAs genes, 22 tRNAs genes and 1 putative control region, and it has the characteristics of the metazoan mitochondrial genome A+T bias. All tRNA genes display the typical clover-leaf secondary structure except tRNASer(AGN), which has lost the dihydroxyuridine arm. The GenBank database contains the mitochondrial genomes of representatives of approximately 22 families of Brachyura, comprising 56 species, including 4 species of freshwater crab...
2018: PloS One
https://www.readbyqxmd.com/read/29438005/maximum-likelihood-expectation-maximization-algorithm-vs-windowed-filtered-backprojection-algorithm-a-case-study
#19
Gengsheng Lawrence Zeng
Objective: The FBP (filtered backprojection) algorithm reduces image noise by smoothing the image. The iterative algorithm reduces image noise by noise weighting and regularization. A myth is that the iterative algorithm is able to reduce the noise without sacrificing image resolution, and thus iterative algorithms especially the ML-EM (maximum-likelihood expectation-maximization) algorithm are used in nuclear medicine to replace the FBP algorithm. Methods: This short paper uses counter examples to show that this myth is not true...
February 2, 2018: Journal of Nuclear Medicine Technology
https://www.readbyqxmd.com/read/29432850/combining-high-throughput-sequencing-and-targeted-loci-data-to-infer-the-phylogeny-of-the-adenocalymma-neojobertia-clade-bignonieae-bignoniaceae
#20
Luiz Henrique M Fonseca, Lúcia G Lohmann
Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae), a diverse lineage of Neotropical plants, using Maximum Likelihood and Bayesian approaches. We used NGS to obtain complete or nearly-complete plastomes of members of this clade, leading to a final dataset with 54 individuals, representing 44 members of ingroup and 10 outgroups...
February 9, 2018: Molecular Phylogenetics and Evolution
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