scholarly journals The Effect of Paralogous Lineages on the Application of Reconciliation Analysis by Cophylogeny Mapping

2005 ◽  
Vol 54 (1) ◽  
pp. 127-145 ◽  
Author(s):  
Andrew P. Jackson
Keyword(s):  
Reconciliation Analysis

scholarly journals You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations

2019 ◽  
Vol 37 (2) ◽  
pp. 442-454 ◽  
Author(s):  
Diego Forni ◽  
Rachele Cagliani ◽  
Mario Clerici ◽  
Uberto Pozzoli ◽  
Manuela Sironi
Keyword(s):  
Geographic Distribution ◽  
Human Population ◽  
Strong Support ◽  
Time Frame ◽  
Genetic Distances ◽  
The Philippines ◽  
Molecular Dating ◽  
Human Populations ◽  
Jc Polyomavirus ◽  
Reconciliation Analysis

Abstract JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise FST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based FST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations.

scholarly journals Genomic evidence of bitter taste in snakes and phylogenetic analysis of bitter taste receptor genes in reptiles

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3708 ◽  
Author(s):  
Huaming Zhong ◽  
Shuai Shang ◽  
Xiaoyang Wu ◽  
Jun Chen ◽  
Wanchao Zhu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bitter Taste ◽  
Taste Receptor ◽  
Model Organisms ◽  
Taste Sensation ◽  
Bitter Taste Receptor ◽  
Taste System ◽  
Phylogenetically Independent Contrasts ◽  
Evolutionary Changes ◽  
Reconciliation Analysis

As nontraditional model organisms with extreme physiological and morphological phenotypes, snakes are believed to possess an inferior taste system. However, the bitter taste sensation is essential to distinguish the nutritious and poisonous food resources and the genomic evidence of bitter taste in snakes is largely scarce. To explore the genetic basis of the bitter taste of snakes and characterize the evolution of bitter taste receptor genes (Tas2rs) in reptiles, we identifiedTas2rgenes in 19 genomes (species) corresponding to three orders of non-avian reptiles. Our results indicated contractions ofTas2rgene repertoires in snakes, however dramatic gene expansions have occurred in lizards. Phylogenetic analysis of theTas2rs with NJ and BI methods revealed thatTas2rgenes of snake species formed two clades, whereas in lizards theTas2rgenes clustered into two monophyletic clades and four large clades. Evolutionary changes (birth and death) of intactTas2rgenes in reptiles were determined by reconciliation analysis. Additionally, the taste signaling pathway calcium homeostasis modulator 1 (Calhm1) gene of snakes was putatively functional, suggesting that snakes still possess bitter taste sensation. Furthermore, Phylogenetically Independent Contrasts (PIC) analyses reviewed a significant correlation between the number ofTas2rgenes and the amount of potential toxins in reptilian diets, suggesting that insectivores such as some lizards may require moreTas2rs genes than omnivorous and carnivorous reptiles.

scholarly journals MEDICATION ERROR OVERVIEW AND PREVENTION STRATEGIES

2021 ◽  
pp. 19-24
Keyword(s):  
Medication Error ◽  
Medication Errors ◽  
Medication Safety ◽  
Improve Patient Safety ◽  
Over The Counter ◽  
Reconciliation Analysis ◽  
Prescribing Medication ◽  
Care Costs ◽  
Improve Patient ◽  
Safety Strategy

This literature review aims to highlight the overview of medication errors and strategies to avoid and decrease medication errors. Availability of various types of over-the-counter and prescribed medication has added to the risk of medication. Also, the medication chain has different steps, and different people are involved in each step, such as prescribing medication, dispensing, and administering medication. Every phase in the medication chain is prone to risks that can lead to medication errors. Medication safety is the responsibility of every healthcare professional involved in the medication chain to deliver effective and safe care to patients with an optimal outcome. A medication error can happen in every health care setting to decrease and prevent medication errors. It is critically important to have complete knowledge of the medication use chain and integrate evidence-based strategies, such as medication reconciliation, analysis of medication error, double-check, and avoiding interruption and distraction into practice. Medication errors can lead to patient harm, prevent on-time discharges, and increase care costs. Medication safety culture can shine in a setting of effectively applying strategy into practice, and everyone's collaboration and commitment to adhere to medication safety strategy can improve patient safety.

scholarly journals Comparing Phylogenetic Codivergence between Polyomaviruses and Their Hosts

2006 ◽  
Vol 80 (12) ◽  
pp. 5663-5669 ◽  
Author(s):  
Marcos Pérez-Losada ◽  
Ryan G. Christensen ◽  
David A. McClellan ◽  
Byron J. Adams ◽  
Raphael P. Viscidi ◽  
...  
Keyword(s):  
Bayesian Methods ◽  
Evolutionary History ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Bk Virus ◽  
Hamster Polyomavirus ◽  
Reconciliation Analysis ◽  
History Of ◽  
Bovine Polyomavirus ◽  
Avian Polyomavirus

ABSTRACT Seventy-two full genomes corresponding to nine mammalian (67 strains) and two avian (5 strains) polyomavirus species were analyzed using maximum likelihood and Bayesian methods of phylogenetic inference. Our fully resolved and well-supported (bootstrap proportions > 90%; posterior probabilities = 1.0) trees separate the bird polyomaviruses (avian polyomavirus and goose hemorrhagic polyomavirus) from the mammalian polyomaviruses, which supports the idea of spitting the genus into two subgenera. Such a split is also consistent with the different viral life strategies of each group. Simian (simian virus 40, simian agent 12 [Sa12], and lymphotropic polyomavirus) and rodent (hamster polyomavirus, mouse polyomavirus, and murine pneumotropic polyomavirus [MPtV]) polyomaviruses did not form monophyletic groups. Using our best hypothesis of polyomavirus evolutionary relationships and established host phylogenies, we performed a cophylogenetic reconciliation analysis of codivergence. Our analyses generated six optimal cophylogenetic scenarios of coevolution, including 12 codivergence events (P< 0.01), suggesting that Polyomaviridae coevolved with their avian and mammal hosts. As individual lineages, our analyses showed evidence of host switching in four terminal branches leading to MPtV, bovine polyomavirus, Sa12, and BK virus, suggesting a combination of vertical and horizontal transfer in the evolutionary history of the polyomaviruses.

scholarly journals Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

2009 ◽  
Vol 106 (14) ◽  
pp. 5714-5719 ◽  
Author(s):  
O. Akerborg ◽  
B. Sennblad ◽  
L. Arvestad ◽  
J. Lagergren
Keyword(s):  
Gene Tree ◽  
Tree Reconstruction ◽  
Reconciliation Analysis

scholarly journals JC Virus Evolution and Its Association with Human Populations

2006 ◽  
Vol 80 (20) ◽  
pp. 9928-9933 ◽  
Author(s):  
Laura A. Shackelton ◽  
Andrew Rambaut ◽  
Oliver G. Pybus ◽  
Edward C. Holmes
Keyword(s):  
Phylogenetic Trees ◽  
Nucleotide Substitution ◽  
Jc Virus ◽  
Population History ◽  
Human Polyomavirus ◽  
Human Populations ◽  
Nucleotide Substitution Rate ◽  
Limited Sampling ◽  
Reconciliation Analysis ◽  
And Migration

ABSTRACT The ubiquitous human polyomavirus JC (JCV) is a small double-stranded DNA virus that establishes a persistent infection, and it is often transmitted from parents to children. There are at least 14 subtypes of the virus associated with different human populations. Because of its presumed codivergence with humans, JCV has been used as a genetic marker for human evolution and migration. Codivergence has also been used as a basis for estimating the rate of nucleotide substitution in JCV. We tested the hypothesis of host-virus codivergence by (i) performing a reconciliation analysis of phylogenetic trees of human and JCV populations and (ii) providing the first estimate of the evolutionary rate of JCV that is independent from the assumption of codivergence. Strikingly, our comparisons of JCV and human phylogenies provided no evidence for codivergence, suggesting that this virus should not be used as a marker for human population history. Further, while the estimated nucleotide substitution rate of JCV has large confidence intervals due to limited sampling, our analysis suggests that this virus may evolve nearly two orders of magnitude faster than predicted under the codivergence hypothesis.

scholarly journals Genome-wide probabilistic reconciliation analysis across vertebrates

2013 ◽  
Vol 14 (Suppl 15) ◽  
pp. S10 ◽  
Author(s):  
Owais Mahmudi ◽  
Joel Sjöstrand ◽  
Bengt Sennblad ◽  
Jens Lagergren
Keyword(s):  
Genome Wide ◽  
Reconciliation Analysis

Integrating GIS and GPS Into Today’s Pipeline

2000 ◽  
Author(s):  
David Hobbs ◽  
Keith Rummell
Keyword(s):  
Los Angeles ◽  
Data Collection ◽  
Field Data ◽  
Lessons Learned ◽  
Multiple Sources ◽  
Positional Accuracy ◽  
Construction Monitoring ◽  
Oil Pipeline ◽  
Reconciliation Analysis ◽  
Pipeline Project

Today’s tools and technologies allow the pipeline industry to collect information and describe company pipeline assets in a productive way. Rooney Engineering, Inc. recently completed a 130-mile crude oil pipeline in the greater Los Angeles area of California with which wide ranges of technologies were utilized over an 8-year period. Review of all phases of this pipeline project offers a unique glimpse of managing and integrating traditional survey and Global Positioning System (GPS) techniques with a Geographic Information System (GIS). While the first portion of the project used traditional methods of photogrammetry and Computer Aided Drafting (CAD) to complete the conceptual design and construction drawings, the second portion utilized a combination of CAD, GIS and GPS technologies to assist the construction team during construction and as-built. Geographically organized data was later applied beyond the phases of pipeline construction; data was later used in one-call, contingency planning and emergency response. This paper will give an overview of the project, including pre-construction drawing preparation, construction zones, terrain types, political jurisdictions, and original staff assignments for data collection. The paper will discuss data dictionary design and management of collected field data, equipment and personnel requirements, and accuracy trade-off. The paper will examine the verification of data for attribute integrity and assignment of positional accuracy tags, along with specific methods of GPS and traditional data collection, while also exploring data management of incoming field data from multiple sources over an extensive timeline. Additionally, the paper will focus on the use of GIS to support construction monitoring and cost reconciliation analysis. Finally, we will review preparation of final drawings, summarize lessons learned, and discuss what the future offers in enhancing pipeline-mapping productivity.

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