Consensus and Confusion in Molluscan Trees: Evaluating Morphological and Molecular Phylogenies

Mollusks are the most morphologically disparate living animal phylum, they have diversified into all habitats, and have a deep fossil record. Monophyly and identity of their eight living classes is undisputed, but relationships between these groups and patterns of their early radiation have remained elusive. Arguments about traditional morphological phylogeny focus on a small number of topological concepts but often without regard to proximity of the individual classes. In contrast, molecular studies have proposed a number of radically different, inherently contradictory, and controversial sister relationships. Here, we assembled a dataset of 42 unique published trees describing molluscan interrelationships. We used these data to ask several questions about the state of resolution of molluscan phylogeny compared to a null model of the variation possible in random trees constructed from a monophyletic assemblage of eight terminals. Although 27 different unique trees have been proposed from morphological inference, the majority of these are not statistically different from each other. Within the available molecular topologies, only four studies to date have included the deep-sea class Monoplacophora; but 36.4% of all trees are not significantly different. We also present supertrees derived from 2 data partitions and 3 methods, including all available molecular molluscan phylogenies, which will form the basis for future hypothesis testing. The supertrees presented here were not constructed to provide yet another hypothesis of molluscan relationships, but rather to algorithmically evaluate the relationships present in the disparate published topologies. Based on the totality of available evidence, certain patterns of relatedness among constituent taxa become clear. The internodal distance is consistently short between a few taxon pairs, particularly supporting the relatedness of Monoplacophora and the chitons, Polyplacophora. Other taxon pairs are rarely or never found in close proximity, such as the vermiform Caudofoveata and Bivalvia. Our results have specific utility for guiding constructive research planning in order to better test relationships in Mollusca as well as other problematic groups. Taxa with consistently proximate relationships should be the focus of a combined approach in a concerted assessment of potential genetic and anatomical homology, while unequivocally distant taxa will make the most constructive choices for exemplar selection in higher-level phylogenomic analyses.

BOB CAT: a Large-Scale Review and Delphi Consensus for Management of Barrett’s Esophagus With No Dysplasia, Indefinite for, or Low-Grade Dysplasia

OBJECTIVES: Barrett’s esophagus (BE) is a common premalignant lesion for which surveillance is recommended. This strategy is limited by considerable variations in clinical practice. We conducted an international, multidisciplinary, systematic search and evidence-based review of BE and provided consensus recommendations for clinical use in patients with nondysplastic, indefinite, and low-grade dysplasia (LGD). METHODS: We defined the scope, proposed statements, and searched electronic databases, yielding 20,558 publications that were screened, selected online, and formed the evidence base. We used a Delphi consensus process, with an 80% agreement threshold, using GRADE (Grading of Recommendations Assessment, Development and Evaluation) to categorize the quality of evidence and strength of recommendations. RESULTS: In total, 80% of respondents agreed with 55 of 127 statements in the final voting rounds. Population endoscopic screening is not recommended and screening should target only very high-risk cases of males aged over 60 years with chronic uncontrolled reflux. A new international definition of BE was agreed upon. For any degree of dysplasia, at least two specialist gastrointestinal (GI) pathologists are required. Risk factors for cancer include male gender, length of BE, and central obesity. Endoscopic resection should be used for visible, nodular areas. Surveillance is not recommended for <5 years of life expectancy. Management strategies for indefinite dysplasia (IND) and LGD were identified, including a de-escalation strategy for lower-risk patients and escalation to intervention with follow-up for higher-risk patients. CONCLUSIONS: In this uniquely large consensus process in gastroenterology, we made key clinical recommendations for the escalation/de-escalation of BE in clinical practice. We made strong recommendations for the prioritization of future research.

New insights into sequence variation in the IGS region of 21 cyathostomin species and the implication for molecular identification

Cyathostomins comprise a group of 50 species of parasitic nematodes that infect equids. Ribosomal DNA sequences, in particular the intergenic spacer (IGS) region, have been utilized via several methodologies to identify pre-parasitic stages of the commonest species that affect horses. These methods rely on the availability of accurate sequence information for each species, as well as detailed knowledge of the levels of intra- and inter-specific variation. Here, the IGS DNA region was amplified and sequenced from 10 cyathostomin species for which sequence was not previously available. Also, additional IGS DNA sequences were generated from individual worms of 8 species already studied. Comparative analysis of these sequences revealed a greater range of intra-specific variation than previously reported (up to 23%); whilst the level of inter-specific variation (3-62%) was similar to that identified in earlier studies. The reverse line blot (RLB) method has been used to exploit the cyathostomin IGS DNA region for species identification. Here, we report validation of novel and existing DNA probes for identification of cyathostomins using this method and highlight their application in differentiating life-cycle stages such as third-stage larvae that cannot be identified to species by morphological means.

Sequence stratigraphy related distribution of diagenetic alterations In Miocene deltaic and shoreface arenites, the Suez Rift, EGYPT.

The distribution of eogenetic alterations in shoreface-offshore and coarse-grained deltaic, calcarenite to hybrid arenites of the Mheiherrat Formation (lower Rudeis), Early Miocene, the Gulf of Suez, Egypt) can be constrained within a sequence stratigraphic framework. The bioclast-rich, shoreface (trangressive systems tract; TST) and shoreface (highstand systems tract; HST) arenites, particularly those below the parasequence boundaries and maximum flooding surface, are cemented by grain-coating microcrystalline, circumgranular isopacheous acicular and columnar, and coarse-crystalline calcite (δ18OVPDB = -3.6 to -0.3 ‰; δ13CVPDB = -2.3 to -0.7 ‰), non-Ferro an dolomite (δ18OVPDB = -3.9 to +0.9‰; δ13CVPDB = -2.5 ‰ to -0.7 ‰), and pyrite. Zeolite, palygorskite and gypsum occur in the HST shoreface arenites, being enhanced by aird climatic condations. The coarse-grained deltaic LST deposits are pervasively cemented by coarse-crystalline, pore-filling calcite and small amounts of microcrystalline calcite (δ18OVPDB = -4.4 to -2.3 ‰; δ13CVPDB = -2.8 to -1.3 ‰) and non-ferroan dolomite (δ18OVPDB = -4.8 to -2.5 ‰; δ13CVPDB = -3.3 to -1.5 ‰). Thus, this study demonstrates that changes in pore-water chemistry, which induced changes in the texture, composition and extent of cementation in the Miocene arenites was controlled by changes in the relative sea level and by the paleo-climatic conditions during deposition of the HST arenites.

Sequence stratigraphy related distribution of diagenetic alterations In Miocene deltaic and shoreface arenites, the Suez Rift, EGYPT.. Available from: https://www.researchgate.net/publication/264545153_Sequence_stratigraphy_related_distribution_of_diagenetic_alterations_In_Miocene_deltaic_and_shoreface_arenites_the_Suez_Rift_EGYPT [accessed Apr 15, 2015].

Recombinant Subgroup B Human Respiratory Syncytial Virus Expressing Enhanced Green Fluorescent Protein Efficiently Replicates in Primary Human Cells and Is Virulent in Cotton Rats

Human respiratory syncytial virus (HRSV) is the most important viral cause of severe respiratory tract disease in infants. Two subgroups (A and B) have been identified, which cocirculate during, or alternate between, yearly epidemics and cause indistinguishable disease. Existing in vitro and in vivo models of HRSV focus almost exclusively on subgroup A viruses. Here, a recombinant (r) subgroup B virus (rHRSV(B05)) was generated based on a consensus genome sequence obtained directly from an unpassaged clinical specimen from a hospitalized infant. An additional transcription unit containing the gene encoding enhanced green fluorescent protein (EGFP) was introduced between the phosphoprotein and matrix genes (position 5) of the genome to generate rHRSV(B05)EGFP(5). The recombinant viruses replicated efficiently in both HEp-2 cells and in well-differentiated normal human bronchial cells grown at air-liquid interface. Intranasal infection of cotton rats (Sigmodon hispidus) resulted in high numbers of EGFP(+) cells in epithelia of the nasal septum and conchae. When administered in a relatively large inoculum volume, the virus also replicated efficiently in bronchiolar epithelial cells and spread extensively in both the upper and lower respiratory tracts. Virus replication was not observed in ciliated epithelial cells of the trachea. This is the first virulent rHRSV strain with the genetic composition of a currently circulating wild-type virus. In vivo tracking of infected cells by means of EGFP fluorescence in the absence of cytopathic changes increases the sensitivity of virus detection in HRSV pathogenesis studies.

IMPORTANCE

Virology as a discipline has depended on monitoring cytopathic effects following virus culture in vitro. However, wild-type viruses isolated from patients often do not cause significant changes to infected cells, necessitating blind passage. This can lead to genetic and phenotypic changes and the generation of high-titer, laboratory-adapted viruses with diminished virulence in animal models of disease. To address this, we determined the genome sequence of an unpassaged human respiratory syncytial virus from a sample obtained directly from an infected infant, assembled a molecular clone, and recovered a wild-type recombinant virus. Addition of a gene encoding enhanced green fluorescent protein allowed this wild-type virus to be tracked in primary human cells and living animals in the absence of significant cytopathic effects. Imaging of fluorescent cells proved to be a highly valuable tool for monitoring the spread of virus and may help improve assays for evaluating novel intervention strategies.

Conflict and Consensus

There are widely differing conceptions as to whether healthy social relations are, in essence, conflictual or consensual; such differences give rise to different approaches to finding peace and managing power. This article outlines the two broad schools of thought from conflict theory (in which society functions through competition) and consensus theory (which sees society developing through cooperation). It outlines the middle ground between them, as found by pluralism and agonism, before considering the ways in which assumptions vis-a-vis conflict and consensus are reflected in different models of democratic system and, in particular, different priorities for post-conflict recovery.

Medical consensus, guidelines, and position papers: A policy for the ECFS

The terms consensus, guideline and position paper are sometimes employed as if they were interchangeable, but the purpose of such documents and the robustness of advice vary as the evidence base does not have the same depth in each. The Board of the European Cystic Fibrosis Society deemed it to be helpful to provide a short commentary on the definition of these terms, on their interconnections and on how ECFS considers them in documents endorsed by the society.

Pre-Main-Sequence Accretion in the Low Metallicity Galactic Star-forming Region Sh 2-284

We present optical spectra of pre-main-sequence (PMS) candidates around the Ha region taken with the Southern African Large Telescope in the low metallicity (Z) Galactic region Sh 2-284, which includes the open cluster Dolidze 25 with an atypical low metallicity of Z similar to 1/5 Z(circle dot). It has been suggested on the basis of both theory and observations that PMS mass-accretion rates, (M) over dot(acc), are a function of Z. We present the first sample of spectroscopic estimates of mass-accretion rates for PMS stars in any low-Z star-forming region. Our data set was enlarged with literature data of H alpha emission in intermediate-resolution R-band spectroscopy. Our total sample includes 24 objects spanning a mass range between 1 and 2 M-circle dot and with a median age of approximately 3.5 Myr. The vast majority (21 out of 24) show evidence for a circumstellar disk on the basis of Two Micron All Sky Survey and Spitzer infrared photometry. We find (M) over dot(acc) in the 1-2 M-circle dot interval to depend quasi-quadratically on stellarmass, with (M) over dot(acc) proportional to M-*(2.4 +/- 0.35), and inversely with stellar age, with (M) over dot(acc) proportional to t(*)(-0.7 +/- 0.4). Furthermore, we compare our spectroscopic (M) over dot(acc) measurements with solar Z Galactic PMS stars in the same mass range, but, surprisingly find no evidence for a systematic change in (M) over dot(acc) with Z. We show that literature accretion-rate studies are influenced by detection limits, and we suggest that (M) over dot(acc) may be controlled by factors other than Z(*), M-*, and age.

An unbiased genetic screen reveals the polygenic nature of the influenza virus anti-interferon response

UNLABELLED: Influenza A viruses counteract the cellular innate immune response at several steps, including blocking RIG I-dependent activation of interferon (IFN) transcription, interferon (IFN)-dependent upregulation of IFN-stimulated genes (ISGs), and the activity of various ISG products; the multifunctional NS1 protein is responsible for most of these activities. To determine the importance of other viral genes in the interplay between the virus and the host IFN response, we characterized populations and selected mutants of wild-type viruses selected by passage through non-IFN-responsive cells. We reasoned that, by allowing replication to occur in the absence of the selection pressure exerted by IFN, the virus could mutate at positions that would normally be restricted and could thus find new optimal sequence solutions. Deep sequencing of selected virus populations and individual virus mutants indicated that nonsynonymous mutations occurred at many phylogenetically conserved positions in nearly all virus genes. Most individual mutants selected for further characterization induced IFN and ISGs and were unable to counteract the effects of exogenous IFN, yet only one contained a mutation in NS1. The relevance of these mutations for the virus phenotype was verified by reverse genetics. Of note, several virus mutants expressing intact NS1 proteins exhibited alterations in the M1/M2 proteins and accumulated large amounts of deleted genomic RNAs but nonetheless replicated to high titers. This suggests that the overproduction of IFN inducers by these viruses can override NS1-mediated IFN modulation. Altogether, the results suggest that influenza viruses replicating in IFN-competent cells have tuned their complete genomes to evade the cellular innate immune system and that serial replication in non-IFN-responsive cells allows the virus to relax from these constraints and find a new genome consensus within its sequence space.

IMPORTANCE: In natural virus infections, the production of interferons leads to an antiviral state in cells that effectively limits virus replication. The interferon response places considerable selection pressure on viruses, and they have evolved a variety of ways to evade it. Although the influenza virus NS1 protein is a powerful interferon antagonist, the contributions of other viral genes to interferon evasion have not been well characterized. Here, we examined the effects of alleviating the selection pressure exerted by interferon by serially passaging influenza viruses in cells unable to respond to interferon. Viruses that grew to high titers had mutations at many normally conserved positions in nearly all genes and were not restricted to the NS1 gene. Our results demonstrate that influenza viruses have fine-tuned their entire genomes to evade the interferon response, and by removing interferon-mediated constraints, viruses can mutate at genome positions normally restricted by the interferon response.

PET/CT imaging for target volume delineation in curative intent radiotherapy of non-small cell lung cancer: IAEA consensus report 2014

This document describes best practice and evidence based recommendations for the use of FDG-PET/CT for the purposes of radiotherapy target volume delineation (TVD) for curative intent treatment of non-small cell lung cancer (NSCLC). These recommendations have been written by an expert advisory group, convened by the International Atomic Energy Agency (IAEA) to facilitate a Coordinated Research Project (CRP) aiming to improve the applications of PET based radiation treatment planning (RTP) in low and middle income countries. These guidelines can be applied in routine clinical practice of radiotherapy TVD, for NSCLC patients treated with concurrent chemoradiation or radiotherapy alone, where FDG is used, and where a calibrated PET camera system equipped for RTP patient positioning is available. Recommendations are provided for PET and CT image visualization and interpretation, and for tumor delineation using planning CT with and without breathing motion compensation.

Consensus on Outcome Measures for Glaucoma Effectiveness Trials: Results From a Delphi and Nominal Group Technique Approaches

PURPOSE: Comparing the relative effectiveness of interventions across glaucoma trials can be problematic due to differences in definitions of outcomes. We sought to identify a key set of clinical outcomes and reach consensus on how best to measure them from the perspective of glaucoma experts.

METHODS: A 2-round electronic Delphi survey was conducted. Round 1 involved 25 items identified from a systematic review. Round 2 was developed based on information gathered in round 1. A 10-point Likert scale was used to quantify importance and consensus of outcomes (7 outcomes) and ways of measuring them (44 measures). Experts were identified through 2 glaucoma societies membership-the UK and Eire Glaucoma Society and the European Glaucoma Society. A Nominal Group Technique (NGT) followed the Delphi process. Results were analyzed using descriptive statistics.

RESULTS: A total of 65 participants completed round 1 out of 320; of whom 56 completed round 2 (86%). Agreement on the importance of outcomes was reached on 48/51 items (94%). Intraocular pressure (IOP), visual field (VF), safety, and anatomic outcomes were classified as highly important. Regarding methods of measurement of IOP, "mean follow-up IOP" using Goldmann applanation tonometry achieved the highest importance, whereas for evaluating VFs "global index mean deviation/defect (MD)" and "rate of VF progression" were the most important. Retinal nerve fiber layer (RNFL) thickness measured by optical coherence tomography (OCT) was identified as highly important. The NGT results reached consensus on "change of IOP (mean of 3 consecutive measurements taken at fixed time of day) from baseline," change of VF-MD values (3 reliable VFs at baseline and follow-up visit) from baseline, and change of RNFL thickness (2 good quality OCT images) from baseline.

CONCLUSIONS: Consensus was reached among glaucoma experts on how best to measure IOP, VF, and anatomic outcomes in glaucoma randomized controlled trials.