Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ßtubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils

The term "carcinoid" is a misnomer: the evidence based on local invasion

<p>Abstract</p> <p>Background</p> <p>Since Oberndorfer proposed the term "carcinoid" in 1907, over 100 years have passed. This attractive term was initially proposed for 6 cases of his own experience with 12 submucosal lesions in the small intestine.</p> <p>Oberndorfer summarized the characteristic features of these lesions as follows: (1) small in size and often multiple, (2) histologically undifferentiated with a suggestion of gland-formation, (3) well-defined without any tendency to infiltrate the surroundings, (4) no metastases, and (5) apparently slow-growing reaching no significant size with a seemingly harmless nature.</p> <p>Review</p> <p>This article stresses the malignant nature of "carcinoid" on the basis of local invasion prior to metastases in the first two sessions, (1) with Oberndorfer's original diagram, and (2) with an experimental observation on extraglandular microcarcinoid in a form of "budding".</p> <p>Next, (3) a statistical comparison between a carcinoid group and a non-carcinoid ordinary carcinoma group is introduced on metastasis rates at an early stage with two prescribed factors of the depth of invasion restricted within the submucosa (sm-lesion) and a small tumor size category of 1 cm to 2 cm: the carcinoid group exhibited metastasis rates higher than those in the ordinary carcinoma group when calculated in the stomach and rectum.</p> <p>In the author's experience, "carcinoids" are malignant not only in the gastrointestinal tract but also in the other sites on the basis of local invasion.</p> <p>Lastly, (4) discussion on the terminology of "carcinoid" as a misnomer is carried out.</p> <p>Adequate terms referring to the entity of this malignant tumor group are discussed. One of the most adequate and brief terms for "carcinoid" that is included now in neuroendocrine tumor group would be "endocrinocarcinoma" as per the author's proposal, followed by NEC (neuroendocrinocarcinoma) or GEC (gut endocrinocarcinoma).</p> <p>Conclusion</p> <p>The term "carcinoid" is a misnomer that can be confirmed on the basis of local invasion prior to metastases. "No metastases without local invasion" is not of a negligible importance.</p

Direction of the formation of anterior lumbar vertebral osteophytes

<p>Abstract</p> <p>Background</p> <p>X-ray images of lumbar degenerative diseases often show not only claw osteophytes, but also pairs of osteophytes that form in a direction away from the adjacent disc. We have investigated the direction of the formation of anterior lumbar vertebral osteophytes across the lumbar vertebrae using a sufficient number of lumbar radiographs, because osteophytes images can provide essential information that will contribute to the understanding of the pathology and progress of lumbar spine degeneration.</p> <p>Methods</p> <p>The direction of the formation of 14,250 pairs of anterior lumbar vertebral osteophytes across the adjacent intervertebral discs in 2,850 patients who were all over 60 years old was investigated. Anterior lumbar vertebral osteophytes were distributed into six groups based on the direction of extension of each pair of osteophytes across the intervertebral disc space.</p> <p>Results</p> <p>In L1–L2 and L2–L3, the number of patients classified into groups B (the pair of osteophytes extended in the direction of the adjacent disc) and C (almost complete bone bridge formation by a pair of osteophytes across the intervertebral disc space) was larger than that classified into group D (the pair of osteophytes extended in a direction away from the adjacent disc). In L3–L4, L4–L5 and L5-S1, the number of patients in group D was greater than that of patients belonging to groups B and C.</p> <p>Conclusion</p> <p>Our study showed that pairs of osteophytes frequently formed in the direction of the adjacent disc in the upper lumbar vertebrae (L1–L2 and L2–L3) and in the direction away from the adjacent disc in middle or lower lumbar vertebrae (L3–L4, L4–L5, and L5-S1).</p

Prevalence of Disorders Recorded in Dogs Attending Primary-Care Veterinary Practices in England

Purebred dog health is thought to be compromised by an increasing occurence of inherited diseases but inadequate prevalence data on common disorders have hampered efforts to prioritise health reforms. Analysis of primary veterinary practice clinical data has been proposed for reliable estimation of disorder prevalence in dogs. Electronic patient record (EPR) data were collected on 148,741 dogs attending 93 clinics across central and south-eastern England. Analysis in detail of a random sample of EPRs relating to 3,884 dogs from 89 clinics identified the most frequently recorded disorders as otitis externa (prevalence 10.2%, 95% CI: 9.1-11.3), periodontal disease (9.3%, 95% CI: 8.3-10.3) and anal sac impaction (7.1%, 95% CI: 6.1-8.1). Using syndromic classification, the most prevalent body location affected was the head-and-neck (32.8%, 95% CI: 30.7-34.9), the most prevalent organ system affected was the integument (36.3%, 95% CI: 33.9-38.6) and the most prevalent pathophysiologic process diagnosed was inflammation (32.1%, 95% CI: 29.8-34.3). Among the twenty most-frequently recorded disorders, purebred dogs had a significantly higher prevalence compared with crossbreds for three: otitis externa (P = 0.001), obesity (P = 0.006) and skin mass lesion (P = 0.033), and popular breeds differed significantly from each other in their prevalence for five: periodontal disease (P = 0.002), overgrown nails (P = 0.004), degenerative joint disease (P = 0.005), obesity (P = 0.001) and lipoma (P = 0.003). These results fill a crucial data gap in disorder prevalence information and assist with disorder prioritisation. The results suggest that, for maximal impact, breeding reforms should target commonly-diagnosed complex disorders that are amenable to genetic improvement and should place special focus on at-risk breeds. Future studies evaluating disorder severity and duration will augment the usefulness of the disorder prevalence information reported herein

Exploring the Ecological History of a Tropical Agroforestry Landscape Using Fossil Pollen and Charcoal Analysis from Four Sites in Western Ghats, India

Contrary to expectations, some human-modified landscapes are considered to sustain both human activities and biodiversity over the long-term. Agroforestry systems are among these landscapes where crops are planted under native shade trees. In this context, ancient agroforestry systems can provide insight into how farmers managed the landscape over time. Such insight can help to quantify the extent to which tropical forests (especially habitat-specialist trees) are responding to local and landscape-level management. Here, we extracted fossil pollen (indicator of past vegetation changes) and macroscopic charcoal (indicator of biomass burning) from four forest hollows’ sedimentary sequences in an ancient agroforestry system in Western Ghats, India. We used a mixed-modelling approach and a principal components analysis (PCA) to determine past trajectories of forest change and species composition dynamics for the last 900 years. In addition, we reconstructed the long-term forest canopy dynamics and examined the persistence of habitat-specialist trees over time. Our results show that the four sites diverged to a surprising degree in both taxa composition and dynamics. However, despite these differences, forest has persisted over 900 years under agricultural activities within agroforestry systems. This long-term analysis highlights the importance of different land-use legacies as a framework to increase the effectiveness of management across tropical agricultural lands

X-Ray Spectroscopy of Stars

(abridged) Non-degenerate stars of essentially all spectral classes are soft X-ray sources. Low-mass stars on the cooler part of the main sequence and their pre-main sequence predecessors define the dominant stellar population in the galaxy by number. Their X-ray spectra are reminiscent, in the broadest sense, of X-ray spectra from the solar corona. X-ray emission from cool stars is indeed ascribed to magnetically trapped hot gas analogous to the solar coronal plasma. Coronal structure, its thermal stratification and geometric extent can be interpreted based on various spectral diagnostics. New features have been identified in pre-main sequence stars; some of these may be related to accretion shocks on the stellar surface, fluorescence on circumstellar disks due to X-ray irradiation, or shock heating in stellar outflows. Massive, hot stars clearly dominate the interaction with the galactic interstellar medium: they are the main sources of ionizing radiation, mechanical energy and chemical enrichment in galaxies. High-energy emission permits to probe some of the most important processes at work in these stars, and put constraints on their most peculiar feature: the stellar wind. Here, we review recent advances in our understanding of cool and hot stars through the study of X-ray spectra, in particular high-resolution spectra now available from XMM-Newton and Chandra. We address issues related to coronal structure, flares, the composition of coronal plasma, X-ray production in accretion streams and outflows, X-rays from single OB-type stars, massive binaries, magnetic hot objects and evolved WR stars.Comment: accepted for Astron. Astrophys. Rev., 98 journal pages, 30 figures (partly multiple); some corrections made after proof stag

Challenges in identifying barriers to adoption in a theory-based implementation study: lessons for future implementation studies

Background: Exploring barriers to the uptake of research based recommendations into practice is an important part of the development of implementation programmes. Techniques to identify barriers can include use of theory-informed questionnaires and qualitative interviews. Conceptualising and measuring theory-informed factors, and engaging health professionals’ to uncover all potential barriers, can be a difficult task. This paper presents a case study of the process of trying to identify, systematically, the key factors influencing health professionals’ referrals for women diagnosed with mild to moderate postnatal depression for psychological treatment. The paper illustrates how the factors were conceptualised and measured and explores the real world challenges experienced, with implications for future implementation studies. Methods: Theory-informed factors were conceptualised and measured using a questionnaire and interviews. The questionnaire was piloted, before being administered to general practitioners, practice nurses and health visitors working in general practices in one area of the UK NHS. The interviews were conducted with a small sample of general practitioners who had not completed the questionnaire, further exploring factors influencing their referral decisions in the local context. Results: The response rate to the questionnaire was low (19%), despite selecting the recommendation to target through engagement with local stakeholders and surveying local health professionals, and despite using two reminders, an incentive prize, and phone calls to practice managers to bolster response rates. Conclusions: Two significant challenges to achieving higher response rates and successfully exploring local context were identified: the difficulties of developing a robust- but feasible- questionnaire to explore theory-informed factors, and targeting recommendations that are important to policy makers, but which health professionals view as unimportant. This case study highlights the “trade-off” between scientifically rigorous collection of data against the pragmatism and flexibility requirements of “real world” implementation. Future implementation studies should explore different ways of identifying factors influencing the adoption of recommendations to bridge this gulf

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal

Functional Interactions between KCNE1 C-Terminus and the KCNQ1 Channel

The KCNE1 gene product (minK protein) associates with the cardiac KvLQT1 potassium channel (encoded by KCNQ1) to create the cardiac slowly activating delayed rectifier, IKs. Mutations throughout both genes are linked to the hereditary cardiac arrhythmias in the Long QT Syndrome (LQTS). KCNE1 exerts its specific regulation of KCNQ1 activation via interactions between membrane-spanning segments of the two proteins. Less detailed attention has been focused on the role of the KCNE1 C-terminus in regulating channel behavior. We analyzed the effects of an LQT5 point mutation (D76N) and the truncation of the entire C-terminus (Δ70) on channel regulation, assembly and interaction. Both mutations significantly shifted voltage dependence of activation in the depolarizing direction and decreased IKs current density. They also accelerated rates of channel deactivation but notably, did not affect activation kinetics. Truncation of the C-terminus reduced the apparent affinity of KCNE1 for KCNQ1, resulting in impaired channel formation and presentation of KCNQ1/KCNE1 complexes to the surface. Complete saturation of KCNQ1 channels with KCNE1-Δ70 could be achieved by relative over-expression of the KCNE subunit. Rate-dependent facilitation of K+ conductance, a key property of IKs that enables action potential shortening at higher heart rates, was defective for both KCNE1 C-terminal mutations, and may contribute to the clinical phenotype of arrhythmias triggered by heart rate elevations during exercise in LQTS mutations. These results support several roles for KCNE1 C-terminus interaction with KCNQ1: regulation of channel assembly, open-state destabilization, and kinetics of channel deactivation