The Plant Ontology: A common reference ontology for plants

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms

Factors in Debris Accumulation at Bridge Piers

Debris accumulation at bridge piers has been a significant problem at a number of bridge sites in Indiana, increasing risks of upstream flooding, scour, and stream instability. The current study aimed at identifying factors contributing to debris accumulation in order to formulate guidelines for the design of new bridges that would minimize their occurrence or impact. Three related approaches were taken: i) a systematic study of the available underwater bridge inspections reports, ii) a program of periodic visits and visual examination of bridge sites that were thought to be prone to debris accumulation, and iii) continued video monitoring of three bridge sites, and analysis of video images recorded during debris-transporting events. The available underwater bridge inspection reports spanned a period of 10 years and covered 370 structures. Heavy debris accumulation was observed at ¡Ö20% of these sites, with the heaviest accumulations being concentrated in southwestern Indiana. Almost all of the sites in south-central and southern Indiana experienced at least moderate debris accumulation at one time. Sites with estimated volume of debris accumulation greater than 1000 cubic yards (¡®mega¡¯ sites), sites where heavy debris accumulation was observed during more than one inspection (¡®chronic¡¯ sites), and sites with at most minor debris accumulation during more than one inspection (¡®lite¡¯ sites) were examined in greater detail with regards to their crosssectional geometry and the placement of the piers, and the specific location of debris accumulation. A program of periodic site inspections was undertaken that eventually covered 22 sites, including 4 ¡®mega¡¯ sites and 6 ¡®chronic¡¯ sites. The sites were visited at intervals of 3 ¨C 4 months over a 16-month period, and visually examined with regards to the occurrence and location of any debris accumulation, and other features, such as the presence of upstream bridges, that might be related to debris accumulation. These observations were combined with cross-section information from underwater bridge inspection reports to corroborate or refine the conclusions drawn from the broader study of underwater bridge inspection reports. Issues that could not be resolved from the bridge inspection reports, such as the behavior over time of debris accumulation, and the relationship to hydrologic events, were of particular interest in the periodic-site inspections. Although some sites suffered what might be classed as ¡®heavy¡¯ accumulation during the study period, no ¡®mega¡¯ accumulation occurred at any site, suggesting that average recurrence intervals for such events are more than 16 months, at least for larger rivers. Finally, video monitoring of debris-transporting events was conducted at three sites including one ¡®mega¡¯ site. This yielded the most detailed information regarding aspects that were visible above the water surface. This included including the variation of debris ¡®discharge¡¯ and amount of debris accumulated with time, typical debris trajectories, and even direct evidence of disaggregation of already accumulated debris. At two of the sites, extensive debris accumulations, possibly approaching ¡®mega¡¯ class at one site, were recorded. In contrast, little debris accumulation was noted at the third site in spite of quite heavy debris transport during at least one large flow event. For larger, longer-duration flow events, debris transport seemed to be concentrated towards the earlier rising part, such as the first 12 ¨C 18 hours, of the event. Little correlation between the lateral location within the stream where debris transport is high and the thalweg in the immediate vicinity of the bridge crossing was found. On the basis of the observations made during the study, recommended practices are suggested for designing bridges with the aim of minimizing debris accumulation

Assessing Photoreceptor Structure Associated with Ellipsoid Zone Disruptions Visualized with Optical Coherence Tomography

Purpose: To compare images of photoreceptor layer disruptions obtained with optical coherence tomography (OCT) and adaptive optics scanning light ophthalmoscopy (AOSLO) in a variety of pathologic states.Methods: Five subjects with photoreceptor ellipsoid zone disruption as per OCT and clinical diagnoses of closed-globe blunt ocular trauma (n = 2), macular telangiectasia type 2 (n = 1), blue-cone monochromacy (n = 1), or cone-rod dystrophy (n = 1) were included. Images were acquired within and around photoreceptor lesions using spectral domain OCT, confocal AOSLO, and split-detector AOSLO.Results: There were substantial differences in the extent and appearance of the photoreceptor mosaic as revealed by confocal AOSLO, split-detector AOSLO, and spectral domain OCT en face view of the ellipsoid zone.Conclusion: Clinically available spectral domain OCT, viewed en face or as B-scan, may lead to misinterpretation of photoreceptor anatomy in a variety of diseases and injuries. This was demonstrated using split-detector AOSLO to reveal substantial populations of photoreceptors in areas of no, low, or ambiguous ellipsoid zone reflectivity with en face OCT and confocal AOSLO. Although it is unclear if these photoreceptors are functional, their presence offers hope for therapeutic strategies aimed at preserving or restoring photoreceptor function

Exactly separable version of the Bohr Hamiltonian with the Davidson potential

An exactly separable version of the Bohr Hamiltonian is developed using a potential of the form u(beta)+u(gamma)/beta^2, with the Davidson potential u(beta)= beta^2 + beta_0^4/beta^2 (where beta_0 is the position of the minimum) and a stiff harmonic oscillator for u(gamma) centered at gamma=0. In the resulting solution, called exactly separable Davidson (ES-D), the ground state band, gamma band and 0_2^+ band are all treated on an equal footing. The bandheads, energy spacings within bands, and a number of interband and intraband B(E2) transition rates are well reproduced for almost all well-deformed rare earth and actinide nuclei using two parameters (beta_0, gamma stiffness). Insights regarding the recently found correlation between gamma stiffness and the gamma-bandhead energy, as well as the long standing problem of producing a level scheme with Interacting Boson Approximation SU(3) degeneracies from the Bohr Hamiltonian, are also obtained.Comment: 35 pages, 11 postscript figures, LaTe

Assessing Retinal Structure In Complete Congenital Stationary Night Blindness and Oguchi Disease

Purpose To examine retinal structure and changes in photoreceptor intensity after dark adaptation in patients with complete congenital stationary night blindness and Oguchi disease. Design Prospective, observational case series. Methods We recruited 3 patients with complete congenital stationary night blindness caused by mutations in GRM6, 2 brothers with Oguchi disease caused by mutations in GRK1, and 1 normal control. Retinal thickness was measured from optical coherence tomography images. Integrity of the rod and cone mosaic was assessed using adaptive optics scanning light ophthalmoscopy. We imaged 5 of the patients after a period of dark adaptation and examined layer reflectivity on optical coherence tomography in a patient with Oguchi disease under light- and dark-adapted conditions. Results Retinal thickness was reduced in the parafoveal region in patients with GRM6 mutations as a result of decreased thickness of the inner retinal layers. All patients had normal photoreceptor density at all locations analyzed. On removal from dark adaptation, the intensity of the rods (but not cones) in the patients with Oguchi disease gradually and significantly increased. In 1 Oguchi disease patient, the outer segment layer contrast on optical coherence tomography was 4-fold higher under dark-adapted versus light-adapted conditions. Conclusions The selective thinning of the inner retinal layers in patients with GRM6 mutations suggests either reduced bipolar or ganglion cell numbers or altered synaptic structure in the inner retina. Our finding that rods, but not cones, change intensity after dark adaptation suggests that fundus changes in Oguchi disease are the result of changes within the rods as opposed to changes at a different retinal locus

Phase Space Description of the Leading Order Quark and Gluon Production from a Space-Time Dependent Chromofield

We derive source terms for the production of quarks and gluons from the QCD vacuum in the presence of a space-time dependent external chromofield A_{cl} to the order of S^{(1)}. We found that the source terms for the parton production processes A_{cl} -> q\bar{q} and A_{cl},A_{cl}A_{cl} -> gg also include the annihilation processes q\bar{q} -> A_{cl} and gg -> A_{cl},A_{cl}A_{cl}. The source terms we derive are applicable for the description of the production of partons with momentum p larger rhan gA which itself must be larger than \Lambda_{QCD}. We observe that these source terms for the production of partons from a space-time dependent chromofield can be used to study the production and equilibration of the quark-gluon plasma during the very early stages of an ultrarelativistic heavy-ion collision.Comment: 30 pages latex (single spaced), 7 eps figures, Revised Version, To appear in Physical Review

Is group cognitive behaviour therapy for postnatal depression evidence-based practice? A systematic review

Background: There is evidence that psychological therapies including cognitive behaviour therapy (CBT) may be effective in reducing postnatal depression (PND) when offered to individuals. In clinical practice, this is also implemented in a group therapy format, which, although not recommended in guidelines, is seen as a cost-effective alternative. To consider the extent to which group methods can be seen as evidence-based, we systematically review and synthesise the evidence for the efficacy of group CBT compared to currently used packages of care for women with PND, and we discuss further factors which may contribute to clinician confidence in implementing an intervention. Methods: Seventeen electronic databases were searched. All full papers were read by two reviewers and a third reviewer was consulted in the event of a disagreement on inclusion. Selected studies were quality assessed, using the Cochrane Risk of Bias Tool, were data extracted by two reviewers using a standardised data extraction form and statistically synthesised where appropriate using the fixed-effect inverse-variance method. Results: Seven studies met the inclusion criteria. Meta-analyses showed group CBT to be effective in reducing depression compared to routine primary care, usual care or waiting list groups. A pooled effect size of d = 0.57 (95% CI 0.34 to 0.80, p < 0.001) was observed at 10–13 weeks post-randomisation, reducing to d = 0.28 (95% CI 0.03 to 0.53, p = 0.025) at 6 months. The non-randomised comparisons against waiting list controls at 10–13 weeks was associated with a larger effect size of d = 0.94 (95% CI 0.42 to 1.47, p < 0.001). However due to the limitations of the available data, such as ill-specified definitions of the CBT component of the group programmes, these results should be interpreted with caution. Conclusions: Although the evidence available is limited, group CBT was shown to be effective. We argue, therefore, that there is sufficient evidence to implement group CBT, conditional upon routinely collected outcomes being benchmarked against those obtained in trials of individual CBT, and with other important factors such as patient preference, clinical experience, and information from the local context taken into account when making the treatment decision

Linkages among runoff, dissolved organic carbon, and the stable oxygen isotope composition of seawater and other water mass indicators in the Arctic Ocean

Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 110 (2005): G02013, doi:10.1029/2005JG000031.Concentrations of dissolved organic carbon (DOC) and δ18O values have been determined following sampling of runoff from a number of major arctic rivers, including the Ob, Yenisey, Lena, Kolyma, Mackenzie and Yukon in 2003-2004. These data are considered in conjunction with marine data for DOC, δ18O values, nutrients, salinity, and fluorometric indicators of DOC that were obtained as part of the Shelf-Basin Interactions program at the continental shelf-basin boundary of the Chukchi and Beaufort Seas. These marine data indicate that the freshwater component is most likely derived from regional sources, such as the Mackenzie, the Bering Strait inflow and possibly eastern Siberian rivers, including the Kolyma, or the Lena but not rivers further west in the Eurasian arctic. Contributions of freshwater from melted sea ice to marine surface waters appeared to be insignificant over annual cycles compared to runoff, although on a seasonal basis, freshwater from melted sea ice was locally dominant following a major sea-ice retreat into the Canada Basin in 2002. DOC concentrations were correlated with the runoff fraction, with an apparent meteoric water DOC concentration of 174 ± 1 μM (standard error). This concentration is lower than the flow-weighted concentrations measured at river mouths of the five largest Arctic rivers (358 to 917 μM), indicating that removal of terrigenous DOC during transport through estuaries, shelves and in the deep basin. DOC data indicate that flow-weighted concentrations in the two largest North American arctic rivers, the Yukon (625μM) and the Mackenzie (382 μM), are lower than in the three largest Eurasian arctic rivers, the Ob (825 μM), the Yenesey (858 μM) and the Lena (917 μM). A fluorometric indicator of chromophoric dissolved organic matter (CDOM) that has provided estimates of terrigenous DOC concentrations in the Eurasian Arctic was not correlated with DOC concentrations in the Amerasian marine waters studied, except below the upper Arctic Ocean halocline. Nutrient distributions and concentrations as well as derived nutrient ratios suggest the CDOM fluorometer may be responding to the release of chromophoric materials from continental shelf sediments. Shipboard incubation experiments with undisturbed sediment cores indicate that continental shelf sediments on the Bering and Chukchi Sea shelves are likely to be a net source of DOC to the Arctic Ocean.The PARTNERS and SBI projects have been supported by the Office of Polar Programs of the U.S. National Science Foundation

Adrenergic gene polymorphisms and cardiovascular risk in the NHLBI-sponsored Women's Ischemia Syndrome Evaluation

<p>Abstract</p> <p>Background</p> <p>Adrenergic gene polymorphisms are associated with cardiovascular and metabolic phenotypes. We investigated the influence of adrenergic gene polymorphisms on cardiovascular risk in women with suspected myocardial ischemia.</p> <p>Methods</p> <p>We genotyped 628 women referred for coronary angiography for eight polymorphisms in the α_1A-, β₁-, β₂- and β₃-adrenergic receptors (<it>ADRA1A</it>, <it>ADRB1, ADRB2</it>, <it>ADRB3</it>, respectively), and their signaling proteins, G-protein β 3 subunit (<it>GNB3</it>) and G-protein α subunit (<it>GNAS</it>). We compared the incidence of death, myocardial infarction, stroke, or heart failure between genotype groups in all women and women without obstructive coronary stenoses.</p> <p>Results</p> <p>After a median of 5.8 years of follow-up, 115 women had an event. Patients with the <it>ADRB1 </it>Gly389 polymorphism were at higher risk for the composite outcome due to higher rates of myocardial infarction (adjusted hazard ratio [HR] 3.63, 95% confidence interval [95%CI] 1.17–11.28; Gly/Gly vs. Arg/Arg HR 4.14, 95%CI 0.88–19.6). The risk associated with <it>ADRB1 </it>Gly389 was limited to those without obstructive CAD (n = 400, P_interaction= 0.03), albeit marginally significant in this subset (HR 1.71, 95%CI 0.91–3.19). Additionally, women without obstructive CAD carrying the <it>ADRB3 </it>Arg64 variant were at higher risk for the composite endpoint (HR 2.10, 95%CI 1.05–4.24) due to subtle increases in risk for all of the individual endpoints. No genetic associations were present in women with obstructive CAD.</p> <p>Conclusion</p> <p>In this exploratory analysis, common coding polymorphisms in the β₁- and β₃-adrenergic receptors increased cardiovascular risk in women referred for diagnostic angiography, and could improve risk assessment, particularly for women without evidence of obstructive CAD.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov NCT00000554.</p

Nonmonotonic d_{x^2-y^2} Superconducting Order Parameter in Nd_{2-x}Ce_xCuO_4

Low energy polarized electronic Raman scattering of the electron doped superconductor Nd_1.85Ce_0.15CuO_4 (T_c=22 K) has revealed a nonmonotonic d_{x^2-y^2} superconducting order parameter. It has a maximum gap of 4.4 k_BT_c at Fermi surface intersections with antiferromagnetic Brillouin zone (the ``hot spots'') and a smaller gap of 3.3 k_BT_c at fermionic Brillouin zone boundaries. The gap enhancement in the vicinity of the ``hot spots'' emphasizes role of antiferromagnetic fluctuations and similarity in the origin of superconductivity for electron- and hole-doped cuprates.Comment: 4 pages, 4 figure