Take these Flowers Old Lady

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A multiple catheter technique for studies or hepatic metabolism and blood flow in dogs with portacaval transposition

A technique is described for in vivo hepatic metabolic studies, employing a multiple catheterization technique in dogs with chronic portacaval transposition. The animals are studied in the unanesthetized state immediately after the insertion of catheters through peripheral cut-downs. The gradient of metabolites entering and leaving the liver can be measured concomitantly with hepatic plasma flow. Additional simultaneous gradients can be obtained across the splanchnic capillary bed, or the hindquarters. Drugs can be introduced into the circulation by a systemic route or by primary injection into the hepatic circulation. The advantages of this approach compared to other methods of evaluating moment to moment hepatic function are discussed. © 1962

Palaeobiology, ecology, and distribution of stromatoporoid faunas in biostromes of the mid-Ludlow of Gotland

Six well exposed mid−Ludlow stromatoporoid−dominated reef biostromes in four localities from the Hemse Group in southeastern Gotland, Sweden comprise a stromatoporoid assemblage dominated by four species; Clathrodictyon mohicanum, “Stromatopora” bekkeri, Plectostroma scaniense, and Lophiostroma schmidtii. All biostromes investigated in this area (of approximately 30 km2) are interpreted to belong to a single faunal assemblage forming a dense accumulation of fossils that is probably the best exposed stromatoporoid−rich deposit of the Silurian. The results from this comprehensive study strengthen earlier interpretations of a combination of genetic and environmental control on growth−forms of the stromatoporoids. Growth styles are similar for stromatoporoids in all six biostromes. Differences in biostrome fabric are due to variations in the degree of disturbance by storms. The uniformity of facies and the widespread low−diversity fauna support the view that palaeoenvironmental conditions were similar across the area where these biostromes crop out, and promoted the extraordinary growth of stromatoporoids in this shallow shelf area

The Prostate Health Index adds predictive value to multi-parametric MRI in detecting significant prostate cancers in a repeat biopsy population

Both multi-parametric MRI (mpMRI) and the Prostate Health Index (PHI) have shown promise in predicting a positive biopsy in men with suspected prostate cancer. Here we investigated the value of combining both tests in men requiring a repeat biopsy. PHI scores were measured in men undergoing re-biopsy with an mpMRI image-guided transperineal approach (n = 279, 94 with negative mpMRIs). The PHI was assessed for ability to add value to mpMRI in predicting all or only significant cancers (Gleason ≥7). In this study adding PHI to mpMRI improved overall and significant cancer prediction (AUC 0.71 and 0.75) compared to mpMRI + PSA alone (AUC 0.64 and 0.69 respectively). At a threshold of ≥35, PHI + mpMRI demonstrated a NPV of 0.97 for excluding significant tumours. In mpMRI negative men, the PHI again improved prediction of significant cancers; AUC 0.76 vs 0.63 (mpMRI + PSA). Using a PHI≥35, only 1/21 significant cancers was missed and 31/73 (42%) men potentially spared a re-biopsy (NPV of 0.97, sensitivity 0.95). Decision curve analysis demonstrated clinically relevant utility of the PHI across threshold probabilities of 5-30%. In summary, the PHI adds predictive performance to image-guided detection of clinically significant cancers and has particular value in determining re-biopsy need in men with a negative mpMRI

The Schistosoma mansoni tegumental-allergen-like (TAL) protein family: influence of developmental expression on human IgE responses

BACKGROUND: A human IgE response to Sm22.6 (a dominant IgE target in Schistosoma mansoni) is associated with the development of partial immunity. Located inside the tegument, the molecule belongs to a family of proteins from parasitic platyhelminths, the Tegument-Allergen-Like proteins (TALs). In addition to containing dynein-light-chain domains, these TALs also contain EF-hand domains similar to those found in numerous EF-hand allergens. METHODOLOGY/PRINCIPAL FINDINGS: S. mansoni genome searches revealed 13 members (SmTAL1-13) within the species. Recent microarray data demonstrated they have a wide range of life-cycle transcriptional profiles. We expressed SmTAL1 (Sm22.6), SmTAL2, 3, 4, 5 and 13 as recombinant proteins and measured IgE and IgG4 in 200 infected males (7–60 years) from a schistosomiasis endemic region in Uganda. For SmTAL1 and 3 (transcribed in schistosomula through adult-worms and adult-worms, respectively) and SmTAL5 (transcribed in cercariae through adult-worms), detectable IgE responses were rare in 7–9 year olds, but increased with age. At all ages, IgE to SmTAL2 (expressed constitutively), was rare while anti-SmTAL2 IgG4 was common. Levels of IgE and IgG4 to SmTAL4 and 13 (transcribed predominantly in the cercariae/skin stage) were all low. CONCLUSIONS: We have not measured SmTAL protein abundance or exposure in live parasites, but the antibody data suggests to us that, in endemic areas, there is priming and boosting of IgE to adult-worm SmTALs by occasional death of long-lived worms, desensitization to egg SmTALs through continuous exposure to dying eggs and low immunogenicity of larval SmTALs due to immunosuppression in the skin by the parasite. Of these, it is the gradual increase in IgE to the worm antigens that parallels age-dependent immunity seen in endemic areas

Changing geo-ecological functions of coral reefs in the Anthropocene

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record The ecology of many coral reefs has changed markedly over recent decades in response to various combinations of local and global stressors. These ecological changes have important implications for the abundance of taxa that regulate the production and erosion of skeletal carbonates, and thus for many of the geo-ecological functions that coral reefs provide, including reef framework production and sediment generation, the maintenance of reef habitat complexity and reef growth potential. These functional attributes underpin many of the ecosystem goods and services that reefs provide to society. Rapidly changing conditions of reefs in the Anthropocene are likely to significantly impact the capacity of reefs to sustain these geo-ecological functions. Although the Anthropocene footprint of disturbance will be expressed differently across ecoregions and habitats, the end point for many reefs may be broadly similar: (a) progressively shifting towards net neutral or negative carbonate budget states; (b) becoming structurally flatter; and (c) having lower vertical growth rates. It is also likely that a progressive depth-homogenisation will occur in terms of these processes. The Anthropocene is likely to be defined by an increasing disconnect between the ecological processes that drive carbonate production on the reef surface, and the net geological outcome of that production, that is, the accumulation of the underlying reef structure. Reef structures are thus likely to become increasingly relict or senescent features, which will reduce reef habitat complexity and sediment generation rates, and limit reef potential to accrete vertically at rates that can track rising sea levels. In the absence of pervasive stressors, recovery of degraded coral communities has been observed, resulting in high net-positive budgets being regained. However, the frequency and intensity of climate-driven bleaching events are predicted to increase over the next decades. This would increase the spatial footprint of disturbances and exacerbate the magnitude of the changes described here, limiting the capacity of many reefs to maintain their geo-ecological functions. The enforcement of effective marine protection or the benefits of geographic isolation or of favourable environmental conditions (“refugia” sites) may offer the hope of more optimistic futures in some locations. A plain language summary is available for this article.Royal Societ

Extreme spatial heterogeneity in carbonate accretion potential on a Caribbean fringing reef linked to local human disturbance gradients

This is the final version. Available on open access from Wiley via the DOI in this recordThe capacity of coral reefs to maintain their structurally complex frameworks and to retain the potential for vertical accretion is vitally important to the persistence of their ecological functioning and the ecosystem services they sustain. However, datasets to support detailed along-coast assessments of framework production rates and accretion potential do not presently exist. Here we estimate, based on gross bioaccretion and bioerosion measures, the carbonate budgets and resultant maximum accretion potential (RAPmax) of the shallow reef zone of leeward Bonaire – between 5 to 12 m depth – at unique fine spatial resolution along this coast (115 sites). Whilst the fringing reef of Bonaire is often reported to be in a better ecological condition than most sites throughout the wider Caribbean region, our data show that the carbonate budgets of the reefs and derived RAPmax rates varied3 considerably across this ~58 km long fringing reef complex. Some areas, in particular the marine reserves, were indeed still dominated by structurally complex coral communities with high net carbonate production (> 10 kg CaCO3 m-2 year-1 35 ), high live coral cover and complex structural topography. The majority of the studied sites, however, were defined by relatively low budget states (< 2 kg CaCO3 m-2 year-1 36 ) or were in a state of net erosion. These data highlight the marked spatial heterogeneity that can occur in budgets states, and thus in reef accretion potential, even between quite closely spaced areas of individual reef complexes. This heterogeneity is linked strongly to the degree of localized land-based impacts along the coast, and resultant differences in the abundance of reef framework building coral species. The major impact of this variability is that those sections of reef defined by low-accretion potential will have limited capacity to maintain their structural integrity and to keep pace with current projections of climate change induced sea-level rise (SLR), thus posing a threat to reef functioning, biodiversity and trophic cascades. Since many Caribbean reefs are more severely degraded than those found around Bonaire, it is to be expected that the findings presented here are rather the rule than the exception, but the study also highlights the need for similar high spatial resolution (along-coast) assessments of budget states and accretion potential to meaningfully explore increasing coastal risk at the country level. The findings also more generally underline the significance of reducing local anthropogenic disturbance and restoring framework-building coral assemblages. Appropriately focussed local preservation efforts may aid in averting future large-scale submergence of Caribbean coral reefs and will constrain the social and economic implications associated with the loss of reef goods and services.Ministry of Economic AffairsWageningen UniversityRoyal Netherlands Institute for Sea Researc

Systematic review of vestibular disorders related to human immunodeficiency virus and acquired immunodeficiency syndrome

INTRODUCTION: Disorders of the auditory and vestibular system are often associated with human immunodeficiency virus infection and acquired immunodeficiency syndrome. However, the extent and nature of these vestibular manifestations are unclear. OBJECTIVE: To systematically review the current peer-reviewed literature on vestibular manifestations and pathology related to human immunodeficiency virus and acquired immunodeficiency syndrome. METHOD: Systematic review of peer-reviewed articles related to vestibular findings in individuals with human immunodeficiency virus infection and acquired immunodeficiency syndrome. Several electronic databases were searched. RESULTS: We identified 442 records, reduced to 210 after excluding duplicates and reviews. These were reviewed for relevance to the scope of the study. DISCUSSION: We identified only 13 reports investigating vestibular functioning and pathology in individuals affected by human immunodeficiency virus and acquired immunodeficiency syndrome. This condition can affect both the peripheral and central vestibular system, irrespective of age and viral disease stage. Peripheral vestibular involvement may affect up to 50 per cent of patients, and central vestibular involvement may be even more prevalent. Post-mortem studies suggest direct involvement of the entire vestibular system, while opportunistic infections such as oto- and neurosyphilis and encephalitis cause secondary vestibular dysfunction resulting in vertigo, dizziness and imbalance. CONCLUSION: Patients with human immunodeficiency virus and acquired immunodeficiency syndrome should routinely be monitored for vestibular involvement, to minimise functional limitations of quality of life.http://journals.cambridge.org/action/displayJournal?jid=JL

Caribbean-wide decline in carbonate production threatens coral reef growth

This a post-print, author-produced version of an article accepted for publication in Nature Communications. Copyright © 2013 Nature Publishing Group . The definitive version is available at http://www.nature.com/ncomms/journal/v4/n1/full/ncomms2409.htmlGlobal-scale deteriorations in coral reef health have caused major shifts in species composition. One projected consequence is a lowering of reef carbonate production rates, potentially impairing reef growth, compromising ecosystem functionality and ultimately leading to net reef erosion. Here, using measures of gross and net carbonate production and erosion from 19 Caribbean reefs, we show that contemporary carbonate production rates are now substantially below historical (mid- to late-Holocene) values. On average, current production rates are reduced by at least 50%, and 37% of surveyed sites were net erosional. Calculated accretion rates (mm year(-1)) for shallow fore-reef habitats are also close to an order of magnitude lower than Holocene averages. A live coral cover threshold of ~10% appears critical to maintaining positive production states. Below this ecological threshold carbonate budgets typically become net negative and threaten reef accretion. Collectively, these data suggest that recent ecological declines are now suppressing Caribbean reef growth potential

The taxonomic name resolution service : an online tool for automated standardization of plant names

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 14 (2013): 16, doi:10.1186/1471-2105-14-16.The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ webcite and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/ webcite.BJE was supported by NSF grant DBI 0850373 and TR by CSIRO Marine and Atmospheric Research, Australia,. BB and BJE acknowledge early financial support from Conservation International and TEAM who funded the development of early prototypes of taxonomic name resolution. The iPlant Collaborative (http://www.iplantcollaborative.org) is funded by a grant from the National Science Foundation (#DBI-0735191)