Activity and abundance of methanotrophic bacteria in a northern mountainous gradient of wetlands

Methane uptake and diversity of methanotrophic bacteria was investigated across six hydrologically connected wetlands in a mountainous forest landscape upstream of lake Langtjern, southern Norway. From floodplain through shrubs, forest and sedges to a Sphagnum covered site, growing season CH4 production was insufficiently consumed to balance release into the atmosphere. Emission increased by soil moisture ranging 0.6-6.8 mg CH4 m-2  h-1 . Top soils of all sites consumed CH4 including at the lowest 78 ppmv CH4 supplied, thus potentially oxidizing 17-51 nmol CH4 g-1 dw h-1 , with highest Vmax 440 nmol g-1 dw h-1 under Sphagnum and lowest Km 559 nM under hummocked Carex. Nine genera and several less understood type I and type II methanotrophs were detected by the key functional gene pmoA involved in methane oxidation. Microarray signal intensities from all sites revealed Methylococcus, the affiliated Lake Washington cluster, Methylocaldum, a Japanese rice cluster, Methylosinus, Methylocystis and the affiliated Peat264 cluster. Notably enriched by site was a floodplain Methylomonas and a Methylocapsa-affiliated watershed cluster in the Sphagnum site. The climate sensitive water table was shown to be a strong controlling factor highlighting its link with the CH4 cycle in elevated wetlands.

Nontrivial maturation metastate-average state in a one-dimensional long-range Ising spin glass: Above and below the upper critical range

Understanding the low-temperature pure state structure of spin glasses remains an open problem in the field of statistical mechanics of disordered systems. Here we study Monte Carlo dynamics, performing simulations of the growth of correlations following a quench from infinite temperature to a temperature well below the spin-glass transition temperature T_{c} for a one-dimensional Ising spin-glass model with diluted long-range interactions. In this model, the probability P_{ij} that an edge {i,j} has nonvanishing interaction falls as a power law with chord distance, P_{ij}∝1/R_{ij}^{2σ}, and we study a range of values of σ with 1/2<σ<1. We consider a correlation function C_{4}(r,t). A dynamic correlation length that shows power-law growth with time ξ(t)∝t^{1/z} can be identified in the data and, for large time t, C_{4}(r,t) decays as a power law r^{-α_{d}} with distance r when r≪ξ(t). The calculation can be interpreted in terms of the maturation metastate averaged Gibbs state, or MMAS, and the decay exponent α_{d} differentiates between a trivial MMAS (α_{d}=0), as expected in the droplet picture of spin glasses, and a nontrivial MMAS (α_{d}≠0), as in the replica-symmetry-breaking (RSB) or chaotic pairs pictures. We find nonzero α_{d} even in the regime σ>2/3 which corresponds to short-range systems below six dimensions. For σ<2/3, the decay exponent α_{d} follows the RSB prediction for the decay exponent α_{s}=3-4σ of the static metastate, consistent with a conjectured statics-dynamics relation, while it approaches α_{d}=1-σ in the regime 2/3<σ<1; however, it deviates from both lines in the vicinity of σ=2/3.

Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation

Gammaproteobacteria from the family Endozoicomonadaceae have emerged as widespread associates of dense marine animal communities. Their abundance in coral reefs involves symbiotic relationships and possibly host nutrition. We explored functions encoded in the genome of an uncultured Endozoicomonadaceae 'Candidatus Acestibacter aggregatus' that lives inside gill cells of large Acesta excavata clams in deep-water coral reefs off mid-Norway. The dominance and deep branching lineage of this symbiont was confirmed using 16S rRNA gene sequencing and phylogenomic analysis from shotgun sequencing data. The 4.5 Mb genome binned in this study has a low GC content of 35% and is enriched in transposon and chaperone gene annotations indicating ongoing adaptation. Genes encoding functions potentially involved with the symbiosis include ankyrins, repeat in toxins, secretion and nutritional systems. Complete pathways were identified for the synthesis of eleven amino acids and six B-vitamins. A minimal chitinolytic machinery was indicated from a glycosyl hydrolase GH18 and a lytic polysaccharide monooxygenase LPMO10. Expression of the latter was confirmed using proteomics. Signal peptides for secretion were identified for six polysaccharide degrading enzymes, ten proteases and three lipases. Our results suggest a nutritional symbiosis fuelled by enzymatic products from extracellular degradation processes.

Contact in the Unitary Fermi Gas across the Superfluid Phase Transition

A quantity known as the contact is a fundamental thermodynamic property of quantum many-body systems with short-range interactions. Determination of the temperature dependence of the contact for the unitary Fermi gas of infinite scattering length has been a major challenge, with different calculations yielding qualitatively different results. Here we use finite-temperature auxiliary-field quantum Monte Carlo (AFMC) methods on the lattice within the canonical ensemble to calculate the temperature dependence of the contact for the homogeneous spin-balanced unitary Fermi gas. We extrapolate to the continuum limit for 40, 66, and 114 particles, eliminating systematic errors due to finite-range effects. We observe a dramatic decrease in the contact as the superfluid critical temperature is approached from below, followed by a gradual weak decrease as the temperature increases in the normal phase. Our theoretical results are in excellent agreement with the most recent precision ultracold atomic gas experiments. We also present results for the energy as a function of temperature in the continuum limit.

Pairing Correlations across the Superfluid Phase Transition in the Unitary Fermi Gas

In the two-component Fermi gas with a contact interaction, a pseudogap regime can exist at temperatures between the superfluid critical temperature T_{c} and a temperature T^{*}>T_{c}. This regime is characterized by pairing correlations without superfluidity. However, in the unitary limit of infinite scattering length, the existence of this regime is still debated. To help address this, we have applied finite-temperature auxiliary-field quantum Monte Carlo (AFMC) methods to study the thermodynamics of the superfluid phase transition and signatures of the pseudogap in the spin-balanced homogeneous unitary Fermi gas. We present results at finite filling factor ν≃0.06 for the condensate fraction, an energy-staggering pairing gap, the spin susceptibility, and the heat capacity, and compare them to experimental data when available. In contrast to previous AFMC simulations, our model space consists of the complete first Brillouin zone of the lattice, and our calculations are performed in the canonical ensemble of fixed particle number. The canonical ensemble AFMC framework enables the calculation of a model-independent gap, providing direct information on pairing correlations without the need for numerical analytic continuation. We use finite-size scaling to estimate T_{c} at the corresponding filling factor. We find that the energy-staggering pairing gap vanishes above T_{c}, showing no pseudogap effects, and that the spin susceptibility shows a substantially reduced signature of a spin gap compared to previously reported AFMC simulations.

Experimentally derived incorporation rates and diet-to-tissue discrimination values for carbon and nitrogen stable isotopes in gray wolves (Canis lupus) fed a marine diet

Recent studies have noted the differential effects of marine versus terrestrial diets on the carbon and nitrogen stable isotope (13C and 15N, respectively) diet-to-tissue discrimination values and incorporation rates for omnivorous and carnivorous mammals. Inaccurate estimates of these parameters may result in misrepresentation of diet composition or in the timing of diet shifts. Here, we present the results of a diet-switch experiment designed to estimate diet-to-tissue discrimination values and incorporation rates for tissues of gray wolves (Canis lupus Linnaeus, 1758) fed a diet of Pacific salmon (genus Oncorhynchus Suckley, 1861). Our results demonstrate substantial differences in both parameters between wolves maintained on a marine (salmon) diet and wolves maintained on terrestrially sourced prey (beef, Bos taurus Linnaeus, 1758). Increased awareness of the significance of marine resources to omnivorous and carnivorous consumers, like wolves, highlights the importance of phenomenological and mechanistic understandings of the effects of fish and other marine prey on dietary investigations based on stable isotopes.

Liquid Chromatographic Determination of Residual Nitrite/Nitrate in Foods: NMKL Collaborative Study

Nitrite and nitrate are used as additives in the food industry to provide color and taste and to control undesirable gas and flavor production by anaerobic bacteria by virtue of their antimicrobial properties. The analytical method that has been widely used to determine nitrite and nitrate involves the use of toxic cadmium. In response to a request from the Nordic Committee on Food Analysis, a study was performed to obtain an alternative chromatographic method to determine residual nitrite and nitrate in meat products. The study was done in 3 stages: (1) comparative evaluation of the performance of 3 liquid chromatographic methods, (2) internal validation of the selected ion chromatographic method, and (3) a collaborative study in which 17 laboratories from European countries participated. Furthermore, the applicability of the method to matrixes other than meat and meat products was demonstrated. The results of the collaborative study show that the European Prestandard prENV 12014-4 is well suited for the determination of nitrite and nitrate in different foods (e.g., meat products, vegetables, baby food, and cheese). The limits of detection for nitrite and nitrate ions are 1 and 10 mg/kg, respectively. Recoveries of residual nitrite/nitrate ranged from 96 to 108%. Repeatability and reproducibility were satisfactory.

Diversity of deep-water coral-associated bacteria and comparison across depth gradients

Environmental conditions influence species composition, including the microbial communities that associate with benthic organisms such as corals. In this study we identified and compared bacteria that associate with three common deep-water corals, Lophelia pertusa, Madrepora oculata and Paragorgia arborea, from a reef habitat on the mid-Norwegian shelf. The 16S rRNA gene amplicon sequencing data obtained revealed that >50% of sequences were represented by only five operational taxonomic units. Three were host-specific and unclassified below class level, belonging to Alphaproteobacteria with affiliation to members of the Rhizobiales order (L. pertusa), Flavobacteria affiliated with members of the Elisabethkingia genus (M. oculata) and Mollicutes sequences affiliated with the Mycoplasma genus (P. arborea). In addition, gammaproteobacterial sequences within the genera Sulfitobacter and Oleispira were found across all three deep-water coral taxa. Although highly abundant in the coral microbiomes, these sequences accounted for <0.1% of the surrounding bacterioplankton, supporting specific relationships. We combined this information with previous studies, undertaking a meta-data analysis of 165 widespread samples across coral hosts and habitats. Patterns in bacterial diversity indicated enrichment of distinct uncultured species in coral microbiomes that differed among deep (>200 m), mesophotic (30–200 m) and shallow (<30 m) reefs.

From Usability Testing to Clinical Simulations: Bringing Context into the Design and Evaluation of Usable and Safe Health Information Technologies

Objectives: The objective of this paper is to explore human factors approaches to understanding the use of health information technology (HIT) by extending usability engineering approaches to include analysis of the impact of clinical context through use of clinical simulations.

Methods: Methods discussed are considered on a continuum from traditional laboratory-based usability testing to clinical simulations. Clinical simulations can be conducted in a simulation laboratory and they can also be conducted in real-world settings. The clinical simulation approach attempts to bring the dimension of clinical context into stronger focus. This involves testing of systems with representative users doing representative tasks, in representative settings/environments.

Results: Application of methods where realistic clinical scenarios are used to drive the study of users interacting with systems under realistic conditions and settings can lead to identification of problems and issues with systems that may not be detected using traditional usability engineering methods. In conducting such studies, careful consideration is needed in creating ecologically valid test scenarios. The evidence obtained from such evaluation can be used to improve both the usability and safety of HIT. In addition, recent work has shown that clinical simulations, in particular those conducted in-situ, can lead to considerable benefits when compared to the costs of running such studies.

Conclusion: In order to bring context of use into the testing of HIT, clinical simulation, involving observing representative users carrying out tasks in representative settings, holds considerable promise.

Solvent Effects on Activity and Conformation of Plasminogen Activator Inhibitor-1

We have studied effects of the solvent composition on the activity and the conformation of human plasminogen activator inhibitor-1 (PAI-1) from HT-1080 fibrosarcoma cells. Non-ionic detergents, including Triton X-100, reduced the inhibitory activity of PAI-1 more than 20-fold at 0° C, but less than 2-fold at 37° C, while glycerol partly prevented the detergent-induced activity-loss at 0° C. The activity-loss was associated with an increase in PAI-1 substrate behaviour. Evaluating the PAI-1 conformation by proteolytic susceptibility of specific peptide bonds, we found that the V8-proteinase susceptibility of the Glu332-Ser333 (P17-P16) bond, part of the hinge between the reactive centre loop (RCL) and β-strand 5A, and the endoproteinase Asp-N susceptibility of several bonds in the β-strand 2A-α-helix E region were increased by detergents at both 0 and 37° C. The susceptibility of the Gln321-Ala322 and the Lys325-Val326 bonds in β-strand 5A to papain and trypsin, respectively, was increased by detergents at 0° C, but not at 37° C, showing a strict correlation between proteinase susceptibility of β-strand 5A and activity-loss at 0° C. Since the β-strand 2A-α-helix E region also showed differential susceptibility to endoproteinase Asp-N in latent, active, and reactive centre-cleaved PAI-1, we propose that a detergent-induced conformational change of the β-strand 2A-α-helix E region influences the movements of β-sheet A, resulting in a cold-induced conformational change of β-strand 5A and thereby an increased substrate behaviour at low temperatures. These results provide new information about the structural basis for serpin substrate behaviour.

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle

During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5'-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge's sulfur cycle.

Methods for Addressing Technology-induced Errors: The Current State

OBJECTIVES

The objectives of this paper are to review and discuss the methods that are being used internationally to report on, mitigate, and eliminate technology-induced errors.

METHODS

The IMIA Working Group for Health Informatics for Patient Safety worked together to review and synthesize some of the main methods and approaches associated with technology- induced error reporting, reduction, and mitigation. The work involved a review of the evidence-based literature as well as guideline publications specific to health informatics.

RESULTS

The paper presents a rich overview of current approaches, issues, and methods associated with: (1) safe HIT design, (2) safe HIT implementation, (3) reporting on technology-induced errors, (4) technology-induced error analysis, and (5) health information technology (HIT) risk management. The work is based on research from around the world.

CONCLUSIONS

Internationally, researchers have been developing methods that can be used to identify, report on, mitigate, and eliminate technology-induced errors. Although there remain issues and challenges associated with the methodologies, they have been shown to improve the quality and safety of HIT. Since the first publications documenting technology-induced errors in healthcare in 2005, we have seen in a short 10 years researchers develop ways of identifying and addressing these types of errors. We have also seen organizations begin to use these approaches. Knowledge has been translated into practice in a short ten years whereas the norm for other research areas is of 20 years.

The effect of 8 or 5 years of denosumab treatment in postmenopausal women with osteoporosis: results from the FREEDOM Extension study

The FREEDOM study and its Extension provide long-term information about the effects of denosumab for the treatment of postmenopausal osteoporosis. Treatment for up to 8 years was associated with persistent reduction of bone turnover, continued increases in bone mineral density, low fracture incidence, and a favorable benefit/risk profile.

INTRODUCTION

This study aims to report the results through year 5 of the FREEDOM Extension study, representing up to 8 years of continued denosumab treatment in postmenopausal women with osteoporosis.

METHODS

Women who completed the 3-year FREEDOM study were eligible to enter the 7-year open-label FREEDOM Extension in which all participants are scheduled to receive denosumab, since placebo assignment was discontinued for ethical reasons. A total of 4550 women enrolled in the Extension (2343 long-term; 2207 cross-over). In this analysis, women in the long-term and cross-over groups received denosumab for up to 8 and 5 years, respectively.

RESULTS

Throughout the Extension, sustained reduction of bone turnover markers (BTMs) was observed in both groups. In the long-term group, mean bone mineral density (BMD) continued to increase significantly at each time point measured, for cumulative 8-year gains of 18.4 and 8.3 % at the lumbar spine and total hip, respectively. In the cross-over group, mean BMD increased significantly from the Extension baseline for 5-year cumulative gains of 13.1 and 6.2 % at the lumbar spine and total hip, respectively. The yearly incidence of new vertebral and nonvertebral fractures remained low in both groups. The incidence of adverse and serious adverse events did not increase over time. Through Extension year 5, eight events of osteonecrosis of the jaw and two events of atypical femoral fracture were confirmed.

CONCLUSIONS

Denosumab treatment for up to 8 years was associated with persistent reductions of BTMs, continued BMD gains, low fracture incidence, and a consistent safety profile.

Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy

BACKGROUND

Hospital-associated infections cause considerable morbidity and mortality, and are expensive to treat. Organisms causing these infections can be sourced from the inanimate environment around a patient. Could the difficulty in eradicating these organisms from the environment be because they reside in dry surface biofilms?

AIM

The intensive care unit (ICU) of a tertiary referral hospital was decommissioned and the opportunity to destructively sample clinical surfaces was taken in order to investigate whether multidrug-resistant organisms (MDROs) had survived the decommissioning process and whether they were present in biofilms.

METHODS

The ICU had two 'terminal cleans' with 500 ppm free chlorine solution; items from bedding, surrounds, and furnishings were then sampled with cutting implements. Sections were sonicated in tryptone soya broth and inoculated on to chromogenic plates to demonstrate MDROs, which were confirmed with the Vitek2 system. Genomic DNA was extracted directly from ICU samples, and subjected to polymerase chain reaction (PCR) for femA to detect Staphylococcus aureus and the microbiome by bacterial tag-encoded FLX amplicon pyrosequencing. Confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) were performed on environmental samples.

FINDINGS

Multidrug-resistant bacteria were cultured from 52% (23/44) of samples cultured. S. aureus PCR was positive in 50%. Biofilm was demonstrated in 93% (41/44) of samples by CLSM and/or SEM. Pyrosequencing demonstrated that the biofilms were polymicrobial and contained species that had multidrug-resistant strains.

CONCLUSION

Dry surface biofilms containing MDROs are found on ICU surfaces despite terminal cleaning with chlorine solution. How these arise and how they might be removed requires further study.

From adverse drug event detection to prevention. A novel clinical decision support framework for medication safety

BACKGROUND

Errors related to medication seriously affect patient safety and the quality of healthcare. It has been widely argued that various types of such errors may be prevented by introducing Clinical Decision Support Systems (CDSSs) at the point of care.

OBJECTIVES

Although significant research has been conducted in the field, still medication safety is a crucial issue, while few research outcomes are mature enough to be considered for use in actual clinical settings. In this paper, we present a clinical decision support framework targeting medication safety with major focus on adverse drug event (ADE) prevention.

METHODS

The novelty of the framework lies in its design that approaches the problem holistically, i.e., starting from knowledge discovery to provide reliable numbers about ADEs per hospital or medical unit to describe their consequences and probable causes, and next employing the acquired knowledge for decision support services development and deployment. Major design features of the framework's services are: a) their adaptation to the context of care (i.e. patient characteristics, place of care, and significance of ADEs), and b) their straightforward integration in the healthcare information technologies (IT) infrastructure thanks to the adoption of a service-oriented architecture (SOA) and relevant standards.

RESULTS

Our results illustrate the successful interoperability of the framework with two commercially available IT products, i.e., a Computerized Physician Order Entry (CPOE) and an Electronic Health Record (EHR) system, respectively, along with a Web prototype that is independent of existing healthcare IT products. The conducted clinical validation with domain experts and test cases illustrates that the impact of the framework is expected to be major, with respect to patient safety, and towards introducing the CDSS functionality in practical use.

CONCLUSIONS

This study illustrates an important potential for the applicability of the presented framework in delivering contextualized decision support services at the point of care and for making a substantial contribution towards ADE prevention. Nonetheless, further research is required in order to quantitatively and thoroughly assess its impact in medication safety.

Automated thresholding and analysis of microCT scanned bread dough

Computer aided x-ray microtomography is an increasingly popular method to investigate the structure of materials. Continuing improvements in the technique are resulting in increasingly larger data sets. The analysis of these data sets generally involves executing a static workflow for multiple samples and is generally performed manually by researchers. Executing these processes requires a significant time investment. A workflow which is able to automate the activities of the user would be useful. In this work, we have developed an automated workflow for the analysis of microtomography scanned bread dough data sets averaging 5 GB in size. Comparing the automated workflow with the manual workflow indicates a significant amount of the time spent (33% in the case of bread dough) on user interactions in manual method. Both workflows return similar results for porosity and pore frequency distribution. Finally, by implementing an automated workflow, users save the time which would be required to manually execute the workflow. This time can be spent on more productive tasks.

Novel RNA oligonucleotide improves liver function and inhibits liver carcinogenesis in vivo

Hepatocellular carcinoma (HCC) occurs predominantly in patients with liver cirrhosis. Here we show an innovative RNA-based targeted approach to enhance endogenous albumin production while reducing liver tumor burden. We designed short-activating RNAs (saRNA) to enhance expression of C/EBPα (CCAAT/enhancer-binding protein-α), a transcriptional regulator and activator of albumin gene expression. Increased levels of both C/EBPα and albumin mRNA in addition to a 3-fold increase in albumin secretion and 50% decrease in cell proliferation was observed in C/EBPα-saRNA transfected HepG2 cells. Intravenous injection of C/EBPα-saRNA in a cirrhotic rat model with multifocal liver tumors increased circulating serum albumin by over 30%, showing evidence of improved liver function. Tumor burden decreased by 80% (P = 0.003) with a 40% reduction in a marker of preneoplastic transformation. Since C/EBPα has known antiproliferative activities by way of retinoblastoma, p21, and cyclins, we used messenger RNA (mRNA) expression liver cancer-specific microarray in C/EBPα-saRNA-transfected HepG2 cells to confirm down-regulation of genes strongly enriched for negative regulation of apoptosis, angiogenesis, and metastasis. Up-regulated genes were enriched for tumor suppressors and positive regulators of cell differentiation. A quantitative polymerase chain reaction (PCR) and western blot analysis of C/EBPα-saRNA-transfected cells suggested that in addition to the known antiproliferative targets of C/EBPα, we also observed suppression of interleukin (IL)6R, c-Myc, and reduced STAT3 phosphorylation.

CONCLUSION

A novel injectable saRNA-oligonucleotide that enhances C/EBPα expression successfully reduces tumor burden and simultaneously improves liver function in a clinically relevant liver cirrhosis/HCC model.

From Usability Testing to Clinical Simulations: Bringing Context into the Design and Evaluation of Usable and Safe Health Information Technologies. Contribution of the IMIA Human Factors Engineering for Healthcare Informatics Working Group

OBJECTIVES

The objective of this paper is to explore human factors approaches to understanding the use of health information technology (HIT) by extending usability engineering approaches to include analysis of the impact of clinical context through use of clinical simulations.

METHODS

Methods discussed are considered on a continuum from traditional laboratory-based usability testing to clinical simulations. Clinical simulations can be conducted in a simulation laboratory and they can also be conducted in real-world settings. The clinical simulation approach attempts to bring the dimension of clinical context into stronger focus. This involves testing of systems with representative users doing representative tasks, in representative settings/environments.

RESULTS

Application of methods where realistic clinical scenarios are used to drive the study of users interacting with systems under realistic conditions and settings can lead to identification of problems and issues with systems that may not be detected using traditional usability engineering methods. In conducting such studies, careful consideration is needed in creating ecologically valid test scenarios. The evidence obtained from such evaluation can be used to improve both the usability and safety of HIT. In addition, recent work has shown that clinical simulations, in particular those conducted in-situ, can lead to considerable benefits when compared to the costs of running such studies.

CONCLUSION

In order to bring context of use into the testing of HIT, clinical simulation, involving observing representative users carrying out tasks in representative settings, holds considerable promise.

First Report of the Pear Trellis Rust Fungus, Gymnosporangium sabinae, on Pyrus calleryana ('Bradford' and 'Chanticleer') and P. communis in New York State

Owing to their relative disease resistance and showy spring flowers, cultivars of Callery pear (Pyrus calleryana) are commonly planted ornamental and streetside trees in New York state and elsewhere in the U.S. Over the past 2 years, we collected a leaf rust on P. calleryana 'Bradford' or 'Chanticleer' (also known as 'Cleveland Select') from Hempstead (Nassau County), East Moriches and Riverhead (Suffolk Co.), Rochester (Monroe Co.), and Staten Island (Richmond Co.), NY. Leaf samples were collected in June and August 2010 and 2011; adaxial surface lesions resembled infection by fungi in the genus Gymnosporangium (Pucciniales). Lesions were yellow- to red-orange with irregular red to purple margins, 1 to 3.5 cm in any one dimension, and contained 20 to 45 black, subepidermal spermogonia. Hypertrophied plant tissue was evident on the abaxial surface below the spermagonia, but aecia were absent. Genomic DNA was extracted from rust-infected tissue on P. calleryana 'Bradford' (East Moriches, Hempstead, Rochester, and Staten Island) and 'Chanticleer' (Riverhead), and the D1/D2 domain of the 28s ribosomal DNA was PCR-amplified using primers 4 and 11 (3) and sequenced. Partial 28s rDNA sequences (GenBank Accession Nos. JN969962 to JN969966) were either identical or nearly so (99%) to that of the trellis rust fungus, G. sabinae (AF426209 and AY512845). G. sabinae produces aecia with conspicuous balanoid peridia from August to November or until leaf drop; both characteristics are unique to the genus (1). We therefore monitored rust-infected Callery pears in Riverhead as well as a common pear (P. communis) in Ithaca, NY, for the appearance of aecia in 2011. The telial state of G. sabinae on taxa in the genus Juniperus sect. Sabina (e.g., J. sabina and J. virginiana) was not observed within the vicinity of affected pears. In late September, aecia of G. sabinae with morphological features identical to those described by Kerns (1) and Yun et al. (4) were collected from a P. calleryana in Riverhead (Cornell Plant Pathology Herbarium; CUP-067943) and a P. communis in Ithaca (CUP-067943): aecia roestelioid, hypophyllous; periderium balanoid, apex intact and conic, cancellate along the sides; aeciospores brown, globoid to broadly ellipsoid, 22.5 to 28.2 × 25.1 to 32.4 μm, walls 3.3 to 4.7 μm thick. A native of Eurasia and North Africa, G. sabinae was first identified in North America on common pear in 1960 in British Columbia and California (2). Thereafter, the fungus was collected on Callery pear in northern Washington in 1988 and recently, in Michigan in 2009 (4). To our knowledge, this is the first report of G. sabinae on P. calleryana 'Bradford' and 'Chanticleer' as well as P. communis in New York and the new records represent a large (>800 km) eastward expansion of the distribution of the pathogen in the U.S. The geographic locations of affected trees described herein suggest that the trellis rust fungus is well-established across New York, and has spread undetected since its introduction. Given the widespread planting of Callery pear and occurrence of susceptible Juniperus spp. in urban landscapes of New York, G. sabinae has the potential to become a perennial problem where epidemiological conditions permit host alternation. References: (2) F. Kerns. A revised taxonomic account of Gymnosporangium, 1973. (4) A. McCain. Plant Dis. Rep. 45:151, 1961. (1) G. Van der Auwera et al. FEBS Lett. 338:133, 1994. (3) H. Yun et al. Plant Dis. 93:841, 2009.

Differential expression of particulate methane monooxygenase genes in the verrucomicrobial methanotroph 'Methylacidiphilum kamchatkense' Kam1

Methane monooxygenases (MMOs) are oxygen-dependent enzymes that catalyze the oxidation of methane to methanol in the methanotrophic bacteria. The thermoacidophilic verrucomicrobial methanotroph 'Methylacidiphilum kamchatkense' Kam1 contains three complete and phylogenetically distinct copies of the pmoCAB gene cluster apparently organized as operons, each encoding all three subunits of particulate MMO (pMMO), and a truncated pmoCA cluster encoding only two of the subunits. Two of the clusters are present as a tandem array, but the other clusters occur in isolation. Here, the expression of these clusters has been assessed using the four pmoA genes as targets in reverse transcriptase quantitative PCR analysis. One of the pmoA genes, designated pmoA2, is at least 35-fold more strongly transcribed than the other pmoA copies. Growth at suboptimal temperature and pH conditions did not significantly change the transcription pattern, indicating that the pmoCAB2 cluster encodes the functional pMMO under methane-fuelled growth conditions. During growth on methanol, expression of pmoA2 was reduced approximately tenfold as compared to growth on methane, suggesting a role for the alternative carbon substrates in gene regulation.

The challenge of informed consent for increased risk living donation and transplantation

The Organ Procurement and Transplantation Network (OPTN) mandates that organ recipients provide "specific informed consent" before accepting organs that the OPTN defines as "increased risk". However, the OPTN does not provide specific guidelines for what information should be disclosed to potential recipients. Such vagueness opens the door to inadequate informed consent. This paper examines the ethical dimensions of informed consent when the prospective living donor has self-reported behaviors associated with increased risk for infection transmission. Donor privacy is a primary ethical concern that conflicts with recipients' informed consent for use of increased risk organs. We propose that both the increased risk status and the specific behavior be disclosed to the recipient. Because the actual risk posed is linked to the type of risk behavior, disclosure is therefore needed to make an informed decision. The donor's risk behavior is material to recipients' decision making because it may impact the donor-recipient relationship. This relationship is the foundation of the donation and acceptance transaction, and thus comprises a critical feature of the recipient's informed consent. Optimizing a recipient's informed consent is essential to protecting patient safety and autonomy.

Evolution of temperature optimum in Thermotogaceae and the prediction of trait values of uncultured organisms

Quantitative characterization of the mode and rate of phenotypic evolution is rarely applied to prokaryotes. Here, we present an analysis of temperature optimum (T_opt) evolution in the thermophilic family Thermotogaceae, which has a large number of cultured representatives. We use log-rate-interval analysis to show that T_opt evolution in Thermotogaceae is consistent with a Brownian motion (BM) evolutionary model. The properties of the BM model are used to a establish confidence intervals on the unknown phenotypic trait value of an uncultured organism, given its distance to a close relative with known trait value. Cross-validation by bootstrapping indicates that the predictions are robust.

Intracellular Oceanospirillales bacteria inhabit gills of Acesta bivalves

A novel bacterium was discovered in the gills of the large bivalve Acesta excavata (Limidae) from coral reefs on the northeast Atlantic margin near the shelf break of the fishing ground Haltenbanken of Norway, and confirmed present in A. excavata from a rock-wall in the Trondheimsfjord. Purified gill DNA contained one dominant bacterial rRNA operon as indicated from analysis of broad range bacterial PCR amplicons in denaturant gradient gels, in clone libraries and by direct sequencing. The sequences originated from an unknown member of the order Oceanospirillales and its 16S rRNA gene fell within a clade of strictly marine invertebrate-associated Gammaproteobacteria. Visual inspection by fluorescent in situ hybridization and transmission electron microscopy indicated a pleomorphic bacterium with no visible cell wall, located in aggregates inside vacuoles scattered within the gill cells cytoplasm. Intracellular Oceanospirillales exist in bathymodiolin mussels (parasites), Osedax worms and whiteflies (symbionts). This bacterium apparently lives in a specific association with the Acesta.

Methanol improves methane uptake in starved methanotrophic microorganisms

Methanotrophs in enrichment cultures grew and sustained atmospheric methane oxidation when supplied with methanol. If they were not supplied with methanol or formate, their atmospheric methane oxidation came to a halt, but it was restored within hours in response to methanol or formate. Indigenous forest soil methanotrophs were also dependent on a supply of methanol upon reduced methane access but only when exposed to a methane-free atmosphere. Their immediate response to each methanol addition, however, was to shut down the oxidation of atmospheric methane and to reactivate atmospheric methane oxidation as the methanol was depleted.

Coma with Vertical Gaze Palsy: Relevance of Angio-CT in Acute Percheron Artery Syndrome

Background

A 63-year-old woman with chronic atrial fibrillation treated with warfarin was admitted to emergency for coma and complete vertical gaze palsy. Investigations: Brain CT and MRI, echo-colour Doppler sonography of the supraaortic vessels, angio-CT of the intracranial vessels, EEG, transesophageal echocardiogram, biohumoral tests. Brain CT and MRI scans showed bilateral thalamic lesions with involvement of the right midbrain; EEG showed a diffuse alpha rhythm prevalent on the posterior regions; echo-colour Doppler sonography of the supraaortic vessels showed marked reduction of blood flow in the right vertebral artery; angio-CT scans showed occlusion of the right vertebral artery and a significant filling defect of the first part of the right posterior cerebral artery (P1) from which the artery of Percheron arises. A follow-up angio-CT showed a complete recanalization of P1. Diagnosis: Percheron artery syndrome. Treatment and Management: Aspirin, neurorehabilitation.

Trends in skin cancer incidence by socioeconomic position in Scotland, 1978-2004

Background:

Non-melanoma skin cancer has been little studied in relation to deprivation.

Methods:

Incident cases diagnosed in 1978–2004 were extracted from the Scottish Cancer Register and assigned to quintiles of Carstairs deprivation scores. Age-standardised incidence rates (ASRs) (European standard population) were calculated by deprivation quintile, sex, period of diagnosis, for the three main types of skin cancer.

Results and conclusion:

As age-standardised incidence of each skin cancer increased significantly over time across all deprivation categories, rates were consistently highest in the least deprived quintile.