Three-dimensional photonic crystals based on macroporous silicon with modulated pore diameter

We report on the fabrication and optical characterization of a three-dimensional (3D) photonic crystal on the basis of macroporous silicon. The structure consists of a 2D array of air pores in silicon whose diameter is varied (modulated) periodically with depth. The bandstructure of the resulting 3D hexagonal photonic crystal is calculated and compared with transmission measurements. The described structure allows to adjust the dispersion relation along the pore axis almost independently from the dispersion relation in the plane perpendicular to the pore axis.

A Population-Based Study of IGF Axis Polymorphisms and the Esophageal Inflammation, Metaplasia, Adenocarcinoma Sequence

BACKGROUND & AIMS: Insulin-like growth factor (IGF) axis plays a key role in cell development, proliferation, and survival and is implicated in the etiology of several cancers. Few studies have examined the relationship between genetic variation of this axis and esophageal adenocarcinoma (EAC) or its precursors. METHODS: In a population-based case-control study, we investigated the association of common polymorphisms of IGF-1, IGF-2, IGF-1 receptor, IGF binding protein -3, growth hormones (GH) 1 and GH2, and GH receptor with reflux esophagitis (RE), Barrett esophagus (BE), and EAC. Two hundred and thirty RE, 224 BE, 227 EAC cases, and 260 controls were studied. Gene polymorphisms were identified using publicly available online resources; 102 IGF axis tag and putatively functional single-nucleotide polymorphisms (SNPs) were analyzed using MassARRAY iPLEX and Taqman assays. Results were analyzed using Haploview.
RESULTS: Three polymorphisms were disease-associated. IGF1 SNP rs6214 was associated with BE (adjusted P = .039). Using GG genotype as reference, odds ratio for BE in AA (wild-type) was 0.43 (95% confidence interval [CI], 0.24-0.75). GH receptor SNP rs6898743 was associated with EAC (adjusted P = .0112). With GG as reference, odds ratio for EAC in CC (wildtype) genotype was 0.42 (95% CI, 0.23-0.76). IGF1 (CA)(17) 185-bp allele was associated with RE (adjusted P = .0116). Using IGF1(non17) as reference, odds ratio for RE in IGF1(17) carriers was 7.29 (95% CI, 1.57-46.7).
CONCLUSIONS: In this study, 3 polymorphisms of IGF genes were associated with EAC or its precursors. These polymorphisms may be markers of disease risk; independent validation of our findings is required. These results suggest the IGF pathway is involved in EAC development.

Twist localizes three-dimensional patterns

A mechanism or the localization of spatially periodic,self-oganized patterns in anisotropic media which requires systems extended in all three spatial dimensions is presented: When the anisotropy axis is twisted, the pattern becomes localized in planes parallel to the anisotropy axis. An analytical description of the effect is developed, and used to interpret recent experiments in the high-frequency regime of electroconvection by Bohatsch and Stannarius [Phys. Rev. E 60, 5591 (1999)]. The localization width is found to be of the order of magnitude of the geometrical average of the pattern wavelength and the inverse twist.

HIF-2alpha Associated Familial Erythrocytosis Supports the PHD2-HIF2-alpha-VHL Axis as the Major Regulator of Erythropoietin Production

Transcriptionally erythropoietin (Epo) synthesis is tightly regulated by the hypoxia inducible factor (HIF), which is composed of one alpha and one beta subunit that are constitutively expressed. The beta subunit is non-variable, but three different alpha subunits give rise to three isoforms of HIF. The alpha subunit is proteasomally regulated in the presence of oxygen by hydroxylation of the proline in the LXXLAP motif of the oxygen dependent degradation (ODD) domain of HIFalpha, catalysed by members of the prolyl hydroxylase domain (PHD) family of enzymes. This allows the von Hippel Lindau (VHL) protein to associate with the alpha subunit, which is subsequently tagged with ubiquitin and degraded by the proteasome. Any defect in the oxygen sensing pathway that allows the alpha subunit to escape proteasomal regulation leads to elevated expression of HIF target genes.

Recently mutations in both VHL and PHD2 have been identified in a cohort of patients with erythrocytosis, but no mutations were found in the ODD domain of HIF1alpha. Instead, investigation of the homologous region in HIF-2alpha revealed four different mutations, Pro534Leu, Met535Val, Gly537Arg and Gly537Trp in seven individuals/families. Affected individuals presented at a young age with elevated serum Epo. Several individuals have a clinical history of thrombosis, but no evidence of a von Hippel Lindau-like syndrome.

To define how the four mutations relate to the erythrocytosis phenotype functional assays were performed in vitro. Binding of PHD2 to the four HIF-2alpha mutants was impaired to varying degrees, with both the Gly537 mutants showing the greatest reduction. The association of VHL with the hydroxylated Met535Val mutant peptide was similar to wild type HIF- 2alpha, but was decreased in the other three HIF-2alpha mutants. Expression of three HIF- 2alpha target genes, adrenomedullin, NDRG1 and VEGF, was significantly up-regulated in cells stably transfected with the mutants under normoxia compared to wild type HIF-2alpha. Mutations in the ODD domain of HIF-2alpha disrupt proteasomal regulation by reducing the association with PHD2 and hence hydroxylation. Furthermore the binding of VHL is also impaired, even when HIF-2alpha is hydroxylated. Examination of the three-dimensional structure of hydroxylated HIF-1alpha bound to VHL confirms that amino acids close to site of hydroxylation (Pro-531 in isoform 2) are important for this association. These observations, together with recent studies utilising murine models of erythrocytosis, support the PHD2-HIF-2alpha-VHL axis as the major regulator of erythropoietin.

The typology of Irish hard rock aquifers based on an integrated hydrogeological and geophysical approach

Groundwater flow in hard-rock aquifers is strongly controlled by the characteristics and distribution of structural heterogeneity. A methodology for catchment-scale characterisation is presented, based on the integration of complementary, multi-scale hydrogeological, geophysical and geological approaches. This was applied to three contrasting catchments underlain by metamorphic rocks in the northern parts of Ireland (Republic of Ireland and Northern Ireland, UK). Cross-validated surface and borehole geophysical investigations confirm the discontinuous overburden, lithological compartmentalisation of the bedrock and important spatial variations of the weathered bedrock profiles at macro-scale. Fracture analysis suggests that the recent (Alpine) tectonic fabric exerts strong control on the internal aquifer structure at meso-scale, which is likely to impact on the anisotropy of aquifer properties. The combination of the interpretation of depth-specific hydraulic-test data with the structural information provided by geophysical tests allows characterisation of the hydrodynamic properties of the identified aquifer units. Regionally, the distribution of hydraulic conductivities can be described by inverse power laws specific to the aquifer litho-type. Observed groundwater flow directions reflect this multi-scale structure. The proposed integrated approach applies widely available investigative tools to identify key dominant structures controlling groundwater flow, characterising the aquifer type for each catchment and resolving the spatial distribution of relevant aquifer units and associated hydrodynamic parameters.

Burkholderia cenocepacia BC2L-C Is a Super Lectin with Dual Specificity and Proinflammatory Activity

Lectins and adhesins are involved in bacterial adhesion to host tissues and mucus during early steps of infection. We report the characterization of BC2L-C, a soluble lectin from the opportunistic pathogen Burkholderia cenocepacia, which has two distinct domains with unique specificities and biological activities. The N-terminal domain is a novel TNF-alpha-like fucose-binding lectin, while the C-terminal part is similar to a superfamily of calcium-dependent bacterial lectins. The C-terminal domain displays specificity for mannose and L-glycero-D-manno-heptose. BC2L-C is therefore a superlectin that binds independently to mannose/heptose glycoconjugates and fucosylated human histo-blood group epitopes. The apo form of the C-terminal domain crystallized as a dimer, and calcium and mannose could be docked in the binding site. The whole lectin is hexameric and the overall structure, determined by electron microscopy and small angle X-ray scattering, reveals a flexible arrangement of three mannose/heptose-specific dimers flanked by two fucose-specific TNF-alpha-like trimers. We propose that BC2L-C binds to the bacterial surface in a mannose/heptose-dependent manner via the C-terminal domain. The TNF-alpha-like domain triggers IL-8 production in cultured airway epithelial cells in a carbohydrate-independent manner, and is therefore proposed to play a role in the dysregulated proinflammatory response observed in B. cenocepacia lung infections. The unique architecture of this newly recognized superlectin correlates with multiple functions including bacterial cell cross-linking, adhesion to human epithelia, and stimulation of inflammation.

LIQUID MARBLES GRANULATED USING SUPER-HYDROPHOBIC METAL POWDERS

Superhydrophobic (SH) particles based on a copper substrate were prepared by a silver deposition technique of different particle sizes from 10µm to 425µm. Such SH particles were found to be pH-responsive and liquid marbles formed using the SH copper substrate destabilised under certain pH conditions. The exposure to high concentrations of acidic or basic gases caused immediate collapse of the liquid marble. However, low concentrations of acidic and basic gases could diffuse across the shell of liquid marbles without adversely affecting the structure. Liquid marbles formed with large SH particles (425
µm) did not fully form a mono-layer around the liquid droplet. This phenomenon, whereby SH particles slide down the surface of the water droplet until an equilibrium position is reached, was studied using a mathematical approach, which related the angle to the vertical axis of the SH particles at t
he equilibrium F, to the shape of liquid marble and the contact angle, ?.

Combining multi-scale geophysical techniques for robust hydro-structural characterisation in catchments underlain by hard rock in post-glacial regions

Accurate conceptual models of groundwater systems are essential for correct interpretation of monitoring data in catchment studies. In surface-water dominated hard rock regions, modern ground and surface water monitoring programmes often have very high resolution chemical, meteorological and hydrological observations but lack an equivalent emphasis on the subsurface environment, the properties of which exert a strong control on flow pathways and interactions with surface waters. The reasons for this disparity are the complexity of the system and the difficulty in accurately characterising the subsurface, except locally at outcrops or in boreholes. This is particularly the case in maritime north-western Europe, where a legacy of glacial activity, combined with large areas underlain by heterogeneous igneous and metamorphic bedrock, make the structure and weathering of bedrock difficult to map or model. Traditional approaches which seek to extrapolate information from borehole to field-scale are of limited application in these environments due to the high degree of spatial heterogeneity. Here we apply an integrative and multi-scale approach, optimising and combining standard geophysical techniques to generate a three-dimensional geological conceptual model of the subsurface in a catchment in NE Ireland. Available airborne LiDAR, electromagnetic and magnetic data sets were analysed for the region. At field-scale surface geophysical methods, including electrical resistivity tomography, seismic refraction, ground penetrating radar and magnetic surveys, were used and combined with field mapping of outcrops and borehole testing. The study demonstrates how combined interpretation of multiple methods at a range of scales produces robust three-dimensional conceptual models and a stronger basis for interpreting groundwater and surface water monitoring data.

Consistent effects of consumer species loss across different habitats

Our knowledge of the effects of consumer species loss on ecosystem functioning is limited by a paucity of manipulative field studies, particularly those that incorporate inter-trophic effects. Further, given the ongoing transformation of natural habitats by anthropogenic activities, studies should assess the relative importance of biodiversity for ecosystem processes across different environmental contexts by including multiple habitat types. We tested the context-dependency of the effects of consumer species loss by conducting a 15-month field experiment in two habitats (mussel beds and rock pools) on a temperate rocky shore, focussing on the responses of algal assemblages following the single and combined removals of key gastropod grazers (Patella vulgata, P. ulyssiponensis, Littorina littorea and Gibbula umbilicalis). In both habitats, the removal of limpets resulted in a larger increase in macroalgal richness than that of either L. littorea or G. umbilicalis. Further, by the end of the study, macroalgal cover and richness were greater following the removal of multiple grazer species compared to single species removals. Despite substantial differences in physical properties and the structure of benthic assemblages between mussel beds and rock pools, the effects of grazer loss on macroalgal cover, richness, evenness and assemblage structure were remarkably consistent across both habitats. There was, however, a transient habitat-dependent effect of grazer removal on macroalgal assemblage structure that emerged after three months, which was replaced by non-interactive effects of grazer removal and habitat after 15 months. This study shows that the effects of the loss of key consumers may transcend large abiotic and biotic differences between habitats in rocky intertidal systems. While it is clear that consumer diversity is a primary driver of ecosystem functioning, determining its relative importance across multiple contexts is necessary to understand the consequences of consumer species loss against a background of environmental change.

Genetic assessment of parentage in the caridean rock shrimp Rhynchocinetes typus based on microsatellite markers

Over the past decade, the common rock shrimp, Rhynchocinetes typus H. Milne Edwards, 1837, has been the focus of extensive investigations on mating behaviour. The species is now perceived as a model system for the study of reproductive strategies and sexual conflict in crustaceans displaying external fertilization. Using molecular markers, the current study assesses whether social mating behaviour in common rock shrimp translates into true genetic parentage. In a large mesocosm tank with >200 individuals of both sexes, the analysis of 15 families (22 eggs per female) for three informative microsatellites unambiguously confirmed multiple paternity in 11 instances (73%) involving, in each case, two to four males. Where more than one male was identified siring a particular brood, reproductive skew was apparent towards a single individual. Results suggest that multiple paternity in this species results from subordinate male coercive behaviour, female solicitation of multiple male matings or a combination of both.

Super suburbia: developing resilience by closing resource cycles in North Belfast

Sustainability can be described as having three interlinked strands, known as the ‘trias energetica’, without which resilience is difficult to achieve. These strands are environmental, social and economic: and if taken as indicators, the suburbs of North Belfast are very poorly performing indeed. Places such as Ligoneal and Glen Cairn have poor housing stock energetically, and also little economic activity. This paper describes propositional work completed by Queens University and Belfast City Council as part of the UK’s Technology Strategy Board’s Future Cities Programme, which aimed to develop new synergies in these neighbourhoods by the insertion of closed cycle economies.

By utilising a research by design methodology, the paper develops a process-based and phased design to develop a new emergent form to these neighbourhoods, one in which new productive systems are embedded into the city, at a small-scales. These include a peak-load hydro-electric project in Ligoneal; a productive landscape in Glen Cairn and a city-wide energy refurbishment utilising neighbourhood waste streams.

These designs allow for a roadmap for development to be created that could change the modus operandi of an area over a relatively short period of time, and show that even modest investments of productive technologies at a local scale could fundamentally change the form and the economic and environmental operation of the city in the future, and create a new resilient city, one that can be less externally dependent and more socially just.

Assessment of Intervention Fidelity and Recommendations for Researchers Conducting Studies on the Diagnosis and Treatment of Chronic Cough in the Adult: CHEST Guideline and Expert Panel Report

BACKGROUND: Successful management of chronic cough has varied in the primary research studies in the reported literature. One of the potential reasons relates to a lack of intervention fidelity to the core elements of the diagnostic and/or therapeutic interventions that were meant to be used by the investigators.

METHODS: We conducted a systematic review to summarize the evidence supporting intervention fidelity as an important methodologic consideration in assessing the effectiveness of clinical practice guidelines used for the diagnosis and management of chronic cough. We developed and used a tool to assess for five areas of intervention fidelity. Medline (PubMed), Scopus, and the Cochrane Database of Systematic Reviews were searched from January 1998 to May 2014. Guideline recommendations and suggestions for those conducting research using guidelines or protocols to diagnose and manage chronic cough in the adult were developed and voted upon using CHEST Organization methodology.

RESULTS: A total of 23 studies (17 uncontrolled prospective observational, two randomized controlled, and four retrospective observational) met our inclusion criteria. These articles included 3,636 patients. Data could not be pooled for meta-analysis because of heterogeneity. Findings related to the five areas of intervention fidelity included three areas primarily related to the provider and two primarily related to the patients. In the area of study design, 11 of 23 studies appeared to be underpinned by a single guideline/protocol; for training of providers, two of 23 studies reported training, and zero of 23 reported the use of an intervention manual; and for the area of delivery of treatment, when assessing the treatment of gastroesophageal reflux disease, three of 23 studies appeared consistent with the most recent guideline/protocol referenced by the authors. For receipt of treatment, zero of 23 studies mentioned measuring concordance of patient-interventionist understanding of the treatment recommended, and zero of 23 mentioned measuring enactment of treatment, with three of 23 measuring side effects and two of 23 measuring adherence. The overall average intervention fidelity score for all 23 studies was poor (20.74 out of 48).

CONCLUSIONS: Only low-quality evidence supports that intervention fidelity strategies were used when conducting primary research in diagnosing and managing chronic cough in adults. This supports the contention that some of the variability in the reporting of patients with unexplained or unresolved chronic cough may be due to lack of intervention fidelity. By following the recommendations and suggestions in this article, researchers will likely be better able to incorporate strategies to address intervention fidelity, thereby strengthening the validity and generalizability of their results that provide the basis for the development of trustworthy guidelines.