Pyrene emission from monolayers 'clicked' onto quartz

A series of quartz surfaces were modifed with a series of crosslinkers and functional groups in order to obtain an azide-terminated monolayer, which was then used to immobilize pyrene onto the surface via alkyne-azide \click" chemistry. During the course of the immobilization, different ratios of tert-butyl diphenyl chlorosilane were used to control the distribution and hence the photophysical properties of the pyrene on the surface. The preparative surface reactions and photophysical properties were investigated with contact angle, X-ray photoelectron spectroscopy, UV-visible absorption and emission spectroscopy. High surface coverage was achieved of just under 1molecule per nm2. At this coverage all emission from the pyrene was in the form of excimer emission. Excimer emission dominated at all surface coverages greater than 0.45 molecules per nm2. Below this coverage the monomer emission could also be observed. The conclusions that can be drawn are important for understanding the interactions of neighboring molecules in molecular monolayers. Our results suggest that at high surface coverage a substantial number of the pyrene molecules are already close enough to their neighbors that pairs of them can be directly excited to form excimer with no requirement for diffusion. This can be stated because the long wavelength end of the pyrene absorption and excitation spectra show a broad tail that is assigned to a charge transfer band resulting from an electron being directly transferred from a ground state pyrene to a neighboring pyrene molecule. Furthermore, absorption spectra shifts also indicate that the pyrene molecules undergo some interactions on the surface when they are closely packed

Wittgenstein's Thought Experiments and Relativity Theory

In this paper, I discuss the similarity between Wittgenstein’s use of thought experiments and Relativity Theory. I begin with introducing Wittgenstein’s idea of “thought experiments” and a tentative classification of different kinds of thought experiments in Wittgenstein’s work. Then, after presenting a short recap of some remarks on the analogy between Wittgenstein’s point of view and Einstein’s, I suggest three analogies between the status of Wittgenstein’s mental experiments and Relativity theory: the topics of time dilation, the search for invariants, and the role of measuring tools in Special Relativity. This last point will help to better define Wittgenstein’s idea of description as the core of his philosophical enterprise

Mg/Ca-temperature and seawater-test chemistry relationships in the shallow-dwelling large benthic foraminifera <i>Operculina ammonoides</i>

The foraminifera Mg/Ca palaeothermometer contributes significantly to our understanding of palaeoceanic temperaturevariation. However, since seawater Mg/Ca has undergone large secular variation and the relationship between seawaterand test Mg/Ca has not been calibrated in detail for any species with a substantial fossil record, it is only possible to assessrelative temperature changes in pre-Pleistocene fossil samples. In order to establish the basis of accurate quantitativeMg/Ca-derived deep-time temperature reconstructions, we have calibrated the relationship between test Mg/Ca, seawaterchemistry and temperature in laboratory cultures of the shallow-dwelling large benthic species Operculina ammonoides.Operculina has a fossil range extending back to the early Paleogene and is the nearest living relative of the abundant genusNummulites. We find a temperature sensitivity of 1.7% C-1 and a linear relationship between the Mg distribution coefficientand seawater Mg/Ca (Mg=Casw) with m = -1.9 x 10-3, within error of the equivalent slope for inorganic calcite. The highertest Mg/Ca of O. ammonoides compared to inorganic calcite may be explained by an elevated pH of the calcifying fluid, implying that these foraminifera do not modify the Mg/Ca ratio of the seawater from which they calcify, differentiating them in thisrespect from most other perforate foraminifera. Applying these calibrations to previously published fossil data results inpalaeo-Mg=Casw reconstruction consistent with independent proxy evidence. Furthermore, our data enable accurate absolutepalaeotemperature reconstructions if Mg=Casw is constrained by another technique (e.g. ridge flank vein carbonate; fluidinclusions). Finally, we examine Li, Na, Sr and Ba incorporation into the test of O. ammonoides and discuss the controlexerted by temperature, seawater chemistry, saturation state and growth rate on these emerging proxies

Transient Brewster angle reflectometry of spiropyran monolayers

Brewster angle reflectometry has been developed as a tool for determining the absorbance and refractive index changes in molecular monolayers containing spiropyran. The method is sensitive to changes in both the real and imaginary parts of the refractive index in the monolayers. It was used to monitor the conversion of spiropyran to merocyanine and the reversal of this reaction when the molecules were immobilised on quartz using silane coupling. An analytical solution of Fresnel formula allowed the transient reflectometry data to be converted into transient absorption information. Absorbances of transients as low as ~10-6 were possible using the current apparatus with a single laser pulse transient measurement. It was found that spiropyran photoconverted to merocyanine with an efficiency of ~0.1. The photochemical reversion of converted merocyanine to spiropyran occurred with efficiencies of 0.03–0.2 and this was probably site dependent. It was found that the thermal conversion from merocyanine to spiropyran was slow and even after 10 min there was no significant thermal reversion. This measurement was possible because the real part of the refractive index of the monolayer could be monitored with time using an off-resonance probe at a wavelength where the merocyanine did not absorb light meaning that the probe did not photobleach the sample. Thus our method also provides a non-intrusive method for probing changes in molecules in thin films

Transient absorption spectroscopy on spiropyran monolayers using nanosecond pump–probe Brewster angle reflectometry

Self-assembled monolayers of 11-(3’,3’-dimethyl-6,8-dinitrospiro[chromene-2,2’-indoline]-1’-yl) undecanoic acid (amphiphilic spiropyran) at the air–water interface are studied using Brewster angle reflectometry. Transient kinetics of the spiropyran to merocyanine conversion are recorded in a UV-pump, VIS-probe configuration. By varying the probe wavelength using an optical parametric oscillator, we are able to reconstruct absorption spectra of intermediate states with a time-resolution of 10 nanoseconds, limited by the temporal convolution of the two laser pulses. After UV irradiation, spiropyran converts to merocyanine in two stages. The first occurs within a timescale of several tens of nanoseconds and is heavily convoluted with the system response time, whereas the second stage occurs over a few hundred nanoseconds. During the rise time there is a small red shift in the transient absorption spectrum of ∼20 nm. We assign the red shift and the slower kinetics to the isomerization of a merocyanine isomer cis about the central methine bond to those that are trans about the same bond

City Know-How

Human health and planetary health are influenced by city lifestyles, city leadership, and city development. For both, worrying trends are leading to increasing concern and it is imperative that human health and environmental impacts become core foci in urban policy. Changing trajectory will require concerted action; the journal Cities & Health is dedicated to supporting the flow of knowledge, in all directions, to help make this happen. We wish to foster communication between researchers, practitioners, policy-makers, communities, and decision-makers in cities. This is the purpose of the City Know-how section of the journal. ‘Research for city practice’ disseminates lessons from research by explaining key messages for city leaders, communities, and the professions involved in city policy and practice. ‘City shorts’ provide glimpses of what is being attempted or achieved ‘on the ground’ and ’case studies’ are where you will find evaluations of interventions. Last, ‘Commentary and debate’ extends conversations we are having to develop and mobilize much needed new thinking. Join in these conversations. In order to strengthen the community of interest, we would like to include many and varied voices, including those from younger practitioners and researchers who are supporting health and health equity in everyday urban lives

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications

Are Ethnic and Gender Specific Equations Needed to Derive Fat Free Mass from Bioelectrical Impedance in Children of South Asian, Black African-Caribbean and White European Origin? Results of the Assessment of Body Composition in Children Study

Background Bioelectrical impedance analysis (BIA) is a potentially valuable method for assessing lean mass and body fat levels in children from different ethnic groups. We examined the need for ethnic- and gender-specific equations for estimating fat free mass (FFM) from BIA in children from different ethnic groups and examined their effects on the assessment of ethnic differences in body fat. Methods Cross-sectional study of children aged 8–10 years in London Primary schools including 325 South Asians, 250 black African-Caribbeans and 289 white Europeans with measurements of height, weight and arm-leg impedance (Z; Bodystat 1500). Total body water was estimated from deuterium dilution and converted to FFM. Multilevel models were used to derive three types of equation {A: FFM = linear combination(height+weight+Z); B: FFM = linear combination(height2/Z); C: FFM = linear combination(height2/Z+weight)}. Results Ethnicity and gender were important predictors of FFM and improved model fit in all equations. The models of best fit were ethnicity and gender specific versions of equation A, followed by equation C; these provided accurate assessments of ethnic differences in FFM and FM. In contrast, the use of generic equations led to underestimation of both the negative South Asian-white European FFM difference and the positive black African-Caribbean-white European FFM difference (by 0.53 kg and by 0.73 kg respectively for equation A). The use of generic equations underestimated the positive South Asian-white European difference in fat mass (FM) and overestimated the positive black African-Caribbean-white European difference in FM (by 4.7% and 10.1% respectively for equation A). Consistent results were observed when the equations were applied to a large external data set. Conclusions Ethnic- and gender-specific equations for predicting FFM from BIA provide better estimates of ethnic differences in FFM and FM in children, while generic equations can misrepresent these ethnic differences

Microbially mediated reduction of FeIII and AsV in Cambodian sediments amended with 13C-labelled hexadecane and kerogen

Microbial activity is generally accepted to play a critical role, with the aid of suitable organic carbon substrates, in the mobilisation of arsenic from sediments into shallow reducing groundwaters. The nature of the organic matter in natural aquifers driving the reduction of AsV to AsIII is of particular importance but is poorly understood. In this study, sediments from an arsenic rich aquifer in Cambodia were amended with two 13C-labelled organic substrates. 13C-hexadecane was used as a model for potentially bioavailable long chain n-alkanes and a 13C-kerogen analogue as a proxy for non-extractable organic matter. During anaerobic incubation for 8 weeks, significant FeIII reduction and AsIII mobilisation were observed in the biotic microcosms only, suggesting that these processes were microbially driven. Microcosms amended with 13C-hexadecane exhibited a similar extent of FeIII reduction to the non-amended microcosms, but marginally higher AsIII release. Moreover, gas chromatography–mass spectrometry analysis showed that 65 % of the added 13C-hexadecane was degraded during the 8-week incubation. The degradation of 13C-hexadecane was microbially driven, as confirmed by DNA stable isotope probing (DNA-SIP). Amendment with 13C-kerogen did not enhance FeIII reduction or AsIII mobilisation, and microbial degradation of kerogen could not be confirmed conclusively by DNA-SIP fractionation or 13C incorporation in the phospholipid fatty acids. These data are, therefore, consistent with the utilisation of long chain n-alkanes (but not kerogen) as electron donors for anaerobic processes, potentially including FeIII and AsV reduction in the subsurface