Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Classification of instability modes in a model of aluminium reduction cells with a uniform magnetic field

A unified view on the interfacial instability in a model of aluminium reduction cells in the presence of a uniform, vertical, background magnetic field is presented. The classification of instability modes is based on the asymptotic theory for high values of parameter β, which characterises the ratio of the Lorentz force based on the disturbance current, and gravity. It is shown that the spectrum of the travelling waves consists of two parts independent of the horizontal cross-section of the cell: highly unstable wall modes and stable or weakly unstable centre, or Sele’s modes. The wall modes with the disturbance of the interface being localised at the sidewalls of the cell dominate the dynamics of instability. Sele’s modes are characterised by a distributed disturbance over the whole horizontal extent of the cell. As β increases these modes are stabilized by the field.

Spectral characterisation of cooled filters for remote sensing

The improvements obtained on cooling atmospheric remote-sensing instruments for space flight applications has promoted research in characterization of the necessary optical filters. By modelling the effects of temperature on the dispersive spectrum of some constituent thin film materials, the cooled performance can be simulated and compared. multilayer filter designs with the measured spectra from actual filters. Two actual filters are discussed, for the 7µm region, one a composite cut-on/cut-off design of 13% HBW and the other an integral narrowband design of 4% HBW.

Codification vs personalisation: A study of the information evaluation practice between aerospace and construction industries

In the emerging digital economy, the management of information in aerospace and construction organisations is facing a particular challenge due to the ever-increasing volume of information and the extensive use of information and communication technologies (ICTs). This paper addresses the problems of information overload and the value of information in both industries by providing some cross-disciplinary insights. In particular it identifies major issues and challenges in the current information evaluation practice in these two industries. Interviews were conducted to get a spectrum of industrial perspectives (director/strategic, project management and ICT/document management) on these issues in particular to information storage and retrieval strategies and the contrasting approaches to knowledge and information management of personalisation and codification. Industry feedback was collected by a follow-up workshop to strengthen the findings of the research. An information-handling agenda is outlined for the development of a future Information Evaluation Methodology (IEM) which could facilitate the practice of the codification of high-value information in order to support through-life knowledge and information management (K&IM) practice.

Water vapour self-continuum and water dimers: 1. Analysis of recent work

Recent laboratory observations and advances in theoretical quantum chemistry allow a reappraisal of the fundamental mechanisms that determine the water vapour self-continuum absorption throughout the infrared and millimetre wave spectral regions. By starting from a framework that partitions bimolecular interactions between water molecules into free-pair states, true bound and quasi-bound dimers, we present a critical review of recent observations, continuum models and theoretical predictions. In the near-infrared bands of the water monomer, we propose that spectral features in recent laboratory-derived self-continuum can be well explained as being due to a combination of true bound and quasi-bound dimers, when the spectrum of quasi-bound dimers is approximated as being double the broadened spectrum of the water monomer. Such a representation can explain both the wavenumber variation and the temperature dependence. Recent observations of the self-continuum absorption in the windows between these near-infrared bands indicate that widely used continuum models can underestimate the true strength by around an order of magnitude. An existing far-wing model does not appear able to explain the discrepancy, and although a dimer explanation is possible, currently available observations do not allow a compelling case to be made. In the 8–12 micron window, recent observations indicate that the modern continuum models either do not properly represent the temperature dependence, the wavelength variation, or both. The temperature dependence is suggestive of a transition from the dominance of true bound dimers at lower temperatures to quasibound dimers at higher temperatures. In the mid- and far-infrared spectral region, recent theoretical calculations indicate that true bound dimers may explain at least between 20% and 40% of the observed self-continuum. The possibility that quasi-bound dimers could cause an additional contribution of the same size is discussed. Most recent theoretical considerations agree that water dimers are likely to be the dominant contributor to the self-continuum in the mm-wave spectral range.

Nickel(II) and copper(II) complexes of Schiff base ligands containing N4O2 and N4S2 donors with pyrrole terminal binding groups: synthesis, characterization, X-ray structures, DFT and electrochemical studies

A series of hexadentate ligands, H2Lm (m = 1−4), [1H-pyrrol-2-ylmethylene]{2-[2-(2-{[1H-pyrrol-2-ylmethylene]amino}phenoxy)ethoxy]phenyl}amine (H2L1), [1H-pyrrol-2-ylmethylene]{2-[4-(2-{[1H-pyrrol-2-ylmethylene]amino}phenoxy)butoxy]phenyl}amine (H2L2), [1H-pyrrol-2-ylmethylene][2-({2-[(2-{[1H-pyrrol-2-ylmethylene]amino}phenyl)thio]ethyl}thio)phenyl]amine (H2L3) and [1H-pyrrol-2-ylmethylene][2-({4-[(2-{[1H-pyrrol-2-lmethylene]amino}phenyl)thio]butyl}thio) phenyl]amine (H2L4) were prepared by condensation reaction of pyrrol-2-carboxaldehyde with {2-[2-(2-aminophenoxy)ethoxy]phenyl}amine, {2-[4-(2-aminophenoxy)butoxy]phenyl}amine, [2-({2-[(2-aminophenyl)thio]ethyl}thio)phenyl]amine and [2-({4-[(2-aminophenyl)thio]butyl}thio)phenyl]amine respectively. Reaction of these ligands with nickel(II) and copper(II) acetate gave complexes of the form MLm (m = 1−4), and the synthesized ligands and their complexes have been characterized by a variety of physico-chemical techniques. The solid and solution states investigations show that the complexes are neutral. The molecular structures of NiL3 and CuL2, which have been determined by single crystal X-ray diffraction, indicate that the NiL3 complex has a distorted octahedral coordination environment around the metal while the CuL2 complex has a seesaw coordination geometry. DFT calculations were used to analyse the electronic structure and simulation of the electronic absorption spectrum of the CuL2 complex using TDDFT gives results that are consistent with the measured spectroscopic behavior of the complex. Cyclic voltammetry indicates that all copper complexes are electrochemically inactive but the nickel complexes with softer thioethers are more easily oxidized than their oxygen analogs.

The engagement of territorial knowledge communities with European spatial planning and the territorial cohesion debate: a Baltic perspective

Recent, dramatic spatial development trends have contributed to the consolidation of a unique territorial governance landscape in the Baltic States. The paper examines the transformation of this evolving institutional landscape for planning practice and knowledge, which has been marked by the disintegration of Soviet institutions and networks, the transition to a market-based economy and the process of accession to the EU. It explores the evolution of territorial knowledge channels in the Baltic States, and the extent and nature of the engagement of actors' communities with the main knowledge arenas and resources of European spatial planning (ESP). The paper concludes that recent shifts in the evolution of these channels suggest the engagement of ESP has concentrated among epistemic communities at State and trans-national levels of territorial governance. The limited policy coordination across a broader spectrum of diverse actors is compounded by institutionally weak and fragmented professional communities of practice, fragmented government structures and marginalized advocacy coalitions.

The Huntington's Disease health-related Quality of Life questionnaire (HDQoL): a disease-specific measure of health-related quality of life

Hocaoglu MB, Gaffan EA, Ho AK. The Huntington's disease health-related quality of life questionnaire: a disease-specific measure of health-related quality of life. Huntington's disease (HD) is a genetic neurodegenerative disorder characterized by motor, cognitive and psychiatric disturbances, and yet there is no disease-specific patient-reported health-related quality of life outcome measure for patients. Our aim was to develop and validate such an instrument, i.e. the Huntington's Disease health-related Quality of Life questionnaire (HDQoL), to capture the true impact of living with this disease. Semi-structured interviews were conducted with the full spectrum of people living with HD, to form a pool of items, which were then examined in a larger sample prior to data-driven item reduction. We provide the statistical basis for the extraction of three different sets of scales from the HDQoL, and present validation and psychometric data on these scales using a sample of 152 participants living with HD. These new patient-derived scales provide promising patient-reported outcome measures for HD.

A mechanism for the effect of tropospheric jet structure on the annular mode-like response to stratospheric forcing

For many climate forcings the dominant response of the extratropical circulation is a latitudinal shift of the tropospheric mid-latitude jets. The magnitude of this response appears to depend on climatological jet latitude in general circulation models (GCMs): lower latitude jets exhibit a larger shift. The reason for this latitude dependence is investigated for a particular forcing, heating of the equatorial stratosphere, which shifts the jet poleward. Spin-up ensembles with a simplified GCM are used to examine the evolution of the response for five different jet structures. These differ in the latitude of the eddy-driven jet, but have similar sub-tropical zonal winds. It is found that lower latitude jets exhibit a larger response due to stronger tropospheric eddy-mean flow feedbacks. A dominant feedback responsible for enhancing the poleward shift is an enhanced equatorward refraction of the eddies, resulting in an increased momentum flux, poleward of the low latitude critical line. The sensitivity of feedback strength to jet structure is associated with differences in the coherence of this behaviour across the spectrum of eddy phase speeds. In the configurations used, the higher latitude jets have a wider range of critical latitude locations. This reduces the coherence of the momentum flux anomalies associated with different phase speeds, with low phase speeds opposing the effect of high phase speeds. This suggests that, for a given sub-tropical zonal wind strength, the latitude of the eddy driven jet affects the feedback through its influence on the width of the region of westerly winds and the range of critical latitudes on the equatorward flank of the jet.

Carolingian culture in the North Sea world: rethinking the cultural dynamics of personal adornment in Viking age England

Boosted by a proliferation in metal-detected finds, categories of personal adornment now constitute a vital archaeological source for interpreting Viking-age cultural interaction in the North Sea region. Previous research in England has explored the potential of this metalwork in relation to the formation of ‘Anglo-Scandinavian’ identity, but without due consideration of a wider spectrum of cultural influences. This article redresses the balance by shifting attention to twenty-eight belt fittings derived from richly embellished baldrics, equestrian equipment, and waist belts manufactured on the Frankish continent during the period of Carolingian hegemony in the later eighth and ninth centuries ad. The metalwork is classified and then contextualized in order to track import mechanisms and to assess the impact of Carolingian culture on the northern peripheries of the Frankish empire. The main conclusion is that the adoption, adaptation, and strategic manipulation of Carolingian/northern Frankish identity formed an embedded component of cultural dynamics in Viking-age England, scrutiny of which sheds new light on patterns of interconnectivity linking peoples of the North Sea world.

Carbon and nitrogen stable isotope ratio analysis of freshwater, brackish and marine fish from Belgian archaeological sites (1st and 2nd millennium AD)

Carbon and nitrogen stable isotope ratios were measured in 157 fish bone collagen samples from 15 different archaeological sites in Belgium which ranged in ages from the 3rd to the 18th c. AD. Due to diagenetic contamination of the burial environment, only 63 specimens produced results with suitable C:N ratios (2.9–3.6). The selected bones encompass a wide spectrum of freshwater, brackish, and marine taxa (N = 18), and this is reflected in the δ13C results (−28.2‰ to −12.9%). The freshwater fish have δ13C values that range from −28.2‰ to −20.2‰, while the marine fish cluster between −15.4‰ and −13.0‰. Eel, a catadromous species (mostly living in freshwater but migrating into the sea to spawn), plots between −24.1‰ and −17.7‰, and the anadromous fish (living in marine environments but migrating into freshwater to spawn) show a mix of freshwater and marine isotopic signatures. The δ15N results also have a large range (7.2‰ to 16.7‰) indicating that these fish were feeding at many different trophic levels in these diverse aquatic environments. The aim of this research is the isotopic characterization of archaeological fish species (ecology, trophic level, migration patterns) and to determine intra-species variation within and between fish populations differing in time and location. Due to the previous lack of archaeological fish isotope data from Northern Europe and Belgium in particular, these results serve as an important ecological backdrop for the future isotopic reconstruction of the diet of human populations dating from the historical period (1st and 2nd millennium AD), where there is zooarchaeological and historical evidence for an increased consumption of marine fish.

In vitro evaluation of single- and multi-strain probiotics: inter-species inhibition between probiotic strains, and inhibition of pathogens

Many studies comparing the effects of single- and multi-strain probiotics on pathogen inhibition compare treatments with different concentrations. They also do not examine the possibility of inhibition between probiotic strains with a mixture. We tested the ability of 14 single-species probiotics to inhibit each other using a cross-streak assay, and agar spot test. We then tested the ability of 15 single-species probiotics and 5 probiotic mixtures to inhibit C. difficile, E. coli and S. Typhimurium, using the agar spot test. Testing was done with mixtures created in two ways: one group contained component species incubated together, the other group of mixtures was made using component species which had been incubated separately, equalised to equal optical density, and then mixed in equal volumes. Inhibition was observed for all combinations of probiotics, suggesting that when used as such there may be inhibition between probiotics, potentially reducing efficacy of the mixture. Significant inter-species variation was seen against each pathogen. When single species were tested against mixtures, the multi-species preparations displayed significantly (p<0.05 or less) greater inhibition of pathogens in 12 out of 24 cases. Despite evidence that probiotic species will inhibit each other when incubated together in vitro, in many cases a probiotic mixture was more effective at inhibiting pathogens than its component species when tested at approximately equal concentrations of biomass. This suggests that using a probiotic mixture might be more effective at reducing gastrointestinal infections, and that creating a mixture using species with different effects against different pathogens may have a broader spectrum of action that a single provided by a single strain.

Non-display uses of digital works: Google Books and beyond

With the advent of mass digitization projects, such as the Google Book Search, a peculiar shift has occurred in the way that copyright works are dealt with. Contrary to what has so far been the case, works are turned into machine-readable data to be automatically processed for various purposes without the expression of works being displayed to the public. In the Google Book Settlement Agreement, this new kind of usage is referred to as ‘non-display uses’ of digital works. The legitimacy of these uses has not yet been tested by Courts and does not comfortably fit in the current copyright doctrine, plainly because the works are not used as works but as something else, namely as data. Since non-display uses may prove to be a very lucrative market in the near future, with the potential to affect the way people use copyright works, we examine non-display uses under the prism of copyright principles to determine the boundaries of their legitimacy. Through this examination, we provide a categorization of the activities carried out under the heading of ‘non-display uses’, we examine their lawfulness under the current copyright doctrine and approach the phenomenon from the spectrum of data protection law that could apply, by analogy, to the use of copyright works as processable data.

Synthesis, crystal structure, and catecholase activity of three trinuclear heterometallic NiII2-MnII complexes derived from a salen-type Schiff base ligand

Three new trinuclear heterometallic nickel(II)manganese(II) complexes, [(NiL)2Mn(NCS)2] (1), [(NiL)2Mn(NCO)2] (2), and [{NiL(EtOH)}2Mn(NO2)2]center dot 2EtOH (3), have been synthesized by using [NiL] as the so-called ligand complex [where H2L = N,N'-bis(salicylidene)-1,3-propanediamine] and have been structurally characterized. Crystal structure analyses revealed that complexes 1 and 2 are angular trinuclear species, in which two terminal four-coordinate square planar [NiL] moieties are coordinated to a central MnII through double phenoxido bridges. The MnII is in a six-coordinate distorted octahedral environment that is bonded additionally to two mutually cis nitrogen atoms of terminal thiocyanate (in 1) and cyanate (in 2). In complex 3, in addition to the double phenoxo bridge, the two terminal NiII ions are linked to the central MnII by means of a nitrite bridge (1?N:2?O) that, together with a coordinated ethanol molecule, gives rise to an octahedral environment around the NiII ions and consequently the structure becomes linear. Catecholase activity of these three complexes was examined by using 3,5-di-tert-butylcatechol (3,5-DTBC) as the substrate. All three complexes mimic catecholase activity and the rate of catechol oxidation follows saturation kinetics with respect to the substrate and first-order kinetics with respect to the catalyst. The EPR spectra of the complexes exhibit characteristic six line spectra, which indicate the presence of high-spin octahedral MnII species in solution state. The ESI-MS positive spectrum of 1 in the presence of 3,5-DTBC has been recorded to investigate possible complexsubstrate intermediates.

Comparative in vitro inhibition of urinary tract pathogens by single- and multi-strain probiotics

PURPOSE: Multi-species probiotic preparations have been suggested as having a wide spectrum of application, although few studies have compared their efficacy with that of individual component strains at equal concentrations. We therefore tested the ability of 4 single probiotics and 4 probiotic mixtures to inhibit the urinary tract pathogens Escherichia coli NCTC 9001 and Enterococcus faecalis NCTC 00775. METHODS: We used an agar spot test to test the ability of viable cells to inhibit pathogens, while a broth inhibition assay was used to assess inhibition by cell-free probiotic supernatants in both pH-neutralised and non-neutralised forms. RESULTS: In the agar spot test, all probiotic treatments showed inhibition, L. acidophilus was the most inhibitory single strain against E. faecalis, L. fermentum the most inhibitory against E. coli. A commercially available mixture of 14 strains (Bio-Kult(®)) was the most effective mixture, against E. faecalis, the 3-lactobacillus mixture the most inhibitory against E. coli. Mixtures were not significantly more inhibitory than single strains. In the broth inhibition assays, all probiotic supernatants inhibited both pathogens when pH was not controlled, with only 2 treatments causing inhibition at a neutral pH. CONCLUSIONS: Both viable cells of probiotics and supernatants of probiotic cultures were able to inhibit growth of two urinary tract pathogens. Probiotic mixtures prevented the growth of urinary tract pathogens but were not significantly more inhibitory than single strains. Probiotics appear to produce metabolites that are inhibitory towards urinary tract pathogens. Probiotics display potential to reduce the incidence of urinary tract infections via inhibition of colonisation.