Systematic study of the static electrical properties of the CO molecule: influence of the basis set size and correlation energy

The influence of the basis set size and the correlation energy in the static electrical properties of the CO molecule is assessed. In particular, we have studied both the nuclear relaxation and the vibrational contributions to the static molecular electrical properties, the vibrational Stark effect (VSE) and the vibrational intensity effect (VIE). From a mathematical point of view, when a static and uniform electric field is applied to a molecule, the energy of this system can be expressed in terms of a double power series with respect to the bond length and to the field strength. From the power series expansion of the potential energy, field-dependent expressions for the equilibrium geometry, for the potential energy and for the force constant are obtained. The nuclear relaxation and vibrational contributions to the molecular electrical properties are analyzed in terms of the derivatives of the electronic molecular properties. In general, the results presented show that accurate inclusion of the correlation energy and large basis sets are needed to calculate the molecular electrical properties and their derivatives with respect to either nuclear displacements or/and field strength. With respect to experimental data, the calculated power series coefficients are overestimated by the SCF, CISD, and QCISD methods. On the contrary, perturbation methods (MP2 and MP4) tend to underestimate them. In average and using the 6-311 + G(3df) basis set and for the CO molecule, the nuclear relaxation and the vibrational contributions to the molecular electrical properties amount to 11.7%, 3.3%, and 69.7% of the purely electronic μ, α, and β values, respectively

Differential sensitivity to tonal frequency and to the rate of modulation of broad-band noise by hearing-impaired listeners

This dissertation examined whether a hearing impairment of the auditory end-organ has the same or a differential effect on the place and periodicity processes. Differential sensitivities for four normally hearing listeners and for both ears of five patients with unilateral Meniere’s disease were measured for tonal frequency and rate of sinusoidally amplitude-modulated noise at common frequencies and rates of the stimulus.

Sensitivity of the ERA40 reanalysis to the observing system: determination of the global atmospheric circulation from reduced observations

The impact of selected observing systems on the European Centre for Medium-Range Weather Forecasts (ECMWF) 40-yr reanalysis (ERA40) is explored by mimicking observational networks of the past. This is accomplished by systematically removing observations from the present observational data base used by ERA40. The observing systems considered are a surface-based system typical of the period prior to 1945/50, obtained by only retaining the surface observations, a terrestrial-based system typical of the period 1950-1979, obtained by removing all space-based observations, and finally a space-based system, obtained by removing all terrestrial observations except those for surface pressure. Experiments using these different observing systems have been limited to seasonal periods selected from the last 10 yr of ERA40. The results show that the surface-based system has severe limitations in reconstructing the atmospheric state of the upper troposphere and stratosphere. The terrestrial system has major limitations in generating the circulation of the Southern Hemisphere with considerable errors in the position and intensity of individual weather systems. The space-based system is able to analyse the larger-scale aspects of the global atmosphere almost as well as the present observing system but performs less well in analysing the smaller-scale aspects as represented by the vorticity field. Here, terrestrial data such as radiosondes and aircraft observations are of paramount importance. The terrestrial system in the form of a limited number of radiosondes in the tropics is also required to analyse the quasi-biennial oscillation phenomenon in a proper way. The results also show the dominance of the satellite observing system in the Southern Hemisphere. These results all indicate that care is required in using current reanalyses in climate studies due to the large inhomogeneity of the available observations, in particular in time.

The moist boundary layer under a mid-latitude weather system

Mid-latitude weather systems are key contributors to the transport of atmospheric water vapour, but less is known about the role of the boundary layer in this transport. We expand a conceptual model of dry boundary-layer structure under synoptic systems to include moist processes, using idealised simulations of cyclone waves to investigate the three-way interaction between the boundary layer, atmospheric moisture and large-scale dynamics. Forced by large-scale thermal advection, boundary-layer structures develop over large areas, analogous to the daytime convective boundary layer, the nocturnal stable boundary layer and transitional regimes between these extremes.

Developing the next-generation climate system models: challenges and achievements

Although climate models have been improving in accuracy and efficiency over the past few decades, it now seems that these incremental improvements may be slowing. As tera/petascale computing becomes massively parallel, our legacy codes are less suitable, and even with the increased resolution that we are now beginning to use, these models cannot represent the multiscale nature of the climate system. This paper argues that it may be time to reconsider the use of adaptive mesh refinement for weather and climate forecasting in order to achieve good scaling and representation of the wide range of spatial scales in the atmosphere and ocean. Furthermore, the challenge of introducing living organisms and human responses into climate system models is only just beginning to be tackled. We do not yet have a clear framework in which to approach the problem, but it is likely to cover such a huge number of different scales and processes that radically different methods may have to be considered. The challenges of multiscale modelling and petascale computing provide an opportunity to consider a fresh approach to numerical modelling of the climate (or Earth) system, which takes advantage of the computational fluid dynamics developments in other fields and brings new perspectives on how to incorporate Earth system processes. This paper reviews some of the current issues in climate (and, by implication, Earth) system modelling, and asks the question whether a new generation of models is needed to tackle these problems.

The European Declarative System, Database, and Languages

The EP2025 EDS project develops a highly parallel information server that supports established high-value interfaces. We describe the motivation for the project, the architecture of the system, and the design and application of its database and language subsystems. The Elipsys logic programming language, its advanced applications, EDS Lisp, and the Metal machine translation system are examined.

Global hydrology modelling and uncertainty: running multiple ensembles with a campus grid.

Uncertainties associated with the representation of various physical processes in global climate models (GCMs) mean that, when projections from GCMs are used in climate change impact studies, the uncertainty propagates through to the impact estimates. A complete treatment of this ‘climate model structural uncertainty’ is necessary so that decision-makers are presented with an uncertainty range around the impact estimates. This uncertainty is often underexplored owing to the human and computer processing time required to perform the numerous simulations. Here, we present a 189-member ensemble of global river runoff and water resource stress simulations that adequately address this uncertainty. Following several adaptations and modifications, the ensemble creation time has been reduced from 750 h on a typical single-processor personal computer to 9 h of high-throughput computing on the University of Reading Campus Grid. Here, we outline the changes that had to be made to the hydrological impacts model and to the Campus Grid, and present the main results. We show that, although there is considerable uncertainty in both the magnitude and the sign of regional runoff changes across different GCMs with climate change, there is much less uncertainty in runoff changes for regions that experience large runoff increases (e.g. the high northern latitudes and Central Asia) and large runoff decreases (e.g. the Mediterranean). Furthermore, there is consensus that the percentage of the global population at risk to water resource stress will increase with climate change.

Iron Uptake and Homeostasis in Microorganisms

Preface. Iron is considered to be a minor element employed, in a variety of forms, by nearly all living organisms. In some cases, it is utilised in large quantities, for instance for the formation of magnetosomes within magnetotactic bacteria or during use of iron as a respiratory donor or acceptor by iron oxidising or reducing bacteria. However, in most cases the role of iron is restricted to its use as a cofactor or prosthetic group assisting the biological activity of many different types of protein. The key metabolic processes that are dependent on iron as a cofactor are numerous; they include respiration, light harvesting, nitrogen fixation, the Krebs cycle, redox stress resistance, amino acid synthesis and oxygen transport. Indeed, it is clear that Life in its current form would be impossible in the absence of iron. One of the main reasons for the reliance of Life upon this metal is the ability of iron to exist in multiple redox states, in particular the relatively stable ferrous (Fe2+) and ferric (Fe3+) forms. The availability of these stable oxidation states allows iron to engage in redox reactions over a wide range of midpoint potentials, depending on the coordination environment, making it an extremely adaptable mediator of electron exchange processes. Iron is also one of the most common elements within the Earth’s crust (5% abundance) and thus is considered to have been readily available when Life evolved on our early, anaerobic planet. However, as oxygen accumulated (the ‘Great oxidation event’) within the atmosphere some 2.4 billion years ago, and as the oceans became less acidic, the iron within primordial oceans was converted from its soluble reduced form to its weakly-soluble oxidised ferric form, which precipitated (~1.8 billion years ago) to form the ‘banded iron formations’ (BIFs) observed today in Precambrian sedimentary rocks around the world. These BIFs provide a geological record marking a transition point away from the ancient anaerobic world towards modern aerobic Earth. They also indicate a period over which the bio-availability of iron shifted from abundance to limitation, a condition that extends to the modern day. Thus, it is considered likely that the vast majority of extant organisms face the common problem of securing sufficient iron from their environment – a problem that Life on Earth has had to cope with for some 2 billion years. This struggle for iron is exemplified by the competition for this metal amongst co-habiting microorganisms who resort to stealing (pirating) each others iron supplies! The reliance of micro-organisms upon iron can be disadvantageous to them, and to our innate immune system it represents a chink in the microbial armour, offering an opportunity that can be exploited to ward off pathogenic invaders. In order to infect body tissues and cause disease, pathogens must secure all their iron from the host. To fight such infections, the host specifically withdraws available iron through the action of various iron depleting processes (e.g. the release of lactoferrin and lipocalin-2) – this represents an important strategy in our defence against disease. However, pathogens are frequently able to deploy iron acquisition systems that target host iron sources such as transferrin, lactoferrin and hemoproteins, and thus counteract the iron-withdrawal approaches of the host. Inactivation of such host-targeting iron-uptake systems often attenuates the pathogenicity of the invading microbe, illustrating the importance of ‘the battle for iron’ in the infection process. The role of iron sequestration systems in facilitating microbial infections has been a major driving force in research aimed at unravelling the complexities of microbial iron transport processes. But also, the intricacy of such systems offers a challenge that stimulates the curiosity. One such challenge is to understand how balanced levels of free iron within the cytosol are achieved in a way that avoids toxicity whilst providing sufficient levels for metabolic purposes – this is a requirement that all organisms have to meet. Although the systems involved in achieving this balance can be highly variable amongst different microorganisms, the overall strategy is common. On a coarse level, the homeostatic control of cellular iron is maintained through strict control of the uptake, storage and utilisation of available iron, and is co-ordinated by integrated iron-regulatory networks. However, much yet remains to be discovered concerning the fine details of these different iron regulatory processes. As already indicated, perhaps the most difficult task in maintaining iron homeostasis is simply the procurement of sufficient iron from external sources. The importance of this problem is demonstrated by the plethora of distinct iron transporters often found within a single bacterium, each targeting different forms (complex or redox state) of iron or a different environmental condition. Thus, microbes devote considerable cellular resource to securing iron from their surroundings, reflecting how successful acquisition of iron can be crucial in the competition for survival. The aim of this book is provide the reader with an overview of iron transport processes within a range of microorganisms and to provide an indication of how microbial iron levels are controlled. This aim is promoted through the inclusion of expert reviews on several well studied examples that illustrate the current state of play concerning our comprehension of how iron is translocated into the bacterial (or fungal) cell and how iron homeostasis is controlled within microbes. The first two chapters (1-2) consider the general properties of microbial iron-chelating compounds (known as ‘siderophores’), and the mechanisms used by bacteria to acquire haem and utilise it as an iron source. The following twelve chapters (3-14) focus on specific types of microorganism that are of key interest, covering both an array of pathogens for humans, animals and plants (e.g. species of Bordetella, Shigella, , Erwinia, Vibrio, Aeromonas, Francisella, Campylobacter and Staphylococci, and EHEC) as well as a number of prominent non-pathogens (e.g. the rhizobia, E. coli K-12, Bacteroides spp., cyanobacteria, Bacillus spp. and yeasts). The chapters relay the common themes in microbial iron uptake approaches (e.g. the use of siderophores, TonB-dependent transporters, and ABC transport systems), but also highlight many distinctions (such as use of different types iron regulator and the impact of the presence/absence of a cell wall) in the strategies employed. We hope that those both within and outside the field will find this book useful, stimulating and interesting. We intend that it will provide a source for reference that will assist relevant researchers and provide an entry point for those initiating their studies within this subject. Finally, it is important that we acknowledge and thank wholeheartedly the many contributors who have provided the 14 excellent chapters from which this book is composed. Without their considerable efforts, this book, and the understanding that it relays, would not have been possible. Simon C Andrews and Pierre Cornelis

High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

A system for studying epithelial-stromal interactions reveals distinct inductive abilities of stromal cells from benign prostatic hyperplasia and prostate cancer

The development of normal and abnormal glandular structures in the prostate is controlled at the endocrine and paracrine levels by reciprocal interactions between epithelium and stroma. To study these processes it is useful to have an efficient method of tissue acquisition for reproducible isolation of cells from defined histologies. Here we assessed the utility of a standardized system for acquisition and growth of prostatic cells from different regions of the prostate with different pathologies, and we compared the abilities of stromal cells from normal peripheral zone (PZ-S), benign prostatic hyperplasia (BPH-S), and cancer (CA-S) to induce the growth of a human prostatic epithelial cell line (BPH-1) in vivo. Using the tissue recombination method, we showed that grafting stromal cells (from any histology) alone, or BPH-1 epithelial cells alone produced no visible grafts. Recombining PZ-S with BPH-1 cells also produced no visible grafts (n = 15). Recombining BPH-S with BPH-1 cells generated small, well-organized and sharply demarcated grafts approximately 3-4 mm in diameter (n = 9), demonstrating a moderate inductive ability of BPH-S. Recombining CA-S with BPH-1 cells generated highly disorganized grafts that completely surrounded the host kidney and invaded into adjacent renal tissue, demonstrating induction of an aggressive phenotype. We conclude that acquisition of tissue from toluidine blue dye stained specimens is an efficient method to generate high quality epithelial and/or stromal cultures. Stromal cells derived by this method from areas of BPH and cancer induce epithelial cell growth in vivo which mimics the natural history of these diseases.

Rapid parallel expression in E-coli and insect cells: Analysis of five lef gene products of the Autographa californica multiple nuclear polyhedrosis virus (AcMNPV)

A number of strategies are emerging for the high throughput (HTP) expression of recombinant proteins to enable structural and functional study. Here we describe a workable HTP strategy based on parallel protein expression in E. coli and insect cells. Using this system we provide comparative expression data for five proteins derived from the Autographa californica polyhedrosis virus genome that vary in amino acid composition and in molecular weight. Although the proteins are part of a set of factors known to be required for viral late gene expression, the precise function of three of the five, late expression factors (lefs) 6, 7 and 10, is unknown. Rapid expression and characterisation has allowed the determination of their ability to bind DNA and shown a cellular location consistent with their properties. Our data point to the utility of a parallel expression strategy to rapidly obtain workable protein expression levels from many open reading frames (ORFs).

High-throughput proteomics using matrix-assisted laser desorption/ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Failure of a control strategy for a hybrid air-conditioning and wind catchers/towers system at Bluewater shopping malls in Kent

Purpose – To evaluate the control strategy for a hybrid natural ventilation wind catchers and air-conditioning system and to assess the contribution of wind catchers to indoor air environments and energy savings if any. Design/methodology/approach – Most of the modeling techniques for assessing wind catchers performance are theoretical. Post-occupancy evaluation studies of buildings will provide an insight into the operation of these building components and help to inform facilities managers. A case study for POE was presented in this paper. Findings – The monitoring of the summer and winter month operations showed that the indoor air quality parameters were kept within the design target range. The design control strategy failed to record data regarding the operation, opening time and position of wind catchers system. Though the implemented control strategy was working effectively in monitoring the operation of mechanical ventilation systems, i.e. AHU, did not integrate the wind catchers with the mechanical ventilation system. Research limitations/implications – Owing to short-falls in the control strategy implemented in this project, it was found difficult to quantify and verify the contribution of the wind catchers to the internal conditions and, hence, energy savings. Practical implications – Controlling the operation of the wind catchers via the AHU will lead to isolation of the wind catchers in the event of malfunctioning of the AHU. Wind catchers will contribute to the ventilation of space, particularly in the summer months. Originality/value – This paper demonstrates the value of POE as indispensable tool for FM professionals. It further provides insight into the application of natural ventilation systems in building for healthier indoor environments at lower energy cost. The design of the control strategy for natural ventilation and air-conditioning should be considered at the design stage involving the FM personnel.