Charge transfer in DNA: hole charge is confined to a single base pair due to solvation effects

We include solvation effects in tight-binding Hamiltonians for hole states in DNA. The corresponding linear-response parameters are derived from accurate estimates of solvation energy calculated for several hole charge distributions in DNA stacks. Two models are considered: (A) the correction to a diagonal Hamiltonian matrix element depends only on the charge localized on the corresponding site and (B) in addition to this term, the reaction field due to adjacent base pairs is accounted for. We show that both schemes give very similar results. The effects of the polar medium on the hole distribution in DNA are studied. We conclude that the effects of polar surroundings essentially suppress charge delocalization in DNA, and hole states in (GC)n sequences are localized on individual guanines

Two complementary molecular energy decomposition schemes: the Mayer and Ziegler-Rauk methods in comparison

In the present paper we discuss and compare two different energy decomposition schemes: Mayer's Hartree-Fock energy decomposition into diatomic and monoatomic contributions [Chem. Phys. Lett. 382, 265 (2003)], and the Ziegler-Rauk dissociation energy decomposition [Inorg. Chem. 18, 1558 (1979)]. The Ziegler-Rauk scheme is based on a separation of a molecule into fragments, while Mayer's scheme can be used in the cases where a fragmentation of the system in clearly separable parts is not possible. In the Mayer scheme, the density of a free atom is deformed to give the one-atom Mulliken density that subsequently interacts to give rise to the diatomic interaction energy. We give a detailed analysis of the diatomic energy contributions in the Mayer scheme and a close look onto the one-atom Mulliken densities. The Mulliken density ρA has a single large maximum around the nuclear position of the atom A, but exhibits slightly negative values in the vicinity of neighboring atoms. The main connecting point between both analysis schemes is the electrostatic energy. Both decomposition schemes utilize the same electrostatic energy expression, but differ in how fragment densities are defined. In the Mayer scheme, the electrostatic component originates from the interaction of the Mulliken densities, while in the Ziegler-Rauk scheme, the undisturbed fragment densities interact. The values of the electrostatic energy resulting from the two schemes differ significantly but typically have the same order of magnitude. Both methods are useful and complementary since Mayer's decomposition focuses on the energy of the finally formed molecule, whereas the Ziegler-Rauk scheme describes the bond formation starting from undeformed fragment densities

Comparison of splice sites in mammals and chicken

We have carried out an initial analysis of the dynamics of the recent evolution of the splice-sites sequences on a large collection of human, rodent (mouse and rat), and chicken introns. Our results indicate that the sequences of splice sites are largely homogeneous within tetrapoda. We have also found that orthologous splice signals between human and rodents and within rodents are more conserved than unrelated splice sites, but the additional conservation can be explained mostly by background intron conservation. In contrast, additional conservation over background is detectable in orthologous mammalian and chicken splice sites. Our results also indicate that the U2 and U12 intron classes seem to have evolved independently since the split of mammals and birds; we have not been able to find a convincing case of interconversion between these two classes in our collections of orthologous introns. Similarly, we have not found a single case of switching between AT-AC and GT-AG subtypes within U12 introns, suggesting that this event has been a rare occurrence in recent evolutionary times. Switching between GT-AG and the noncanonical GC-AG U2 subtypes, on the contrary, does not appear to be unusual; in particular, T to C mutations appear to be relatively well tolerated in GT-AG introns with very strong donor sites.

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

The construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, we show that the analysis of random sequence reads (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity of a bacterial community from metagenomic libraries. We generated 10,010 RSRs from a metagenomic library of microorganisms found in human faecal samples. Then searched them using the program BLASTN against a prokaryotic sequence database to assign a taxon to each RSR. The results were compared with those obtained by screening and analysing the clones containing 16S rDNA sequences in the whole library. We found that the biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA. We also show that RSRs are suitable to compare the biodiversity between different metagenomic libraries. RSRs can thus provide a good estimate of the biodiversity of a metagenomic library and, as an alternative to 16S, this approach is both faster and cheaper.

Deployment of self-expandable stents in aneurysmatic cerebral vessels: comparison of different computational approaches for interventional planning

In the last few years, there has been a growing focus on faster computational methods to support clinicians in planning stenting procedures. This study investigates the possibility of introducing computational approximations in modelling stent deployment in aneurysmatic cerebral vessels to achieve simulations compatible with the constraints of real clinical workflows. The release of a self-expandable stent in a simplified aneurysmatic vessel was modelled in four different initial positions. Six progressively simplified modelling approaches (based on Finite Element method and Fast Virtual Stenting – FVS) have been used. Comparing accuracy of the results, the final configuration of the stent is more affected by neglecting mechanical properties of materials (FVS) than by adopting 1D instead of 3D stent models. Nevertheless, the differencesshowed are acceptable compared to those achieved by considering different stent initial positions. Regarding computationalcosts, simulations involving 1D stent features are the only ones feasible in clinical context.

A comparison of full-rate full-diversity 2x2 space-time codes for WiMAX systems

Multiple-input multiple-output (MIMO) techniques have become an essential part of broadband wireless communications systems. For example, the recently developed IEEE 802.16e specifications for broadband wireless access include three MIMOprofiles employing 2×2 space-time codes (STCs), and two of these MIMO schemes are mandatory on the downlink of Mobile WiMAX systems. One of these has full rate, and the other has full diversity, but neither of them has both of the desired features. The third profile, namely, Matrix C, which is not mandatory, is both a full rate and a full diversity code, but it has a high decoder complexity. Recently, the attention was turned to the decodercomplexity issue and including this in the design criteria, several full-rate STCs were proposed as alternatives to Matrix C. In this paper, we review these different alternatives and compare them to Matrix C in terms of performances and the correspondingreceiver complexities.

Do the Wealthy Risk More Money? An Experimental Comparison

Are poor people more or less likely to take money risks than wealthy folks? We find that risk attraction is more prevalent among the wealthy when the amounts of money at risk are small (not surprising, since ten dollars is a smaller amount for a wealthy person than for a poor one), but, interestingly, for the larger amounts of money at risk the fraction of the nonwealthy displaying risk attraction exceeds that of the wealthy. We also replicate our previous finding that many people display risk attraction for small money amounts, but risk aversion for large ones. We argue that preferences yielding risk attraction for small money amounts, together with risk aversion for larger amounts, at all levels of wealth, while contradicting the expected utility hypothesis, may be well-defined, independently of reference points, on the choice space.

A comparison of stock market mechanisms

This paper studies the relationship between the amount of publicinformation that stock market prices incorporate and the equilibriumbehavior of market participants. The analysis is framed in a static, NREEsetup where traders exchange vectors of assets accessing multidimensionalinformation under two alternative market structures. In the first(the unrestricted system), both informed and uninformed speculators cancondition their demands for each traded asset on all equilibrium prices;in the second (the restricted system), they are restricted to conditiontheir demand on the price of the asset they want to trade. I show thatinformed traders incentives to exploit multidimensional privateinformation depend on the number of prices they can condition upon whensubmitting their demand schedules, and on the specific price formationprocess one considers. Building on this insight, I then give conditionsunder which the restricted system is more efficient than the unrestrictedsystem.

Comparison of information structures

We introduce two ways of comparing information structures, say ${\cal I}$ and${\cal J}$. First we say that ${\cal I}$ is richer than ${\cal J}$ when forevery compact game $G$, all correlated equilibrium distributions of $G$ inducedby ${\cal J}$ are also induced by ${\cal I}$. Second, we say that ${\cal J}$is faithfully reproducable from ${\cal I}$ when all the players can computefrom their information in ${\cal I}$ ``new information'' that they could havereceived from ${\cal J}$. We prove that ${\cal I}$ is richer than ${\cal J}$if and only if ${\cal J}$ is faithfully reproducable from ${\cal I}$.

Do the eealthy risk more money? An experimental comparison

Are poor people more or less likely to take money risks than wealthy folks?We find that risk attraction is more prevalent among the wealthy when theamounts of money at risk are small (not surprising, since ten dollars is asmaller amount for a wealthy person than for a poor one), but, interestingly,for the larger amounts of money at risk the fraction of the nonwealthydisplaying risk attraction exceeds that of the wealthy.We also replicate our previous finding that many people display riskattraction for small money amounts, but risk aversion for large ones. Weargue that preferences yielding risk attraction for small money amounts,together with risk aversion for larger amounts, at all levels of wealth, while contradicting the expected utility hypothesis, may be well-defined,independently of reference points, on the choice space.

Country effects in ISSP-1993 environmental data: Comparison of SEM approaches

Structural equation models (SEM) are commonly used to analyze the relationship between variables some of which may be latent, such as individual ``attitude'' to and ``behavior'' concerning specific issues. A number of difficulties arise when we want to compare a large number of groups, each with large sample size, and the manifest variables are distinctly non-normally distributed. Using an specific data set, we evaluate the appropriateness of the following alternative SEM approaches: multiple group versus MIMIC models, continuous versus ordinal variables estimation methods, and normal theory versus non-normal estimation methods. The approaches are applied to the ISSP-1993 Environmental data set, with the purpose of exploring variation in the mean level of variables of ``attitude'' to and ``behavior''concerning environmental issues and their mutual relationship across countries. Issues of both theoretical and practical relevance arise in the course of this application.

International accounting harmonisation - A comparison of Spain, Sweden and Austria

Despite attempts to secure harmonisation of accounting practice,significant variations in accounting rules and practice continueto arise in European countries, variations which give rise tocompliance costs for multinational companies.Firstly, this paper considers the relevance of internationalaccounting harmonisation for European business. It then proceedsto examine accounting regulation in three countries: Spain, Swedenand Austria, highlighting the key regulatory issues of the 'trueand fair' view requirement and the link between taxation andaccounting. The three countries are selected because of theinteresting contrasts which they provide; these contrasts areexamined in detail in the paper.The work is based upon a series of interviews carried out withleading accounting practitioners in the three countries during1996-97.The paper concludes that there are significant obstacles toaccounting harmonisation in Europe and that there is potentialfor continuing diversity of national accounting practice.

Comparison and evaluation of states of health

Starting from a finite or countable set of states of health, and assumingthe existence of an objective transitive preference relation on that set,we propose a way of performing interpersonal comparisons of states ofhealth. In so doing, we first consider the population divided into types,and consider that two individuals of a different type have a comparablestate of health whenever they sit at the same centile of their respectivetype. A way of comparing and evaluating states of health for differentgroups is then proposed and rationalized. This can be viewed as both analternative and an extension of the traditional QALY approach.